AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG042060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042060 MtrunA17_Chr8g0348391 96.997 333 10 0 1 333 1 333 0.0 660
MsaG042060 MtrunA17_Chr1g0181771 53.992 263 95 5 52 308 35 277 9.55e-85 258
MsaG042060 MtrunA17_Chr6g0469431 65.405 185 49 4 1 185 1 170 6.22e-74 228
MsaG042060 MtrunA17_Chr3g0109791 40.884 181 90 3 24 187 17 197 2.24e-26 107
MsaG042060 MtrunA17_Chr6g0469441 75.439 57 14 0 242 298 23 79 1.49e-25 98.2
MsaG042060 MtrunA17_Chr6g0481061 54.255 94 35 2 53 138 46 139 1.62e-25 106
MsaG042060 MtrunA17_Chr5g0433851 44.186 172 70 6 49 201 28 192 2.89e-24 102
MsaG042060 MtrunA17_Chr7g0276421 59.459 74 30 0 41 114 3 76 4.33e-24 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042060 AT4G01280.1 55.844 308 121 6 1 305 1 296 6.24e-109 320
MsaG042060 AT4G01280.2 55.806 310 119 8 1 305 1 297 4.49e-108 318
MsaG042060 AT5G52660.2 53.968 315 118 5 14 312 9 312 3.95e-103 306
MsaG042060 AT5G52660.1 53.968 315 117 5 14 312 9 311 6.31e-103 305
MsaG042060 AT1G01520.1 53.035 313 112 9 1 306 1 285 6.39e-102 301
MsaG042060 AT1G01520.3 53.094 307 109 9 1 300 1 279 2.49e-98 292
MsaG042060 AT3G09600.1 53.125 288 104 7 28 306 11 276 1.97e-89 270
MsaG042060 AT3G09600.7 53.125 288 104 7 28 306 11 276 1.97e-89 270
MsaG042060 AT1G01520.2 52.098 286 102 9 1 279 1 258 9.08e-87 262
MsaG042060 AT1G01520.4 52.098 286 102 9 1 279 1 258 9.08e-87 262
MsaG042060 AT3G09600.4 53.597 278 98 7 28 296 11 266 3.73e-86 261
MsaG042060 AT3G09600.2 53.597 278 98 7 28 296 11 266 7.89e-86 260
MsaG042060 AT3G09600.6 53.597 278 98 7 28 296 11 266 7.89e-86 260
MsaG042060 AT5G02840.3 52.222 270 98 6 48 304 32 283 1.06e-84 257
MsaG042060 AT5G02840.1 53.817 262 90 6 48 296 32 275 2.23e-84 257
MsaG042060 AT5G02840.2 53.817 262 90 6 48 296 32 275 2.23e-84 257
MsaG042060 AT5G02840.4 52.653 245 85 6 48 279 32 258 1.61e-73 228
MsaG042060 AT5G02840.5 52.869 244 84 6 48 278 32 257 2.57e-73 228
MsaG042060 AT3G09600.3 49.573 234 91 6 82 306 5 220 6.60e-62 197
MsaG042060 AT3G09600.8 49.573 234 91 6 82 306 5 220 6.60e-62 197
MsaG042060 AT3G09600.5 49.099 222 90 4 82 296 5 210 1.99e-58 188
MsaG042060 AT3G09600.9 49.099 222 90 4 82 296 5 210 1.99e-58 188
MsaG042060 AT1G01520.5 42.500 160 74 5 153 307 56 202 9.21e-32 118
MsaG042060 AT5G37260.1 50.000 142 60 3 53 185 25 164 1.46e-28 112
MsaG042060 AT5G17300.1 45.860 157 66 4 53 196 44 194 2.16e-28 114
MsaG042060 AT1G18330.1 53.684 95 36 1 53 139 39 133 3.92e-25 103
MsaG042060 AT3G10113.1 53.684 95 36 1 53 139 54 148 5.70e-25 103
MsaG042060 AT1G18330.2 53.684 95 36 1 53 139 65 159 8.04e-25 103
MsaG042060 AT1G01060.4 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT1G01060.8 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT1G01060.2 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT1G01060.3 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT1G01060.1 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT1G01060.7 47.414 116 50 2 44 149 4 118 4.24e-24 103
