AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1433480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1433480 MtrunA17_Chr1g0205341 90.393 229 17 3 1 228 1 225 3.00e-129 363
Msa1433480 MtrunA17_Chr1g0185481 47.794 136 49 2 68 182 134 268 1.49e-34 124
Msa1433480 MtrunA17_Chr7g0259991 42.604 169 61 6 34 181 48 201 9.25e-32 115
Msa1433480 MtrunA17_Chr2g0331871 38.356 73 42 1 118 187 208 280 8.08e-13 66.6
Msa1433480 MtrunA17_Chr1g0210351 33.600 125 68 5 55 178 89 199 4.62e-12 63.5
Msa1433480 MtrunA17_Chr7g0267101 38.136 118 63 4 75 189 98 208 8.53e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1433480 AT1G05420.1 45.299 117 60 2 71 184 107 222 4.81e-24 95.9
Msa1433480 AT1G05420.2 45.299 117 60 2 71 184 123 238 5.49e-24 96.3
Msa1433480 AT2G32100.1 37.241 145 60 2 69 182 94 238 3.07e-21 89.0
Msa1433480 AT4G14860.1 54.545 66 30 0 121 186 111 176 1.44e-17 77.8
Msa1433480 AT1G79960.1 36.170 94 52 1 87 180 175 260 1.75e-12 65.9
Msa1433480 AT2G36050.1 31.532 111 56 3 76 180 77 173 8.38e-11 60.5

Find 66 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGGTTTACAGAGTATTT+TGG 0.228255 tig0027315:+22927 None:intergenic
CTCTTCACACTACCTCTTCT+TGG 0.295616 tig0027315:+22954 None:intergenic
CGTAGAAATAGTCTTCTTCT+TGG 0.335486 tig0027315:+23111 None:intergenic
CTTGGTCGTGGTGGTGGTGG+TGG 0.362617 tig0027315:+23129 None:intergenic
TATCGCCACGGTAGTTTCTC+AGG 0.363292 tig0027315:-22649 Msa1433480:CDS
AGCTGTTTAGAGAATAGTTT+TGG 0.372531 tig0027315:+23269 None:intergenic
TGTTAGATGTTACTAATGAT+TGG 0.384737 tig0027315:-22854 Msa1433480:CDS
GAGAAACTACCGTGGCGATA+TGG 0.397249 tig0027315:+22652 None:intergenic
TGAGGTTGGGAGAGAATTGT+AGG 0.399313 tig0027315:+23218 None:intergenic
AGGAGACTCTGTGATGGAAT+TGG 0.407788 tig0027315:+23010 None:intergenic
TGGCGTTGGTTATTGAGCTT+TGG 0.408724 tig0027315:+22672 None:intergenic
GTTAGATGTTACTAATGATT+GGG 0.414482 tig0027315:-22853 Msa1433480:CDS
GTGGTAGTGTGTTGTGGATG+AGG 0.449355 tig0027315:+23200 None:intergenic
CAAGGTAGAGTGTCGTTAGA+AGG 0.451760 tig0027315:+22990 None:intergenic
TAGTGTGTTGTGGATGAGGT+TGG 0.452668 tig0027315:+23204 None:intergenic
TGTGATGGAATTGGAGCTGC+CGG 0.453476 tig0027315:+23019 None:intergenic
GTGATGGAATTGGAGCTGCC+GGG 0.463677 tig0027315:+23020 None:intergenic
GGAGAATGATGAAGAGGAGG+AGG 0.466907 tig0027315:+22725 None:intergenic
GGGTGAAGGTGGTATTGAAA+TGG 0.466993 tig0027315:+23150 None:intergenic
GAACGGAGGAAATCAACATA+AGG 0.476551 tig0027315:+22909 None:intergenic
