AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27370


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27370.t1 MTR_1g021440 65.179 224 69 3 1 221 37 254 3.16e-96 283
MS.gene27370.t1 MTR_1g021440 65.179 224 69 3 1 221 37 254 1.35e-94 282
MS.gene27370.t1 MTR_1g021320 60.300 267 59 4 1 221 197 462 1.48e-94 294
MS.gene27370.t1 MTR_1g021320 76.613 124 29 0 1 124 40 163 3.77e-61 205
MS.gene27370.t1 MTR_1g021440 67.647 204 58 2 1 201 37 235 1.10e-93 276
MS.gene27370.t1 MTR_1g021440 67.647 204 58 2 1 201 37 235 3.95e-92 275
MS.gene27370.t1 MTR_1g021350 61.674 227 59 6 1 221 36 240 5.70e-85 256
MS.gene27370.t1 MTR_1g021330 62.162 222 55 4 1 221 41 234 8.88e-84 254
MS.gene27370.t1 MTR_1g021435 60.444 225 46 5 1 221 37 222 4.37e-78 239
MS.gene27370.t1 MTR_1g021380 57.143 224 49 5 1 221 36 215 5.31e-74 228
MS.gene27370.t1 MTR_1g021400 57.658 222 56 3 1 221 45 229 1.06e-72 225
MS.gene27370.t1 MTR_1g021410 56.696 224 56 5 1 221 37 222 2.26e-67 211
MS.gene27370.t1 MTR_1g021500 52.423 227 76 6 1 214 41 248 2.42e-62 201
MS.gene27370.t1 MTR_1g021500 52.423 227 76 6 1 214 41 248 6.23e-62 201
MS.gene27370.t1 MTR_1g021360 54.412 204 41 4 1 203 197 349 2.13e-60 196
MS.gene27370.t1 MTR_1g021360 73.600 125 33 0 1 125 40 164 5.32e-60 195
MS.gene27370.t1 MTR_1g021290 68.595 121 38 0 1 121 170 290 7.44e-52 171
MS.gene27370.t1 MTR_1g021290 73.267 101 27 0 1 101 42 142 2.91e-48 162
MS.gene27370.t1 MTR_1g021270 38.372 86 52 1 2 87 31 115 3.22e-14 71.2
MS.gene27370.t1 MTR_7g050710 37.838 74 46 0 2 75 29 102 4.67e-12 64.3
MS.gene27370.t1 MTR_3g098790 37.500 80 50 0 1 80 28 107 6.41e-12 64.3
MS.gene27370.t1 MTR_7g050640 37.333 75 47 0 1 75 28 102 1.02e-11 60.5
MS.gene27370.t1 MTR_7g050580 37.975 79 49 0 2 80 29 107 1.13e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27370.t1 AT4G33280 56.250 96 41 1 1 95 38 133 6.90e-31 115
MS.gene27370.t1 AT4G33280 56.250 96 41 1 1 95 38 133 1.62e-30 115
MS.gene27370.t1 AT4G33280 56.250 96 41 1 1 95 38 133 3.24e-30 115
MS.gene27370.t1 AT4G34400 39.759 83 50 0 1 83 30 112 2.84e-17 79.7
MS.gene27370.t1 AT4G34400 39.759 83 50 0 1 83 30 112 2.84e-17 79.7
MS.gene27370.t1 AT3G06220 33.784 74 49 0 2 75 25 98 9.98e-13 64.3
MS.gene27370.t1 AT3G18990 34.694 98 55 1 2 90 22 119 1.02e-12 66.6
MS.gene27370.t1 AT3G18990 34.694 98 55 1 2 90 22 119 1.02e-12 66.6
MS.gene27370.t1 AT3G06160 36.000 75 48 0 1 75 39 113 8.69e-12 63.9