MsaG042060 AT2G46830.1 58.108 74 31 0 48 121 8 81 4.62e-23 100

Find 85 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGGACTCTTTAAATTAA+TGG 0.132035 8:-16145003 None:intergenic
TGTAGCTGATTGGTTGAATT+TGG 0.174297 8:-16144769 None:intergenic
CTTCTTCGATCCTTCAACTA+TGG 0.224424 8:+16139980 MsaT042060.1:CDS
TAGTAATCGTATATGGTTTC+CGG 0.225922 8:-16140100 None:intergenic
ATTACCGTTTCAACATTTAT+TGG 0.251333 8:-16144811 None:intergenic
AAACCTTGTGGTGTTGGATT+AGG 0.259526 8:-16139954 None:intergenic
TGCGCGGGCAAGCCTGTTAA+AGG 0.275255 8:+16143260 MsaT042060.1:CDS
AACCTTGTGGTGTTGGATTA+GGG 0.281198 8:-16139953 None:intergenic
CTAGATTTAGTAATCGTATA+TGG 0.282999 8:-16140107 None:intergenic
GTGGTAGATGGCGGCGGCGG+TGG 0.322284 8:-16140032 None:intergenic
CTTACATGATCCTCAAATTC+AGG 0.323692 8:-16145020 None:intergenic
TTACCGTTTCAACATTTATT+GGG 0.342283 8:-16144810 None:intergenic
GAAGCCTCCTAACCTTTAAC+AGG 0.352956 8:-16143272 None:intergenic
CTGCTATAGCAACAATTAAC+AGG 0.357595 8:-16143197 None:intergenic
GCTGCCGCGGCGGTGGTAGA+TGG 0.357714 8:-16140044 None:intergenic
GTAGATGGCGGCGGCGGTGG+AGG 0.361039 8:-16140029 None:intergenic
GGTTTCCGGATCTTCTTATT+CGG 0.369421 8:-16140086 None:intergenic
CGGTATACTTGTGCAAAATC+TGG 0.393716 8:-16144724 None:intergenic
ACAGTCATGGATTTGCTGCT+TGG 0.394971 8:-16145309 None:intergenic
CCTTCAACTATGGGTCTTCC+CGG 0.395759 8:+16139990 MsaT042060.1:CDS
AACTTTGCCTTCTCGCAGTC+AGG 0.399115 8:-16145279 None:intergenic
TTGCAATGGCCCCATGACTT+GGG 0.403594 8:-16142888 None:intergenic
ATTTCAGATTCGATCGTGAT+TGG 0.404744 8:+16142232 MsaT042060.1:intron
TTTCTCTTTGGCCGAGGAGG+AGG 0.419148 8:-16142721 None:intergenic
GATGGCGGCGGCGGTGGAGG+AGG 0.423564 8:-16140026 None:intergenic
TTTAAAGAGTCCTGAATTTG+AGG 0.425190 8:+16145010 MsaT042060.1:CDS
TAGAGAGAGTTGGACTGATC+AGG 0.431081 8:+16140127 MsaT042060.1:CDS
GCACAAGTATACCGCTTCAT+TGG 0.434161 8:+16144733 MsaT042060.1:CDS
TTAAAATTCAGAGATGATAA+AGG 0.436438 8:-16142992 None:intergenic
AAATGCCGTTCTGTCTACTT+AGG 0.437086 8:+16145341 MsaT042060.1:CDS
AATGAGAAGCAAAGTAGTAA+AGG 0.438530 8:+16143224 MsaT042060.1:CDS
ATGAGAAGCAAAGTAGTAAA+GGG 0.449900 8:+16143225 MsaT042060.1:CDS
GATAAAGGCAGATTAGTAAC+TGG 0.450205 8:-16142977 None:intergenic
AAGAAGATTGAAGCCTTTGT+TGG 0.457494 8:+16142255 MsaT042060.1:CDS
GACACAGGATGGACTGGATC+TGG 0.459539 8:+16143164 MsaT042060.1:CDS
TTCTTCGATCCTTCAACTAT+GGG 0.461447 8:+16139981 MsaT042060.1:CDS
TGTAGTCACTTGTGGCAAAC+TGG 0.462660 8:-16143029 None:intergenic
CTGTGCTATAAATGTAAGTT+GGG 0.464024 8:-16142931 None:intergenic
GTTGCAATGGCCCCATGACT+TGG 0.481177 8:-16142889 None:intergenic
AAGTAGAAACCTTGTGGTGT+TGG 0.483699 8:-16139960 None:intergenic
GCGGCGGTGGTAGATGGCGG+CGG 0.497804 8:-16140038 None:intergenic
