AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1423060


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1423060 MtrunA17_Chr7g0265731 98.157 217 4 0 1 217 1 217 8.77e-154 425
Msa1423060 MtrunA17_Chr6g0486051 48.466 163 66 1 55 217 2 146 1.79e-50 160
Msa1423060 MtrunA17_Chr2g0287981 40.876 137 78 2 79 214 62 196 1.23e-29 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1423060 AT3G52960.1 62.979 235 68 5 1 217 1 234 3.42e-98 285
Msa1423060 AT1G65980.1 58.282 163 66 1 55 217 2 162 2.92e-62 191
Msa1423060 AT1G60740.1 53.988 163 73 1 55 217 2 162 9.47e-60 185
Msa1423060 AT1G65970.1 53.988 163 73 1 55 217 2 162 3.82e-59 184
Msa1423060 AT1G65990.1 46.309 149 74 2 55 203 2 144 5.72e-37 135
Msa1423060 AT3G06050.1 43.066 137 75 2 79 214 64 198 1.22e-32 117
Msa1423060 AT1G65980.2 59.740 77 31 0 55 131 2 78 1.56e-27 100
Msa1423060 AT3G06050.2 47.945 73 38 0 79 151 64 136 8.39e-20 83.6

Find 59 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGAGAATCGGAGAGGTTT+TGG 0.170077 tig0025511:-30880 None:intergenic
TTTGAGAGGGAGGGTGAATT+TGG 0.195781 tig0025511:-30842 None:intergenic
GGAGATGGTGGCGGAGATTT+TGG 0.207407 tig0025511:-30908 None:intergenic
AGGTAGGAGAAGGTGGATTC+AGG 0.275143 tig0025511:-30946 None:intergenic
GCAGTCCTCTTCGCCGTTCC+AGG 0.310776 tig0025511:+31027 Msa1423060:CDS
AACCTGTTGGATTGGGTGTT+AGG 0.351123 tig0025511:+31277 Msa1423060:CDS
GTCAAGACGTTATGCTTTGT+TGG 0.388577 tig0025511:+31299 Msa1423060:CDS
TGCTCACAGAAACACGTTCC+TGG 0.400832 tig0025511:+31066 Msa1423060:CDS
TGTTAGGTCAGAGACGGTTA+TGG 0.417735 tig0025511:-30992 None:intergenic
TGATACAATCGCTTGCATTT+CGG 0.418524 tig0025511:+31128 Msa1423060:CDS
GGTCAGAGACGGTTATGGTT+TGG 0.420880 tig0025511:-30987 None:intergenic
GAATTTGGAAGAGAGGGTTT+TGG 0.429478 tig0025511:-30827 None:intergenic
GTGATTTCACAAGAGCGATT+GGG 0.431034 tig0025511:+31232 Msa1423060:CDS
AGATAAGAGTGAGGTGGTGG+TGG 0.441187 tig0025511:-30797 None:intergenic
GGTAGGAGAAGGTGGATTCA+GGG 0.445681 tig0025511:-30945 None:intergenic
GACCTAACACCCAATCCAAC+AGG 0.452953 tig0025511:-31279 None:intergenic
TTGAAACGGTTGAATTTGAG+AGG 0.455027 tig0025511:-30856 None:intergenic
AGCGATAAACCTGTTGGATT+GGG 0.455914 tig0025511:+31270 Msa1423060:CDS
AGCGTGGAAGGAGGATTTGA+AGG 0.464799 tig0025511:+31173 Msa1423060:CDS
GCTGATTTCTCCACGAATCC+AGG 0.469358 tig0025511:-31084 None:intergenic
GGACTTCACCGGCAGGGTCG+AGG 0.473218 tig0025511:-30966 None:intergenic
GGTGATTTCACAAGAGCGAT+TGG 0.474269 tig0025511:+31231 Msa1423060:CDS