MS.gene27370.t1 AT3G06160 36.000 75 48 0 1 75 24 98 1.05e-11 63.5
MS.gene27370.t1 AT3G06160 36.000 75 48 0 1 75 24 98 1.05e-11 63.5
MS.gene27370.t1 AT3G06160 36.000 75 48 0 1 75 24 98 1.05e-11 63.5
MS.gene27370.t1 AT3G06160 36.000 75 48 0 1 75 83 157 1.06e-11 63.9
MS.gene27370.t1 AT5G60130 38.636 88 49 2 1 83 28 115 1.29e-11 62.4
MS.gene27370.t1 AT5G60130 38.636 88 49 2 1 83 2 89 2.24e-11 62.4
MS.gene27370.t1 AT5G66980 40.506 79 43 1 1 75 24 102 2.39e-11 62.4
MS.gene27370.t1 AT5G60130 38.636 88 49 2 1 83 28 115 2.99e-11 62.0
MS.gene27370.t1 AT5G60130 38.636 88 49 2 1 83 28 115 3.23e-11 62.0
MS.gene27370.t1 AT5G60130 38.636 88 49 2 1 83 25 112 3.26e-11 62.0

Find 46 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTCCACTAGGACCTTTA+AGG 0.183323 1.2:+3139559 None:intergenic
CCTGAAAATGTGAACCTTAA+AGG 0.211774 1.2:-3139573 MS.gene27370:CDS
GCTGGTCTTCCCCGCTTCTT+AGG 0.270434 1.2:+3139039 None:intergenic
AGTGGAGTTGTGTGGAATAT+AGG 0.300231 1.2:-3139546 MS.gene27370:CDS
AACTTCGTTAACAGGCTTCT+TGG 0.341598 1.2:+3139074 None:intergenic
CCAGGCGTAACTTCGTTAAC+AGG 0.352395 1.2:+3139066 None:intergenic
GTCTTCCCCGCTTCTTAGGC+TGG 0.353235 1.2:+3139043 None:intergenic
AATGCGGTTCTGAGAAATTT+CGG 0.363117 1.2:-3139248 MS.gene27370:CDS
CCCCGCTTCTTAGGCTGGCC+AGG 0.381562 1.2:+3139048 None:intergenic
CCAGCAAAATCAGCTACTTC+TGG 0.385623 1.2:-3139021 MS.gene27370:CDS
GTGGAGTTGTGTGGAATATA+GGG 0.421556 1.2:-3139545 MS.gene27370:CDS
TTTGTTAGAAAATGTGGAAA+AGG 0.421612 1.2:-3139354 MS.gene27370:CDS
GCATCAGCCATGACCTGCTC+AGG 0.424246 1.2:+3139138 None:intergenic
TGAGTCTGCTTCCCCTGAGC+AGG 0.449413 1.2:-3139151 MS.gene27370:CDS
GCGAGAAAGCAATTGTTGAT+TGG 0.450466 1.2:-3138999 MS.gene27370:CDS
TGCTTCCCCTGAGCAGGTCA+TGG 0.458901 1.2:-3139145 MS.gene27370:CDS
GAAGTCAACACTGCTTCTAA+TGG 0.464985 1.2:-3139279 MS.gene27370:CDS
GCCTGGCCAGCCTAAGAAGC+GGG 0.466869 1.2:-3139049 MS.gene27370:CDS
AGAGCCTGCTTTCTCGCATA+AGG 0.473371 1.2:+3139380 None:intergenic
CGAGAAAGCAATTGTTGATT+GGG 0.485091 1.2:-3138998 MS.gene27370:CDS
GCGGTTCCCTCCCAAACAAC+CGG 0.485847 1.2:-3139105 MS.gene27370:CDS
TCTTACTTTGTTAGAAAATG+TGG 0.486876 1.2:-3139360 MS.gene27370:CDS
TACTTCACAAACGGTTGGCA+TGG 0.494310 1.2:-3139498 MS.gene27370:CDS
GACACCGTTTACTTCACAAA+CGG 0.514012 1.2:-3139507 MS.gene27370:CDS
CCAACCGTTTGTGAAGTAAA+CGG 0.534062 1.2:+3139503 None:intergenic