TTCTCTTTGGCCGAGGAGGA+GGG 0.498194 8:-16142720 None:intergenic
GCAATGGCCCCATGACTTGG+GGG 0.499676 8:-16142886 None:intergenic
AGGATCCGAATAAGAAGATC+CGG 0.501021 8:+16140081 MsaT042060.1:CDS
GGTAGATGCTGCCGCGGCGG+TGG 0.502495 8:-16140051 None:intergenic
GCGGTGGTAGATGGCGGCGG+CGG 0.503415 8:-16140035 None:intergenic
TCTGTGCTATAAATGTAAGT+TGG 0.503663 8:-16142932 None:intergenic
TTACTAAATCTAGAGAGAGT+TGG 0.504946 8:+16140117 MsaT042060.1:CDS
AATGCCGTTCTGTCTACTTA+GGG 0.505971 8:+16145342 MsaT042060.1:CDS
TTTCTCAAAGTTCAGAAGAG+TGG 0.511728 8:+16142682 MsaT042060.1:CDS
CCGGGAAGACCCATAGTTGA+AGG 0.518414 8:-16139990 None:intergenic
AGTAGTAAAGGGATTAATCA+AGG 0.521159 8:+16143236 MsaT042060.1:CDS
TGCAATGGCCCCATGACTTG+GGG 0.524759 8:-16142887 None:intergenic
GGACCCAATAAATGTTGAAA+CGG 0.526498 8:+16144807 MsaT042060.1:CDS
TGTGGCAAACTGGTTGGTGG+TGG 0.532827 8:-16143019 None:intergenic
AGTTTGCCACAAGTGACTAC+AGG 0.540275 8:+16143031 MsaT042060.1:CDS
GGGATTAATCAAGGCTGCGC+GGG 0.541462 8:+16143245 MsaT042060.1:CDS
GACTCTTTAAATTAATGGAG+AGG 0.542865 8:-16144998 None:intergenic
TAAGTTGGGTCAACAAAAGC+AGG 0.550856 8:-16142917 None:intergenic
TTAGACGACACAGGATGGAC+TGG 0.557873 8:+16143158 MsaT042060.1:intron
CTTATTCGGATCCTCAGAAA+CGG 0.558704 8:-16140072 None:intergenic
GCCGCGGCGGTGGTAGATGG+CGG 0.561725 8:-16140041 None:intergenic
ACAGATTCATCATCTGTGCT+TGG 0.570501 8:+16142950 MsaT042060.1:CDS
GTCACTTGTGGCAAACTGGT+TGG 0.579535 8:-16143025 None:intergenic
ACTTGTGGCAAACTGGTTGG+TGG 0.590217 8:-16143022 None:intergenic
GCTACAGAGGCTAAAACAGA+TGG 0.597480 8:+16144786 MsaT042060.1:CDS
AACAAACCTGTAGTCACTTG+TGG 0.599352 8:-16143037 None:intergenic
AAAGCAGGTGAAGGTTGCAA+TGG 0.602544 8:-16142902 None:intergenic
GGCAGCATCTACCGTTTCTG+AGG 0.602637 8:+16140061 MsaT042060.1:CDS
GGAGGAAGATTGTTAACACC+GGG 0.609913 8:-16140008 None:intergenic
AACCCTAATCCAACACCACA+AGG 0.612459 8:+16139951 MsaT042060.1:CDS
GCCGCCATCTACCACCGCCG+CGG 0.615415 8:+16140040 MsaT042060.1:CDS
CAATGGCCCCATGACTTGGG+GGG 0.621728 8:-16142885 None:intergenic
AACGGTAGATGCTGCCGCGG+CGG 0.625748 8:-16140054 None:intergenic
ATATGATCCTGACTGCGAGA+AGG 0.632407 8:+16145272 MsaT042060.1:CDS
GGGTCAACAAAAGCAGGTGA+AGG 0.638863 8:-16142911 None:intergenic
CAAATACACTGCCAATGAAG+CGG 0.640062 8:-16144744 None:intergenic
GTGAACATGTCCCTCCTCCT+CGG 0.640352 8:+16142710 MsaT042060.1:CDS
GTTTGTTAGACGACACAGGA+TGG 0.648020 8:+16143153 MsaT042060.1:intron
AGGAGGAAGATTGTTAACAC+CGG 0.648350 8:-16140009 None:intergenic
ATTCAACCAATCAGCTACAG+AGG 0.653756 8:+16144773 MsaT042060.1:CDS
AGAAACGGTAGATGCTGCCG+CGG 0.663186 8:-16140057 None:intergenic
TCGAAGAAGTAGAAACCTTG+TGG 0.666073 8:-16139966 None:intergenic
AGGGATTAATCAAGGCTGCG+CGG 0.673504 8:+16143244 MsaT042060.1:CDS
AACACCCTAAGTAGACAGAA+CGG 0.678268 8:-16145346 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 16139939 16145362 16139939 ID=MsaG042060