GAGCGATAAACCTGTTGGAT+TGG 0.482422 tig0025511:+31269 Msa1423060:CDS
GGAGGGTGAATTTGGAAGAG+AGG 0.482927 tig0025511:-30834 None:intergenic
AACGGTTGAATTTGAGAGGG+AGG 0.500645 tig0025511:-30852 None:intergenic
GAGTTTGTCGCCGACGGAGA+TGG 0.504087 tig0025511:-30923 None:intergenic
GGGAGATAAGAGTGAGGTGG+TGG 0.509192 tig0025511:-30800 None:intergenic
GAGGGTGAATTTGGAAGAGA+GGG 0.514701 tig0025511:-30833 None:intergenic
TATGCTTTGTTGGCTGAAGA+TGG 0.518833 tig0025511:+31309 Msa1423060:CDS
TTCTCCTACCTCGACCCTGC+CGG 0.521198 tig0025511:+30958 Msa1423060:CDS
CATGTTGGTGTGAAAGCTCC+TGG 0.523565 tig0025511:-31045 None:intergenic
TTCAGGGAGTTTGTCGCCGA+CGG 0.523891 tig0025511:-30929 None:intergenic
ACCGTCTCTGACCTAACAAA+AGG 0.536577 tig0025511:+30997 Msa1423060:CDS
ACGGTTGAATTTGAGAGGGA+GGG 0.537771 tig0025511:-30851 None:intergenic
GATTTGAGCGATAAACCTGT+TGG 0.550461 tig0025511:+31264 Msa1423060:CDS
GGCAGGGTCGAGGTAGGAGA+AGG 0.551945 tig0025511:-30956 None:intergenic
GTCGCCGACGGAGATGGTGG+CGG 0.556756 tig0025511:-30917 None:intergenic
GGGGAAGAGGAGAATCGGAG+AGG 0.566799 tig0025511:-30886 None:intergenic
ATCAGCGGAGCTAAAAGCGA+AGG 0.573209 tig0025511:+31101 Msa1423060:CDS
TGATTTCACAAGAGCGATTG+GGG 0.578015 tig0025511:+31233 Msa1423060:CDS
TTTGTCGCCGACGGAGATGG+TGG 0.580050 tig0025511:-30920 None:intergenic
TGGTTTGGACTTCACCGGCA+GGG 0.580205 tig0025511:-30972 None:intergenic
GAAACACGTTCCTGGATTCG+TGG 0.581971 tig0025511:+31074 Msa1423060:CDS
GGTTATGGTTTGGACTTCAC+CGG 0.599625 tig0025511:-30977 None:intergenic
ATCTCCGCCACCATCTCCGT+CGG 0.611751 tig0025511:+30913 Msa1423060:CDS
AGGTGGTGGTGGAAGATGAG+AGG 0.612703 tig0025511:-30786 None:intergenic
TGAAACGGTTGAATTTGAGA+GGG 0.618873 tig0025511:-30855 None:intergenic
AGGGTCGAGGTAGGAGAAGG+TGG 0.620333 tig0025511:-30953 None:intergenic
AAGCTCCTGGAACGGCGAAG+AGG 0.622049 tig0025511:-31032 None:intergenic
TTTGGGAGATAAGAGTGAGG+TGG 0.623641 tig0025511:-30803 None:intergenic
TTCACCGGCAGGGTCGAGGT+AGG 0.624603 tig0025511:-30962 None:intergenic
TGTGATGAAAGCGTGGAAGG+AGG 0.635880 tig0025511:+31164 Msa1423060:CDS
GTTTGTGATGAAAGCGTGGA+AGG 0.651012 tig0025511:+31161 Msa1423060:CDS
TCAGCGGAGCTAAAAGCGAA+GGG 0.675110 tig0025511:+31102 Msa1423060:CDS
ACGTGTTTCTGTGAGCATGT+TGG 0.678748 tig0025511:-31060 None:intergenic
TTTGAAGGTGAACGATGAAG+TGG 0.684338 tig0025511:+31188 Msa1423060:CDS
ATGCGTTTGTGATGAAAGCG+TGG 0.693181 tig0025511:+31157 Msa1423060:CDS
TGGTGTGAAAGCTCCTGGAA+CGG 0.694733 tig0025511:-31040 None:intergenic