CTTCTTGGTCGTGGTGGTGG+TGG 0.481550 tig0027315:+23126 None:intergenic
TGATTTCCTCCGTTCTATGC+AGG 0.483346 tig0027315:-22901 Msa1433480:CDS
GTGGTGGTGGTGGGTGAAGG+TGG 0.483521 tig0027315:+23139 None:intergenic
TTGGTCGTGGTGGTGGTGGT+GGG 0.488030 tig0027315:+23130 None:intergenic
CTTCTTCTTGGTCGTGGTGG+TGG 0.488768 tig0027315:+23123 None:intergenic
AGTGTGTTGTGGATGAGGTT+GGG 0.497151 tig0027315:+23205 None:intergenic
AATAGTCTTCTTCTTGGTCG+TGG 0.507672 tig0027315:+23117 None:intergenic
TGATGGAATTGGAGCTGCCG+GGG 0.520934 tig0027315:+23021 None:intergenic
AAGAAGAGGTAGTGTGAAGA+GGG 0.521773 tig0027315:-22952 Msa1433480:CDS
TGGAAAGTGCAAGGTGATGA+TGG 0.523328 tig0027315:+23170 None:intergenic
AGGTTCTTCTTCTCCTCCCC+CGG 0.527466 tig0027315:-23038 Msa1433480:CDS
CACCACGGAGCTTCCACCAC+CGG 0.528976 tig0027315:-23087 Msa1433480:CDS
CGGTAGTTTCTCAGGGAAGT+TGG 0.530160 tig0027315:-22641 Msa1433480:CDS
GGAGGAGAATGATGAAGAGG+AGG 0.534241 tig0027315:+22722 None:intergenic
AACGGAGGAAATCAACATAA+GGG 0.534785 tig0027315:+22910 None:intergenic
TTTGGAGAAGATAGCGGTGG+CGG 0.537055 tig0027315:+22690 None:intergenic
AGAGGAGGAGAATGATGAAG+AGG 0.539046 tig0027315:+22719 None:intergenic
ACAGAAGAAAAGTCCGGTGG+TGG 0.542301 tig0027315:+23074 None:intergenic
TAGCGGTGGCGGAGATGAAG+AGG 0.545559 tig0027315:+22701 None:intergenic
GATGAAGTGGTAGTGTGTTG+TGG 0.564172 tig0027315:+23194 None:intergenic
GAATCATTTCCTGCATAGAA+CGG 0.567536 tig0027315:+22892 None:intergenic
AAGATAAAATATCAACAAGA+AGG 0.574451 tig0027315:+22748 None:intergenic
CAAGAAGAGGTAGTGTGAAG+AGG 0.577676 tig0027315:-22953 Msa1433480:CDS
CTTGGTATCAACGAGTTGCA+AGG 0.582336 tig0027315:+22972 None:intergenic
CTTCTGTCTTCGCGTCTCAG+AGG 0.595550 tig0027315:-23058 Msa1433480:CDS
GATGGAATTGGAGCTGCCGG+GGG 0.596484 tig0027315:+23022 None:intergenic
CGGTGGCGGAGATGAAGAGG+AGG 0.598051 tig0027315:+22704 None:intergenic
CTACCGTGGCGATATGGCGT+TGG 0.601430 tig0027315:+22658 None:intergenic
AGTCTTCTTCTTGGTCGTGG+TGG 0.610248 tig0027315:+23120 None:intergenic
GAGGTTGGGAGAGAATTGTA+GGG 0.614608 tig0027315:+23219 None:intergenic
AGGTGATGATGGTGATGAAG+TGG 0.616233 tig0027315:+23181 None:intergenic
GCGAAGACAGAAGAAAAGTC+CGG 0.617433 tig0027315:+23068 None:intergenic
ATCGCCACGGTAGTTTCTCA+GGG 0.618065 tig0027315:-22648 Msa1433480:CDS
TTGAGCTTTGGAGAAGATAG+CGG 0.632157 tig0027315:+22684 None:intergenic
ATATACTTGTGAGTATGCGT+AGG 0.648661 tig0027315:+22789 None:intergenic