CCTGTTAACGAAGTTACGCC+TGG 0.535294 1.2:-3139066 MS.gene27370:CDS
AATGAAAAGACTTCTAATGC+TGG 0.546042 1.2:-3139177 MS.gene27370:CDS
CCGTTTACTTCACAAACGGT+TGG 0.558722 1.2:-3139503 MS.gene27370:CDS
CATCAGCCATGACCTGCTCA+GGG 0.563227 1.2:+3139139 None:intergenic
CGCCTGGCCAGCCTAAGAAG+CGG 0.563693 1.2:-3139050 MS.gene27370:CDS
GAAAGCAATTGTTGATTGGG+TGG 0.568458 1.2:-3138995 MS.gene27370:CDS
ATATTCCACACAACTCCACT+AGG 0.578077 1.2:+3139549 None:intergenic
GAGACCTTATGCGAGAAAGC+AGG 0.587625 1.2:-3139384 MS.gene27370:CDS
GCAAGAGGGCGACAAGGCAA+AGG 0.587651 1.2:-3139322 MS.gene27370:CDS
GGCTGATGCAGTCACTATTG+CGG 0.596142 1.2:-3139124 MS.gene27370:CDS
TACTGAGCAAGAGGGCGACA+AGG 0.599125 1.2:-3139328 MS.gene27370:CDS
GTGAACCTTAAAGGTCCTAG+TGG 0.609317 1.2:-3139564 MS.gene27370:CDS
AAAAGGTCATACTGAGCAAG+AGG 0.615156 1.2:-3139337 MS.gene27370:CDS
AAGGTCCTAGTGGAGTTGTG+TGG 0.624686 1.2:-3139554 MS.gene27370:CDS
GCTTGTAGCAAGGAAAACTC+AGG 0.631925 1.2:-3138973 None:intergenic
CCTGGCCAGCCTAAGAAGCG+GGG 0.640983 1.2:-3139048 MS.gene27370:CDS
GTCAACACTGCTTCTAATGG+CGG 0.645750 1.2:-3139276 MS.gene27370:CDS
TGATTGGGTGGCTTGTAGCA+AGG 0.654638 1.2:-3138983 MS.gene27370:CDS
TCTAATGGCGGTGTTGAATG+CGG 0.661026 1.2:-3139264 MS.gene27370:CDS
AAAGGTCATACTGAGCAAGA+GGG 0.680883 1.2:-3139336 MS.gene27370:CDS
ATCAGCCATGACCTGCTCAG+GGG 0.726483 1.2:+3139140 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGAAGTTTTAATATTTCA+TGG - chr1.2:3139181-3139200 MS.gene27370:CDS 15.0%
!!! AAATTGTCTGAAAATGTTTT+AGG + chr1.2:3138983-3139002 None:intergenic 20.0%
! TCTTACTTTGTTAGAAAATG+TGG - chr1.2:3139229-3139248 MS.gene27370:CDS 25.0%
! TTTGTTAGAAAATGTGGAAA+AGG - chr1.2:3139235-3139254 MS.gene27370:CDS 25.0%
!! TTTTCATTGGTATTTTCGAA+AGG + chr1.2:3139400-3139419 None:intergenic 25.0%
AATGAAAAGACTTCTAATGC+TGG - chr1.2:3139412-3139431 MS.gene27370:CDS 30.0%
! AGCATTAGAAGTCTTTTCAT+TGG + chr1.2:3139413-3139432 None:intergenic 30.0%
!!! CTCCTTTTTTTCAAGTACAA+TGG - chr1.2:3139148-3139167 MS.gene27370:CDS 30.0%
CCTGAAAATGTGAACCTTAA+AGG - chr1.2:3139016-3139035 MS.gene27370:CDS 35.0%
CGCCATTGTACTTGAAAAAA+AGG + chr1.2:3139153-3139172 None:intergenic 35.0%
! CGAGAAAGCAATTGTTGATT+GGG - chr1.2:3139591-3139610 MS.gene27370:CDS 35.0%
!! AATGCGGTTCTGAGAAATTT+CGG - chr1.2:3139341-3139360 MS.gene27370:CDS 35.0%
!! TTTTCGAAAGGTACAGCTAA+TGG + chr1.2:3139388-3139407 None:intergenic 35.0%