TGGATTCGTGGAGAAATCAG+CGG 0.698367 tig0025511:+31086 Msa1423060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTGTTAAGCTTTTCAATT+TGG + tig0025511:31332-31351 Msa1423060:CDS 25.0%
! TGTTAAGCTTTTCAATTTGG+AGG + tig0025511:31335-31354 Msa1423060:CDS 30.0%
TGAAACGGTTGAATTTGAGA+GGG - tig0025511:30858-30877 None:intergenic 35.0%
TTGAAACGGTTGAATTTGAG+AGG - tig0025511:30859-30878 None:intergenic 35.0%
!!! CTGCTTTTTTGCCTTTTGTT+AGG - tig0025511:31011-31030 None:intergenic 35.0%
TGATACAATCGCTTGCATTT+CGG + tig0025511:31128-31147 Msa1423060:CDS 35.0%
! AAGCTTTTCAATTTGGAGGA+AGG + tig0025511:31339-31358 Msa1423060:CDS 35.0%
!!! GAAGAGAGGGTTTTGGTTTT+GGG - tig0025511:30823-30842 None:intergenic 40.0%
! GAATTTGGAAGAGAGGGTTT+TGG - tig0025511:30830-30849 None:intergenic 40.0%
TTTGAAGGTGAACGATGAAG+TGG + tig0025511:31188-31207 Msa1423060:CDS 40.0%
! AAGTGGTGCTTTTGTCTGAT+GGG + tig0025511:31205-31224 Msa1423060:CDS 40.0%
GTGATTTCACAAGAGCGATT+GGG + tig0025511:31232-31251 Msa1423060:CDS 40.0%
TGATTTCACAAGAGCGATTG+GGG + tig0025511:31233-31252 Msa1423060:CDS 40.0%
GATTTGAGCGATAAACCTGT+TGG + tig0025511:31264-31283 Msa1423060:CDS 40.0%
AGCGATAAACCTGTTGGATT+GGG + tig0025511:31270-31289 Msa1423060:CDS 40.0%
GTCAAGACGTTATGCTTTGT+TGG + tig0025511:31299-31318 Msa1423060:CDS 40.0%
! TATGCTTTGTTGGCTGAAGA+TGG + tig0025511:31309-31328 Msa1423060:CDS 40.0%
! CTTTTCAATTTGGAGGAAGG+TGG + tig0025511:31342-31361 Msa1423060:CDS 40.0%
TTTGGGAGATAAGAGTGAGG+TGG - tig0025511:30806-30825 None:intergenic 45.0%
!!! GGTTTTGGGAGATAAGAGTG+AGG - tig0025511:30809-30828 None:intergenic 45.0%
!!! GGAAGAGAGGGTTTTGGTTT+TGG - tig0025511:30824-30843 None:intergenic 45.0%
GAGGGTGAATTTGGAAGAGA+GGG - tig0025511:30836-30855 None:intergenic 45.0%
TTTGAGAGGGAGGGTGAATT+TGG - tig0025511:30845-30864 None:intergenic 45.0%
ACGGTTGAATTTGAGAGGGA+GGG - tig0025511:30854-30873 None:intergenic 45.0%
AACGGTTGAATTTGAGAGGG+AGG - tig0025511:30855-30874 None:intergenic 45.0%
!!! GGAGAGGTTTTGGGTTGAAA+CGG - tig0025511:30873-30892 None:intergenic 45.0%
! AGGAGAATCGGAGAGGTTTT+GGG - tig0025511:30882-30901 None:intergenic 45.0%
!! TTTTGGGGGAAGAGGAGAAT+CGG - tig0025511:30894-30913 None:intergenic 45.0%
! GGTTATGGTTTGGACTTCAC+CGG - tig0025511:30980-30999 None:intergenic 45.0%
TGTTAGGTCAGAGACGGTTA+TGG - tig0025511:30995-31014 None:intergenic 45.0%
ACCGTCTCTGACCTAACAAA+AGG + tig0025511:30997-31016 Msa1423060:CDS 45.0%
! GCCTTTTGTTAGGTCAGAGA+CGG - tig0025511:31001-31020 None:intergenic 45.0%