GTTAGAAGGAGACTCTGTGA+TGG 0.651959 tig0027315:+23004 None:intergenic
AACTCGTTGATACCAAGAAG+AGG 0.656940 tig0027315:-22966 Msa1433480:CDS
AGCTTTGGAGAAGATAGCGG+TGG 0.665519 tig0027315:+22687 None:intergenic
ATTTGAGCTTGAAGAAACAG+AGG 0.670569 tig0027315:+23243 None:intergenic
GTCCGGTGGTGGAAGCTCCG+TGG 0.684749 tig0027315:+23085 None:intergenic
TCATTTCCTGCATAGAACGG+AGG 0.700476 tig0027315:+22895 None:intergenic
AGACTATTTCTACGACACCA+CGG 0.705726 tig0027315:-23102 Msa1433480:CDS
TAACCAACGCCATATCGCCA+CGG 0.709212 tig0027315:-22661 Msa1433480:CDS
GTATTGAAATGGAAAGTGCA+AGG 0.712044 tig0027315:+23161 None:intergenic
AAGACAGAAGAAAAGTCCGG+TGG 0.739392 tig0027315:+23071 None:intergenic
ACTTCCCTGAGAAACTACCG+TGG 0.784562 tig0027315:+22644 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTAAAAATATTAAATGTCA+AGG - tig0027315:23262-23281 Msa1433480:CDS 15.0%
!! AAGATAAAATATCAACAAGA+AGG + tig0027315:23135-23154 None:intergenic 20.0%
! TGTTAGATGTTACTAATGAT+TGG - tig0027315:23026-23045 Msa1433480:CDS 25.0%
! GTTAGATGTTACTAATGATT+GGG - tig0027315:23027-23046 Msa1433480:CDS 25.0%
! AGCTGTTTAGAGAATAGTTT+TGG + tig0027315:22614-22633 None:intergenic 30.0%
!! TAAGGGTTTACAGAGTATTT+TGG + tig0027315:22956-22975 None:intergenic 30.0%
ATTTGAGCTTGAAGAAACAG+AGG + tig0027315:22640-22659 None:intergenic 35.0%
! GTATTGAAATGGAAAGTGCA+AGG + tig0027315:22722-22741 None:intergenic 35.0%
CGTAGAAATAGTCTTCTTCT+TGG + tig0027315:22772-22791 None:intergenic 35.0%
AACGGAGGAAATCAACATAA+GGG + tig0027315:22973-22992 None:intergenic 35.0%
GAATCATTTCCTGCATAGAA+CGG + tig0027315:22991-23010 None:intergenic 35.0%
ATATACTTGTGAGTATGCGT+AGG + tig0027315:23094-23113 None:intergenic 35.0%
AATAGTCTTCTTCTTGGTCG+TGG + tig0027315:22766-22785 None:intergenic 40.0%
!! AGACTATTTCTACGACACCA+CGG - tig0027315:22778-22797 Msa1433480:CDS 40.0%
AACTCGTTGATACCAAGAAG+AGG - tig0027315:22914-22933 Msa1433480:CDS 40.0%
AAGAAGAGGTAGTGTGAAGA+GGG - tig0027315:22928-22947 Msa1433480:CDS 40.0%
GAACGGAGGAAATCAACATA+AGG + tig0027315:22974-22993 None:intergenic 40.0%
!! TTGAGCTTTGGAGAAGATAG+CGG + tig0027315:23199-23218 None:intergenic 40.0%
GAGGTTGGGAGAGAATTGTA+GGG + tig0027315:22664-22683 None:intergenic 45.0%
TGAGGTTGGGAGAGAATTGT+AGG + tig0027315:22665-22684 None:intergenic 45.0%
AGTGTGTTGTGGATGAGGTT+GGG + tig0027315:22678-22697 None:intergenic 45.0%
TAGTGTGTTGTGGATGAGGT+TGG + tig0027315:22679-22698 None:intergenic 45.0%