!!! CCTTTAAGGTTCACATTTTC+AGG + chr1.2:3139019-3139038 None:intergenic 35.0%
AAAAGGTCATACTGAGCAAG+AGG - chr1.2:3139252-3139271 MS.gene27370:CDS 40.0%
AAAGGTCATACTGAGCAAGA+GGG - chr1.2:3139253-3139272 MS.gene27370:CDS 40.0%
AACTTCGTTAACAGGCTTCT+TGG + chr1.2:3139518-3139537 None:intergenic 40.0%
AGTGGAGTTGTGTGGAATAT+AGG - chr1.2:3139043-3139062 MS.gene27370:CDS 40.0%
ATATTCCACACAACTCCACT+AGG + chr1.2:3139043-3139062 None:intergenic 40.0%
CCAACCGTTTGTGAAGTAAA+CGG + chr1.2:3139089-3139108 None:intergenic 40.0%
GAAGTCAACACTGCTTCTAA+TGG - chr1.2:3139310-3139329 MS.gene27370:CDS 40.0%
GACACCGTTTACTTCACAAA+CGG - chr1.2:3139082-3139101 MS.gene27370:CDS 40.0%
GCGAGAAAGCAATTGTTGAT+TGG - chr1.2:3139590-3139609 MS.gene27370:CDS 40.0%
GTGGAGTTGTGTGGAATATA+GGG - chr1.2:3139044-3139063 MS.gene27370:CDS 40.0%
! GAAAGCAATTGTTGATTGGG+TGG - chr1.2:3139594-3139613 MS.gene27370:CDS 40.0%
CAACTCCACTAGGACCTTTA+AGG + chr1.2:3139033-3139052 None:intergenic 45.0%
CCAGCAAAATCAGCTACTTC+TGG - chr1.2:3139568-3139587 MS.gene27370:CDS 45.0%
CCGTTTACTTCACAAACGGT+TGG - chr1.2:3139086-3139105 MS.gene27370:CDS 45.0%
GCTTGTAGCAAGGAAAACTC+AGG - chr1.2:3139616-3139635 MS.gene27370:CDS 45.0%
GTCAACACTGCTTCTAATGG+CGG - chr1.2:3139313-3139332 MS.gene27370:CDS 45.0%
GTGAACCTTAAAGGTCCTAG+TGG - chr1.2:3139025-3139044 MS.gene27370:CDS 45.0%
TACTTCACAAACGGTTGGCA+TGG - chr1.2:3139091-3139110 MS.gene27370:CDS 45.0%
! TCTAATGGCGGTGTTGAATG+CGG - chr1.2:3139325-3139344 MS.gene27370:CDS 45.0%
!! AGGCTTCTTGGTCTTTTTGC+CGG + chr1.2:3139506-3139525 None:intergenic 45.0%
!! CCAGAAGTAGCTGATTTTGC+TGG + chr1.2:3139571-3139590 None:intergenic 45.0%
!! GGTCTTTTTGCCGGTTGTTT+GGG + chr1.2:3139497-3139516 None:intergenic 45.0%
!! TGGTCTTTTTGCCGGTTGTT+TGG + chr1.2:3139498-3139517 None:intergenic 45.0%
!! TTTTTGCCGGTTGTTTGGGA+GGG + chr1.2:3139493-3139512 None:intergenic 45.0%
AAGGTCCTAGTGGAGTTGTG+TGG - chr1.2:3139035-3139054 MS.gene27370:CDS 50.0%
AGAGCCTGCTTTCTCGCATA+AGG + chr1.2:3139212-3139231 None:intergenic 50.0%
CCAGGCGTAACTTCGTTAAC+AGG + chr1.2:3139526-3139545 None:intergenic 50.0%
CCTGTTAACGAAGTTACGCC+TGG - chr1.2:3139523-3139542 MS.gene27370:CDS 50.0%
GAGACCTTATGCGAGAAAGC+AGG - chr1.2:3139205-3139224 MS.gene27370:CDS 50.0%
GGCTGATGCAGTCACTATTG+CGG - chr1.2:3139465-3139484 MS.gene27370:CDS 50.0%
! TGATTGGGTGGCTTGTAGCA+AGG - chr1.2:3139606-3139625 MS.gene27370:CDS 50.0%
