AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG000239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000239 MtrunA17_Chr1g0154241 95.636 275 9 1 1 275 1 272 0.0 540
MsaG000239 MtrunA17_Chr1g0154211 64.794 267 85 3 5 268 6 266 3.51e-118 344
MsaG000239 MtrunA17_Chr1g0154101 62.626 297 63 5 6 256 168 462 4.08e-114 347
MsaG000239 MtrunA17_Chr1g0154101 76.101 159 37 1 2 159 5 163 1.68e-81 261
MsaG000239 MtrunA17_Chr1g0154251 64.368 261 79 5 2 249 7 266 3.29e-110 327
MsaG000239 MtrunA17_Chr1g0154111 60.741 270 76 5 5 272 9 250 2.79e-101 307
MsaG000239 MtrunA17_Chr1g0154111 56.710 231 65 8 36 257 368 572 2.83e-68 222
MsaG000239 MtrunA17_Chr1g0154191 61.686 261 56 6 1 256 1 222 5.76e-98 291
MsaG000239 MtrunA17_Chr1g0154171 59.922 257 62 5 5 258 6 224 6.16e-90 271
MsaG000239 MtrunA17_Chr1g0154131 54.753 263 55 6 2 263 164 363 6.06e-82 254
MsaG000239 MtrunA17_Chr1g0154131 74.684 158 40 0 3 160 7 164 7.94e-81 251
MsaG000239 MtrunA17_Chr1g0154161 75.000 152 35 2 5 155 13 162 1.13e-74 231
MsaG000239 MtrunA17_Chr1g0154151 55.085 236 56 6 36 268 19 207 8.89e-73 226
MsaG000239 MtrunA17_Chr1g0154071 74.046 131 34 0 6 136 12 142 2.59e-65 211
MsaG000239 MtrunA17_Chr1g0154071 66.667 147 48 1 10 156 145 290 2.75e-62 204
MsaG000239 MtrunA17_Chr1g0154041 36.275 102 64 1 21 122 15 115 3.25e-16 78.2
MsaG000239 MtrunA17_Chr3g0131891 34.021 97 63 1 20 115 17 113 1.19e-13 70.1
MsaG000239 MtrunA17_Chr7g0233561 35.106 94 61 0 22 115 19 112 3.17e-13 68.6
MsaG000239 MtrunA17_Chr7g0233571 34.375 96 62 1 21 115 9 104 1.08e-12 65.9
MsaG000239 MtrunA17_Chr7g0233531 37.975 79 49 0 37 115 2 80 7.86e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000239 AT4G33280.2 56.452 124 52 2 8 130 11 133 9.71e-44 150
MsaG000239 AT4G33280.1 56.452 124 52 2 8 130 11 133 2.68e-43 150
MsaG000239 AT4G33280.3 56.452 124 52 2 8 130 11 133 6.99e-43 151
MsaG000239 AT4G34400.2 37.113 97 60 1 22 118 17 112 2.10e-17 81.6
MsaG000239 AT4G34400.1 37.113 97 60 1 22 118 17 112 2.10e-17 81.6
MsaG000239 AT3G18990.1 34.951 103 58 1 32 125 17 119 1.09e-13 70.5
MsaG000239 AT3G18990.2 34.951 103 58 1 32 125 17 119 1.18e-13 70.5
MsaG000239 AT3G06220.1 32.584 89 59 1 22 110 11 98 1.65e-13 67.4
MsaG000239 AT3G06160.1 34.831 89 57 1 22 110 26 113 5.69e-13 68.6
MsaG000239 AT3G06160.5 34.831 89 57 1 22 110 11 98 8.10e-13 67.8
MsaG000239 AT3G06160.4 34.831 89 57 1 22 110 11 98 8.10e-13 67.8
MsaG000239 AT3G06160.3 34.831 89 57 1 22 110 11 98 8.10e-13 67.8
MsaG000239 AT3G06160.2 34.831 89 57 1 22 110 70 157 9.89e-13 67.8
MsaG000239 AT5G66980.1 41.463 82 44 1 33 110 21 102 1.60e-12 67.0
MsaG000239 AT5G60130.5 38.202 89 50 2 35 118 27 115 6.88e-12 64.3
MsaG000239 AT5G60130.3 38.202 89 50 2 35 118 1 89 1.35e-11 63.9
MsaG000239 AT5G60130.4 38.202 89 50 2 35 118 24 112 1.88e-11 63.9
MsaG000239 AT5G60130.1 38.202 89 50 2 35 118 27 115 2.00e-11 63.9
MsaG000239 AT5G60130.2 38.202 89 50 2 35 118 27 115 2.22e-11 63.5