! ACGTGTTTCTGTGAGCATGT+TGG - tig0025511:31063-31082 None:intergenic 45.0%
TGGATTCGTGGAGAAATCAG+CGG + tig0025511:31086-31105 Msa1423060:CDS 45.0%
ATGCGTTTGTGATGAAAGCG+TGG + tig0025511:31157-31176 Msa1423060:CDS 45.0%
! GTTTGTGATGAAAGCGTGGA+AGG + tig0025511:31161-31180 Msa1423060:CDS 45.0%
! GAAGTGGTGCTTTTGTCTGA+TGG + tig0025511:31204-31223 Msa1423060:CDS 45.0%
! GTGCTTTTGTCTGATGGGAA+TGG + tig0025511:31210-31229 Msa1423060:CDS 45.0%
GGTGATTTCACAAGAGCGAT+TGG + tig0025511:31231-31250 Msa1423060:CDS 45.0%
GAGCGATAAACCTGTTGGAT+TGG + tig0025511:31269-31288 Msa1423060:CDS 45.0%
! AACCTGTTGGATTGGGTGTT+AGG + tig0025511:31277-31296 Msa1423060:CDS 45.0%
! GGTGGTGCTTTTACTTTCAG+TGG + tig0025511:31360-31379 Msa1423060:CDS 45.0%
! AGATAAGAGTGAGGTGGTGG+TGG - tig0025511:30800-30819 None:intergenic 50.0%
GGAGGGTGAATTTGGAAGAG+AGG - tig0025511:30837-30856 None:intergenic 50.0%
! GAGGAGAATCGGAGAGGTTT+TGG - tig0025511:30883-30902 None:intergenic 50.0%
!!! AGATGGTGGCGGAGATTTTG+GGG - tig0025511:30909-30928 None:intergenic 50.0%
!!! GAGATGGTGGCGGAGATTTT+GGG - tig0025511:30910-30929 None:intergenic 50.0%
! GGTAGGAGAAGGTGGATTCA+GGG - tig0025511:30948-30967 None:intergenic 50.0%
! AGGTAGGAGAAGGTGGATTC+AGG - tig0025511:30949-30968 None:intergenic 50.0%
GGTCAGAGACGGTTATGGTT+TGG - tig0025511:30990-31009 None:intergenic 50.0%
TGGTGTGAAAGCTCCTGGAA+CGG - tig0025511:31043-31062 None:intergenic 50.0%
CATGTTGGTGTGAAAGCTCC+TGG - tig0025511:31048-31067 None:intergenic 50.0%
TGCTCACAGAAACACGTTCC+TGG + tig0025511:31066-31085 Msa1423060:CDS 50.0%
GAAACACGTTCCTGGATTCG+TGG + tig0025511:31074-31093 Msa1423060:CDS 50.0%
! GCTGATTTCTCCACGAATCC+AGG - tig0025511:31087-31106 None:intergenic 50.0%
ATCAGCGGAGCTAAAAGCGA+AGG + tig0025511:31101-31120 Msa1423060:CDS 50.0%
TCAGCGGAGCTAAAAGCGAA+GGG + tig0025511:31102-31121 Msa1423060:CDS 50.0%
! TGTGATGAAAGCGTGGAAGG+AGG + tig0025511:31164-31183 Msa1423060:CDS 50.0%
AGCGTGGAAGGAGGATTTGA+AGG + tig0025511:31173-31192 Msa1423060:CDS 50.0%
GACCTAACACCCAATCCAAC+AGG - tig0025511:31282-31301 None:intergenic 50.0%
!! AGGTGGTGGTGGAAGATGAG+AGG - tig0025511:30789-30808 None:intergenic 55.0%
GGGAGATAAGAGTGAGGTGG+TGG - tig0025511:30803-30822 None:intergenic 55.0%
!!! GATGGTGGCGGAGATTTTGG+GGG - tig0025511:30908-30927 None:intergenic 55.0%
!!! GGAGATGGTGGCGGAGATTT+TGG - tig0025511:30911-30930 None:intergenic 55.0%
TTCAGGGAGTTTGTCGCCGA+CGG - tig0025511:30932-30951 None:intergenic 55.0%