! GATGAAGTGGTAGTGTGTTG+TGG + tig0027315:22689-22708 None:intergenic 45.0%
!! AGGTGATGATGGTGATGAAG+TGG + tig0027315:22702-22721 None:intergenic 45.0%
! TGGAAAGTGCAAGGTGATGA+TGG + tig0027315:22713-22732 None:intergenic 45.0%
! GGGTGAAGGTGGTATTGAAA+TGG + tig0027315:22733-22752 None:intergenic 45.0%
AAGACAGAAGAAAAGTCCGG+TGG + tig0027315:22812-22831 None:intergenic 45.0%
GCGAAGACAGAAGAAAAGTC+CGG + tig0027315:22815-22834 None:intergenic 45.0%
! AGGAGACTCTGTGATGGAAT+TGG + tig0027315:22873-22892 None:intergenic 45.0%
GTTAGAAGGAGACTCTGTGA+TGG + tig0027315:22879-22898 None:intergenic 45.0%
!! CAAGGTAGAGTGTCGTTAGA+AGG + tig0027315:22893-22912 None:intergenic 45.0%
CTTGGTATCAACGAGTTGCA+AGG + tig0027315:22911-22930 None:intergenic 45.0%
CTCTTCACACTACCTCTTCT+TGG + tig0027315:22929-22948 None:intergenic 45.0%
CAAGAAGAGGTAGTGTGAAG+AGG - tig0027315:22927-22946 Msa1433480:CDS 45.0%
TGATTTCCTCCGTTCTATGC+AGG - tig0027315:22979-22998 Msa1433480:CDS 45.0%
TCATTTCCTGCATAGAACGG+AGG + tig0027315:22988-23007 None:intergenic 45.0%
AGAGGAGGAGAATGATGAAG+AGG + tig0027315:23164-23183 None:intergenic 45.0%
!! TGGCGTTGGTTATTGAGCTT+TGG + tig0027315:23211-23230 None:intergenic 45.0%
! GTGGTAGTGTGTTGTGGATG+AGG + tig0027315:22683-22702 None:intergenic 50.0%
AGTCTTCTTCTTGGTCGTGG+TGG + tig0027315:22763-22782 None:intergenic 50.0%
ACAGAAGAAAAGTCCGGTGG+TGG + tig0027315:22809-22828 None:intergenic 50.0%
! TGTGATGGAATTGGAGCTGC+CGG + tig0027315:22864-22883 None:intergenic 50.0%
GGAGAATGATGAAGAGGAGG+AGG + tig0027315:23158-23177 None:intergenic 50.0%
GGAGGAGAATGATGAAGAGG+AGG + tig0027315:23161-23180 None:intergenic 50.0%
! TTTGGAGAAGATAGCGGTGG+CGG + tig0027315:23193-23212 None:intergenic 50.0%
!! AGCTTTGGAGAAGATAGCGG+TGG + tig0027315:23196-23215 None:intergenic 50.0%
TAACCAACGCCATATCGCCA+CGG - tig0027315:23219-23238 Msa1433480:CDS 50.0%
GAGAAACTACCGTGGCGATA+TGG + tig0027315:23231-23250 None:intergenic 50.0%
TATCGCCACGGTAGTTTCTC+AGG - tig0027315:23231-23250 Msa1433480:CDS 50.0%
ATCGCCACGGTAGTTTCTCA+GGG - tig0027315:23232-23251 Msa1433480:CDS 50.0%
ACTTCCCTGAGAAACTACCG+TGG + tig0027315:23239-23258 None:intergenic 50.0%
CGGTAGTTTCTCAGGGAAGT+TGG - tig0027315:23239-23258 Msa1433480:CDS 50.0%
CTTCTTCTTGGTCGTGGTGG+TGG + tig0027315:22760-22779 None:intergenic 55.0%
CTTCTGTCTTCGCGTCTCAG+AGG - tig0027315:22822-22841 Msa1433480:CDS 55.0%
AGGTTCTTCTTCTCCTCCCC+CGG - tig0027315:22842-22861 Msa1433480:CDS 55.0%