Chr8 mRNA 16139939 16145362 16139939 ID=MsaT042060.1;Parent=MsaG042060
Chr8 exon 16139939 16140180 16139939 ID=MsaT042060.1.exon1;Parent=MsaT042060.1
Chr8 CDS 16139939 16140180 16139939 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16142239 16142296 16142239 ID=MsaT042060.1.exon2;Parent=MsaT042060.1
Chr8 CDS 16142239 16142296 16142239 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16142658 16142781 16142658 ID=MsaT042060.1.exon3;Parent=MsaT042060.1
Chr8 CDS 16142658 16142781 16142658 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16142873 16143052 16142873 ID=MsaT042060.1.exon4;Parent=MsaT042060.1
Chr8 CDS 16142873 16143052 16142873 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16143162 16143281 16143162 ID=MsaT042060.1.exon5;Parent=MsaT042060.1
Chr8 CDS 16143162 16143281 16143162 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16144719 16144828 16144719 ID=MsaT042060.1.exon6;Parent=MsaT042060.1
Chr8 CDS 16144719 16144828 16144719 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16144978 16145037 16144978 ID=MsaT042060.1.exon7;Parent=MsaT042060.1
Chr8 CDS 16144978 16145037 16144978 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Chr8 exon 16145255 16145362 16145255 ID=MsaT042060.1.exon8;Parent=MsaT042060.1
Chr8 CDS 16145255 16145362 16145255 ID=cds.MsaT042060.1;Parent=MsaT042060.1
Gene Sequence

>MsaT042060.1

ATGGTATCTATAAACCCTAATCCAACACCACAAGGTTTCTACTTCTTCGATCCTTCAACTATGGGTCTTCCCGGTGTTAACAATCTTCCTCCTCCACCGCCGCCGCCATCTACCACCGCCGCGGCAGCATCTACCGTTTCTGAGGATCCGAATAAGAAGATCCGGAAACCATATACGATTACTAAATCTAGAGAGAGTTGGACTGATCAGGAACATGATAAGTTTCTAGAAGCTCTTCAATTATTCGATCGTGATTGGAAGAAGATTGAAGCCTTTGTTGGTTCAAAAACAGTTATCCAGATACGAAGTCATGCACAGAAGTATTTTCTCAAAGTTCAGAAGAGTGGAACAAGTGAACATGTCCCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCACCCATACCCTCAAAAAGCTCCCAAAAATGCTCCTACTGCATCCCCCCAAGTCATGGGGCCATTGCAACCTTCACCTGCTTTTGTTGACCCAACTTACATTTATAGCACAGATTCATCATCTGTGCTTGGTACACCAGTTACTAATCTGCCTTTATCATCTCTGAATTTTAACGCTCCACCACCAACCAGTTTGCCACAAGTGACTACAGACGACACAGGATGGACTGGATCTGGACAAGCTGTTCCTGTTAATTGTTGCTATAGCAGCAGCAATGAGAAGCAAAGTAGTAAAGGGATTAATCAAGGCTGCGCGGGCAAGCCTGTTAAAGTCATGCCAGATTTTGCACAAGTATACCGCTTCATTGGCAGTGTATTTGATCCAAATTCAACCAATCAGCTACAGAGGCTAAAACAGATGGACCCAATAAATGTTGAAACGGCACTGTTGTTGATGAGAAACCTCTCCATTAATTTAAAGAGTCCTGAATTTGAGGATCATAAGAGGCTACTGTCATCATATGATCCTGACTGCGAGAAGGCAAAGTTTGCTAATCCAAGCAGCAAATCCATGACTGTAAAATCTGAAAATGCCGTTCTGTCTACTTAG
Protein sequence

>MsaT042060.1

MVSINPNPTPQGFYFFDPSTMGLPGVNNLPPPPPPPSTTAAAASTVSEDPNKKIRKPYTITKSRESWTDQEHDKFLEALQLFDRDWKKIEAFVGSKTVIQIRSHAQKYFLKVQKSGTSEHVPPPRPKRKAAHPYPQKAPKNAPTASPQVMGPLQPSPAFVDPTYIYSTDSSSVLGTPVTNLPLSSLNFNAPPPTSLPQVTTDDTGWTGSGQAVPVNCCYSSSNEKQSSKGINQGCAGKPVKVMPDFAQVYRFIGSVFDPNSTNQLQRLKQMDPINVETALLLMRNLSINLKSPEFEDHKRLLSSYDPDCEKAKFANPSSKSMTVKSENAVLST*