! TGGTTTGGACTTCACCGGCA+GGG - tig0025511:30975-30994 None:intergenic 55.0%
! ATGGTTTGGACTTCACCGGC+AGG - tig0025511:30976-30995 None:intergenic 55.0%
GGGGAAGAGGAGAATCGGAG+AGG - tig0025511:30889-30908 None:intergenic 60.0%
!! GGCGGAGATTTTGGGGGAAG+AGG - tig0025511:30902-30921 None:intergenic 60.0%
ATCTCCGCCACCATCTCCGT+CGG + tig0025511:30913-30932 Msa1423060:CDS 60.0%
TTTGTCGCCGACGGAGATGG+TGG - tig0025511:30923-30942 None:intergenic 60.0%
GAGTTTGTCGCCGACGGAGA+TGG - tig0025511:30926-30945 None:intergenic 60.0%
AGGGTCGAGGTAGGAGAAGG+TGG - tig0025511:30956-30975 None:intergenic 60.0%
TTCTCCTACCTCGACCCTGC+CGG + tig0025511:30958-30977 Msa1423060:CDS 60.0%
AAGCTCCTGGAACGGCGAAG+AGG - tig0025511:31035-31054 None:intergenic 60.0%
GGCAGGGTCGAGGTAGGAGA+AGG - tig0025511:30959-30978 None:intergenic 65.0%
TTCACCGGCAGGGTCGAGGT+AGG - tig0025511:30965-30984 None:intergenic 65.0%
GCAGTCCTCTTCGCCGTTCC+AGG + tig0025511:31027-31046 Msa1423060:CDS 65.0%
! GTCGCCGACGGAGATGGTGG+CGG - tig0025511:30920-30939 None:intergenic 70.0%
GGACTTCACCGGCAGGGTCG+AGG - tig0025511:30969-30988 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0025511 gene 30757 31410 30757 ID=Msa1423060;Name=Msa1423060
tig0025511 mRNA 30757 31410 30757 ID=Msa1423060-mRNA-1;Parent=Msa1423060;Name=Msa1423060-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|217
tig0025511 exon 30757 31410 30757 ID=Msa1423060-mRNA-1:exon:3005;Parent=Msa1423060-mRNA-1
tig0025511 CDS 30757 31410 30757 ID=Msa1423060-mRNA-1:cds;Parent=Msa1423060-mRNA-1
Gene Sequence

>Msa1423060

ATGGCAACATCACTCTCTTTCTCTAGACTCCTCTCATCTTCCACCACCACCTCACTCTTATCTCCCAAAACCAAAACCCTCTCTTCCAAATTCACCCTCCCTCTCAAATTCAACCGTTTCAACCCAAAACCTCTCCGATTCTCCTCTTCCCCCAAAATCTCCGCCACCATCTCCGTCGGCGACAAACTCCCTGAATCCACCTTCTCCTACCTCGACCCTGCCGGTGAAGTCCAAACCATAACCGTCTCTGACCTAACAAAAGGCAAAAAAGCAGTCCTCTTCGCCGTTCCAGGAGCTTTCACACCAACATGCTCACAGAAACACGTTCCTGGATTCGTGGAGAAATCAGCGGAGCTAAAAGCGAAGGGAGTTGATACAATCGCTTGCATTTCGGTGAACGATGCGTTTGTGATGAAAGCGTGGAAGGAGGATTTGAAGGTGAACGATGAAGTGGTGCTTTTGTCTGATGGGAATGGTGATTTCACAAGAGCGATTGGGGTTGAGCTTGATTTGAGCGATAAACCTGTTGGATTGGGTGTTAGGTCAAGACGTTATGCTTTGTTGGCTGAAGATGGTGTTGTTAAGCTTTTCAATTTGGAGGAAGGTGGTGCTTTTACTTTCAGTGGTGCTGATGATATTCTCAAAGTTCTTTGA

Protein sequence

>Msa1423060

MATSLSFSRLLSSSTTTSLLSPKTKTLSSKFTLPLKFNRFNPKPLRFSSSPKISATISVGDKLPESTFSYLDPAGEVQTITVSDLTKGKKAVLFAVPGAFTPTCSQKHVPGFVEKSAELKAKGVDTIACISVNDAFVMKAWKEDLKVNDEVVLLSDGNGDFTRAIGVELDLSDKPVGLGVRSRRYALLAEDGVVKLFNLEEGGAFTFSGADDILKVL*