TGATGGAATTGGAGCTGCCG+GGG + tig0027315:22862-22881 None:intergenic 55.0%
! GTGATGGAATTGGAGCTGCC+GGG + tig0027315:22863-22882 None:intergenic 55.0%
!! TTGGTCGTGGTGGTGGTGGT+GGG + tig0027315:22753-22772 None:intergenic 60.0%
!! CTTCTTGGTCGTGGTGGTGG+TGG + tig0027315:22757-22776 None:intergenic 60.0%
GATGGAATTGGAGCTGCCGG+GGG + tig0027315:22861-22880 None:intergenic 60.0%
!! TAGCGGTGGCGGAGATGAAG+AGG + tig0027315:23182-23201 None:intergenic 60.0%
CTACCGTGGCGATATGGCGT+TGG + tig0027315:23225-23244 None:intergenic 60.0%
!! GTGGTGGTGGTGGGTGAAGG+TGG + tig0027315:22744-22763 None:intergenic 65.0%
!! GTGGTGGTGGTGGTGGGTGA+AGG + tig0027315:22747-22766 None:intergenic 65.0%
!! CTTGGTCGTGGTGGTGGTGG+TGG + tig0027315:22754-22773 None:intergenic 65.0%
CACCACGGAGCTTCCACCAC+CGG - tig0027315:22793-22812 Msa1433480:CDS 65.0%
!! CGGTGGCGGAGATGAAGAGG+AGG + tig0027315:23179-23198 None:intergenic 65.0%
!! GTCCGGTGGTGGAAGCTCCG+TGG + tig0027315:22798-22817 None:intergenic 70.0%
GGAATTGGAGCTGCCGGGGG+AGG + tig0027315:22858-22877 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0027315 gene 22608 23294 22608 ID=Msa1433480;Name=Msa1433480
tig0027315 mRNA 22608 23294 22608 ID=Msa1433480-mRNA-1;Parent=Msa1433480;Name=Msa1433480-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|228
tig0027315 exon 22608 23294 22608 ID=Msa1433480-mRNA-1:exon:8690;Parent=Msa1433480-mRNA-1
tig0027315 CDS 22608 23294 22608 ID=Msa1433480-mRNA-1:cds;Parent=Msa1433480-mRNA-1
Gene Sequence

>Msa1433480

ATGCCAAAACTATTCTCTAAACAGCTACACCTCTGTTTCTTCAAGCTCAAATACCCTACAATTCTCTCCCAACCTCATCCACAACACACTACCACTTCATCACCATCATCACCTTGCACTTTCCATTTCAATACCACCTTCACCCACCACCACCACCACGACCAAGAAGAAGACTATTTCTACGACACCACGGAGCTTCCACCACCGGACTTTTCTTCTGTCTTCGCGTCTCAGAGGTTCTTCTTCTCCTCCCCCGGCAGCTCCAATTCCATCACAGAGTCTCCTTCTAACGACACTCTACCTTGCAACTCGTTGATACCAAGAAGAGGTAGTGTGAAGAGGGTGCCAAAATACTCTGTAAACCCTTATGTTGATTTCCTCCGTTCTATGCAGGAAATGATTCAATCTCAACAACAAGTGTTAGATGTTACTAATGATTGGGATTATCTTCATGAACTTCTCTTATGCTATCTTGCTCTTAATCCTACGCATACTCACAAGTATATTGTTCAAGCTTTCATTCACCTTCTTGTTGATATTTTATCTTCCTCCTCCTCTTCATCATTCTCCTCCTCTTCATCTCCGCCACCGCTATCTTCTCCAAAGCTCAATAACCAACGCCATATCGCCACGGTAGTTTCTCAGGGAAGTTGGTGTAAAAATATTAAATGTCAAGGTTTTAAATAG
Protein sequence

>Msa1433480

MPKLFSKQLHLCFFKLKYPTILSQPHPQHTTTSSPSSPCTFHFNTTFTHHHHHDQEEDYFYDTTELPPPDFSSVFASQRFFFSSPGSSNSITESPSNDTLPCNSLIPRRGSVKRVPKYSVNPYVDFLRSMQEMIQSQQQVLDVTNDWDYLHELLLCYLALNPTHTHKYIVQAFIHLLVDILSSSSSSSFSSSSSPPPLSSPKLNNQRHIATVVSQGSWCKNIKCQGFK*