Find 56 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTCCACTAGGACCTTTA+AGG 0.183323 1:+3176870 None:intergenic
CCTGAAAATGTGAACCTTAA+AGG 0.211774 1:-3176884 MsaT000239.1:CDS
TGAAATGGATGAACTGAAAA+TGG 0.224125 1:+3177646 None:intergenic
GCTGGTCTTCCCCGCTTCTT+AGG 0.270434 1:+3176350 None:intergenic
AGTGGAGTTGTGTGGAATAT+AGG 0.300231 1:-3176857 MsaT000239.1:CDS
CATGGGAGGAAGACATTTAC+TGG 0.340818 1:-3177671 MsaT000239.1:CDS
AACTTCGTTAACAGGCTTCT+TGG 0.341598 1:+3176385 None:intergenic
CCAGGCGTAACTTCGTTAAC+AGG 0.352395 1:+3176377 None:intergenic
GTCTTCCCCGCTTCTTAGGC+TGG 0.353235 1:+3176354 None:intergenic
AATGCGGTTCTGAGAAATTT+CGG 0.363117 1:-3176559 MsaT000239.1:CDS
CCCCGCTTCTTAGGCTGGCC+AGG 0.381562 1:+3176359 None:intergenic
CCAGCAAAATCAGCTACTTC+TGG 0.385623 1:-3176332 MsaT000239.1:CDS
GTGGAGTTGTGTGGAATATA+GGG 0.421556 1:-3176856 MsaT000239.1:CDS
TTTGTTAGAAAATGTGGAAA+AGG 0.421612 1:-3176665 MsaT000239.1:CDS
GCATCAGCCATGACCTGCTC+AGG 0.424246 1:+3176449 None:intergenic
TGAGTCTGCTTCCCCTGAGC+AGG 0.449413 1:-3176462 MsaT000239.1:CDS
GCGAGAAAGCAATTGTTGAT+TGG 0.450466 1:-3176310 MsaT000239.1:CDS
TGGGAAGTGTGAACCGATCA+TGG 0.456499 1:-3177689 MsaT000239.1:CDS
TGCTTCCCCTGAGCAGGTCA+TGG 0.458901 1:-3176456 MsaT000239.1:CDS
GAAGTCAACACTGCTTCTAA+TGG 0.464985 1:-3176590 MsaT000239.1:CDS
GCCTGGCCAGCCTAAGAAGC+GGG 0.466869 1:-3176360 MsaT000239.1:CDS
TGCGAAGAAATTGAGTGAAA+TGG 0.470492 1:+3177631 None:intergenic
AGAGCCTGCTTTCTCGCATA+AGG 0.473371 1:+3176691 None:intergenic
CCAACCGTTTGTGAAGTAAA+CGG 0.478109 1:+3176814 None:intergenic
CGAGAAAGCAATTGTTGATT+GGG 0.485091 1:-3176309 MsaT000239.1:CDS
GCGGTTCCCTCCCAAACAAC+CGG 0.485847 1:-3176416 MsaT000239.1:CDS
TCTTACTTTGTTAGAAAATG+TGG 0.486876 1:-3176671 MsaT000239.1:CDS
GACACCGTTTACTTCACAAA+CGG 0.514012 1:-3176818 MsaT000239.1:CDS
TACTTCACAAACGGTTGGCA+AGG 0.517034 1:-3176809 MsaT000239.1:CDS
CCTGTTAACGAAGTTACGCC+TGG 0.535294 1:-3176377 MsaT000239.1:CDS
GAAATGGATGAACTGAAAAT+GGG 0.537991 1:+3177647 None:intergenic
AATGAAAAGACTTCTAATGC+TGG 0.546042 1:-3176488 MsaT000239.1:CDS
CCGTTTACTTCACAAACGGT+TGG 0.558722 1:-3176814 MsaT000239.1:CDS
CATCAGCCATGACCTGCTCA+GGG 0.563227 1:+3176450 None:intergenic
CGCCTGGCCAGCCTAAGAAG+CGG 0.563693 1:-3176361 MsaT000239.1:CDS
GAAAGCAATTGTTGATTGGG+TGG 0.568458 1:-3176306 MsaT000239.1:CDS
AAATGTCTTCCTCCCATGAT+CGG 0.572099 1:+3177676 None:intergenic
CGTGAAGATCGTGAAATTGA+AGG 0.574504 1:-3174113 MsaT000239.1:CDS
ATATTCCACACAACTCCACT+AGG 0.578077 1:+3176860 None:intergenic
GAGACCTTATGCGAGAAAGC+AGG 0.587625 1:-3176695 MsaT000239.1:CDS
GCAAGAGGGCGACAAGGCAA+AGG 0.587651 1:-3176633 MsaT000239.1:CDS
GGGAAGTGTGAACCGATCAT+GGG 0.593667 1:-3177688 MsaT000239.1:CDS
GGCTGATGCAGTCACTATTG+CGG 0.596142 1:-3176435 MsaT000239.1:CDS
TACTGAGCAAGAGGGCGACA+AGG 0.599125 1:-3176639 MsaT000239.1:CDS
GTGAACCTTAAAGGTCCTAG+TGG 0.609317 1:-3176875 MsaT000239.1:CDS
AAAAGGTCATACTGAGCAAG+AGG 0.615156 1:-3176648 MsaT000239.1:CDS
AAGGTCCTAGTGGAGTTGTG+TGG 0.624686 1:-3176865 MsaT000239.1:CDS
GCTTGTAGCAAGGAAAACTC+AGG 0.631925 1:-3176284 MsaT000239.1:intron
CCTGGCCAGCCTAAGAAGCG+GGG 0.640983 1:-3176359 MsaT000239.1:CDS
GTCAACACTGCTTCTAATGG+CGG 0.645750 1:-3176587 MsaT000239.1:CDS
AAGTGTGAACCGATCATGGG+AGG 0.649028 1:-3177685 MsaT000239.1:CDS
TGATTGGGTGGCTTGTAGCA+AGG 0.654638 1:-3176294 MsaT000239.1:CDS
GAAGATCGTGAAATTGAAGG+TGG 0.655920 1:-3174110 MsaT000239.1:CDS
TCTAATGGCGGTGTTGAATG+CGG 0.661026 1:-3176575 MsaT000239.1:CDS
AAAGGTCATACTGAGCAAGA+GGG 0.680883 1:-3176647 MsaT000239.1:CDS
ATCAGCCATGACCTGCTCAG+GGG 0.726483 1:+3176451 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 3174103 3177712 3174103 ID=MsaG000239
Chr1 mRNA 3174103 3177712 3174103 ID=MsaT000239.1;Parent=MsaG000239
Chr1 exon 3174103 3174161 3174103 ID=MsaT000239.1.exon3;Parent=MsaT000239.1
Chr1 CDS 3174103 3174161 3174103 ID=cds.MsaT000239.1;Parent=MsaT000239.1
Chr1 exon 3176285 3176948 3176285 ID=MsaT000239.1.exon2;Parent=MsaT000239.1
Chr1 CDS 3176285 3176948 3176285 ID=cds.MsaT000239.1;Parent=MsaT000239.1
Chr1 exon 3177608 3177712 3177608 ID=MsaT000239.1.exon1;Parent=MsaT000239.1
Chr1 CDS 3177608 3177712 3177608 ID=cds.MsaT000239.1;Parent=MsaT000239.1
Gene Sequence