!! CTTTTTGCCGGTTGTTTGGG+AGG + chr1.2:3139494-3139513 None:intergenic 50.0%
ATCAGCCATGACCTGCTCAG+GGG + chr1.2:3139452-3139471 None:intergenic 55.0%
CATCAGCCATGACCTGCTCA+GGG + chr1.2:3139453-3139472 None:intergenic 55.0%
TACTGAGCAAGAGGGCGACA+AGG - chr1.2:3139261-3139280 MS.gene27370:CDS 55.0%
GCAAGAGGGCGACAAGGCAA+AGG - chr1.2:3139267-3139286 MS.gene27370:CDS 60.0%
GCATCAGCCATGACCTGCTC+AGG + chr1.2:3139454-3139473 None:intergenic 60.0%
GCGGTTCCCTCCCAAACAAC+CGG - chr1.2:3139484-3139503 MS.gene27370:CDS 60.0%
GTCTTCCCCGCTTCTTAGGC+TGG + chr1.2:3139549-3139568 None:intergenic 60.0%
TGAGTCTGCTTCCCCTGAGC+AGG - chr1.2:3139438-3139457 MS.gene27370:CDS 60.0%
TGCTTCCCCTGAGCAGGTCA+TGG - chr1.2:3139444-3139463 MS.gene27370:CDS 60.0%
!! GCTGGTCTTCCCCGCTTCTT+AGG + chr1.2:3139553-3139572 None:intergenic 60.0%
CCTGGCCAGCCTAAGAAGCG+GGG - chr1.2:3139541-3139560 MS.gene27370:CDS 65.0%
CGCCTGGCCAGCCTAAGAAG+CGG - chr1.2:3139539-3139558 MS.gene27370:CDS 65.0%
GCCTGGCCAGCCTAAGAAGC+GGG - chr1.2:3139540-3139559 MS.gene27370:CDS 65.0%
! CCCCGCTTCTTAGGCTGGCC+AGG + chr1.2:3139544-3139563 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 3138974 3139637 3138974 ID=MS.gene27370
chr1.2 mRNA 3138974 3139637 3138974 ID=MS.gene27370.t1;Parent=MS.gene27370
chr1.2 exon 3138974 3139637 3138974 ID=MS.gene27370.t1.exon1;Parent=MS.gene27370.t1
chr1.2 CDS 3138974 3139637 3138974 ID=cds.MS.gene27370.t1;Parent=MS.gene27370.t1
Gene Sequence

>MS.gene27370

GCACTTCCTAAAACATTTTCAGACAATTTAAAGAAGAAGTTGCCTGAAAATGTGAACCTTAAAGGTCCTAGTGGAGTTGTGTGGAATATAGGGCTGACAACTAAAGATGACACCGTTTACTTCACAAACGGTTGGCATGGATTTGTGAATGATCACTCTTTGAAAGAGAGTGATCTCCTTTTTTTCAAGTACAATGGCGAATCGTTGTTTGAAGTTTTAATATTTCATGGCGAGACCTTATGCGAGAAAGCAGGCTCTTACTTTGTTAGAAAATGTGGAAAAGGTCATACTGAGCAAGAGGGCGACAAGGCAAAGGTTGCAAAGAATTCTGTTGAAGAAGTCAACACTGCTTCTAATGGCGGTGTTGAATGCGGTTCTGAGAAATTTCGGAAGCTTGACACTATAAGAACACCATTAGCTGTACCTTTCGAAAATACCAATGAAAAGACTTCTAATGCTGGTGTTGAGTCTGCTTCCCCTGAGCAGGTCATGGCTGATGCAGTCACTATTGCGGTTCCCTCCCAAACAACCGGCAAAAAGACCAAGAAGCCTGTTAACGAAGTTACGCCTGGCCAGCCTAAGAAGCGGGGAAGACCAGCAAAATCAGCTACTTCTGGCGAGAAAGCAATTGTTGATTGGGTGGCTTGTAGCAAGGAAAACTCAG

Protein sequence

>MS.gene27370.t1

ALPKTFSDNLKKKLPENVNLKGPSGVVWNIGLTTKDDTVYFTNGWHGFVNDHSLKESDLLFFKYNGESLFEVLIFHGETLCEKAGSYFVRKCGKGHTEQEGDKAKVAKNSVEEVNTASNGGVECGSEKFRKLDTIRTPLAVPFENTNEKTSNAGVESASPEQVMADAVTIAVPSQTTGKKTKKPVNEVTPGQPKKRGRPAKSATSGEKAIVDWVACSKENS