>MsaT000239.1

ATGGGAAGTGTGAACCGATCATGGGAGGAAGACATTTACTGGACCCATTTTCAGTTCATCCATTTCACTCAATTTCTTCGCAACACTGATTTTCAACAACAACTTGCACTTCCTAAAACATTTTCAGACAATTTAAAGAAGAAGTTGCCTGAAAATGTGAACCTTAAAGGTCCTAGTGGAGTTGTGTGGAATATAGGGCTGACAACTAAAGATGACACCGTTTACTTCACAAACGGTTGGCAAGGATTTGTGAATGATCACTCTTTGAAAGAGAGTGATCTCCTTTTTTTCAAGTACAATGGCGAATCGTTGTTTGAAGTTTTAATATTTCATGGCGAGACCTTATGCGAGAAAGCAGGCTCTTACTTTGTTAGAAAATGTGGAAAAGGTCATACTGAGCAAGAGGGCGACAAGGCAAAGGTTGCAAAGAATTCTGTTGAAGAAGTCAACACTGCTTCTAATGGCGGTGTTGAATGCGGTTCTGAGAAATTTCGGAAGCTTGACACTATAAGAACACCATTAGCTGTACCTTTCGAAAATACCAATGAAAAGACTTCTAATGCTGGTGTTGAGTCTGCTTCCCCTGAGCAGGTCATGGCTGATGCAGTCACTATTGCGGTTCCCTCCCAAACAACCGGCAAAAAGACCAAGAAGCCTGTTAACGAAGTTACGCCTGGCCAGCCTAAGAAGCGGGGAAGACCAGCAAAATCAGCTACTTCTGGCGAGAAAGCAATTGTTGATTGGGTGGCTTGTAGCAAGGAAAACTCAGGGAGCAAAGAGAAAGATGTTGATGATCGTGAAGATCGTGAAATTGAAGGTGGAAGCTGA
Protein sequence

>MsaT000239.1

MGSVNRSWEEDIYWTHFQFIHFTQFLRNTDFQQQLALPKTFSDNLKKKLPENVNLKGPSGVVWNIGLTTKDDTVYFTNGWQGFVNDHSLKESDLLFFKYNGESLFEVLIFHGETLCEKAGSYFVRKCGKGHTEQEGDKAKVAKNSVEEVNTASNGGVECGSEKFRKLDTIRTPLAVPFENTNEKTSNAGVESASPEQVMADAVTIAVPSQTTGKKTKKPVNEVTPGQPKKRGRPAKSATSGEKAIVDWVACSKENSGSKEKDVDDREDREIEGGS*