AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG025513

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025513 MtrunA17_Chr5g0402321 81.890 254 21 2 1 254 1 229 1.49e-146 409
MsaG025513 MtrunA17_Chr4g0066271 45.872 109 57 1 14 122 109 215 9.51e-27 107
MsaG025513 MtrunA17_Chr7g0250201 49.020 102 49 2 19 118 43 143 6.58e-22 93.6
MsaG025513 MtrunA17_Chr1g0179531 31.111 135 74 4 22 143 133 261 7.44e-16 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025513 AT3G24860.1 34.082 267 141 5 11 253 54 309 8.26e-44 150
MsaG025513 AT2G44730.1 44.348 115 54 2 9 119 51 159 1.14e-22 95.9
MsaG025513 AT3G10030.1 36.634 101 58 2 22 122 161 255 3.21e-15 75.1
MsaG025513 AT3G10030.2 36.634 101 58 2 22 122 161 255 3.55e-15 75.1
MsaG025513 AT3G54390.1 28.151 238 134 7 22 238 38 259 4.12e-15 73.9
MsaG025513 AT3G54390.2 28.151 238 134 7 22 238 54 275 5.25e-15 73.6
MsaG025513 AT3G58630.2 31.624 117 67 2 22 128 26 139 3.95e-14 71.2
MsaG025513 AT3G58630.1 31.624 117 67 2 22 128 26 139 4.82e-14 70.9

Find 81 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCTTGTTACTGTTGGTTTC+TGG 0.153076 5:-9328402 None:intergenic
TGATGAGGTTAATGGTTTCT+TGG 0.248878 5:-9327991 None:intergenic
GTAGGCTCTGATGAGGTTAA+TGG 0.265129 5:-9327999 None:intergenic
GATTCTATTGGAAAGGCATT+TGG 0.282980 5:+9328652 MsaT025513.1:CDS
TGGAGGATTGTTGATTCTAT+TGG 0.285128 5:+9328640 MsaT025513.1:CDS
ACGACATTGAAGAGCGGTTT+TGG 0.311108 5:-9328128 None:intergenic
TGCAGAGAGGATTGTAGGTT+TGG 0.345673 5:+9328528 MsaT025513.1:CDS
TCTTGGTGGGTCCATGGAAT+GGG 0.347722 5:-9327974 None:intergenic
TTCTTGGTGGGTCCATGGAA+TGG 0.347924 5:-9327975 None:intergenic
GATTAGAGATGGAGAATAAG+AGG 0.371813 5:+9328593 MsaT025513.1:CDS
ATTCTATTGGAAAGGCATTT+GGG 0.373738 5:+9328653 MsaT025513.1:CDS
CCGTCGCTATCGTCGGAGAT+AGG 0.382179 5:-9328313 None:intergenic
TTTCAGATCGGTGGCGTTGA+CGG 0.386482 5:-9328168 None:intergenic
ATGGGTTGAGGTTTCTTTGT+GGG 0.390802 5:-9327956 None:intergenic
GAAATGGTATTCACTCAAAC+GGG 0.393548 5:+9328027 MsaT025513.1:CDS
GCCCACTCCGCGGCAGTCAA+TGG 0.394607 5:+9328050 MsaT025513.1:CDS
GGAGGAGGAAGACGAAGAGG+AGG 0.400142 5:+9328465 MsaT025513.1:CDS
CCGCCGCTTCTTCTCGATCC+TGG 0.407620 5:+9328215 MsaT025513.1:CDS
AGCTTTGCAGAGAGGATTGT+AGG 0.418283 5:+9328523 MsaT025513.1:CDS
CCCATTGACTGCCGCGGAGT+GGG 0.424106 5:-9328051 None:intergenic
GAAAGAGGTCTGACGGAGAT+AGG 0.427949 5:-9328280 None:intergenic
ATGGTTTCTTGGTGGGTCCA+TGG 0.435098 5:-9327980 None:intergenic
ACAGTGCTGCTAGGTCTGTT+AGG 0.436809 5:+9328353 MsaT025513.1:CDS
TGATGATGAAGAGGAGGAGG+AGG 0.437652 5:+9328450 MsaT025513.1:CDS
TGGGTCCATGGAATGGGTTG+AGG 0.452120 5:-9327968 None:intergenic
CCCACTCCGCGGCAGTCAAT+GGG 0.457508 5:+9328051 MsaT025513.1:CDS
TGTTGTTGTCTTGTTACTGT+TGG 0.461863 5:-9328409 None:intergenic
GAGGAGGAAGACGAAGAGGA+GGG 0.463856 5:+9328466 MsaT025513.1:CDS
GGATCGAGAAGAAGCGGCGG+AGG 0.465439 5:-9328212 None:intergenic
AGAGAGGTTTAGATTAGAGA+TGG 0.466781 5:+9328582 MsaT025513.1:CDS
TTGAGGTTTCTTTGTGGGAA+GGG 0.468718 5:-9327951 None:intergenic
TCAGAGCCTACCAAGAGAAA+TGG 0.468909 5:+9328011 MsaT025513.1:CDS
AACTGATGATGAAGAGGAGG+AGG 0.476758 5:+9328447 MsaT025513.1:CDS
TCCCATTGACTGCCGCGGAG+TGG 0.479922 5:-9328052 None:intergenic
AGAAATGGTATTCACTCAAA+CGG 0.486979 5:+9328026 MsaT025513.1:CDS
GTATGATACTTGAATCTCAA+TGG 0.493726 5:+9328620 MsaT025513.1:CDS
GAGGTTAATGGTTTCTTGGT+GGG 0.497980 5:-9327987 None:intergenic
GGAGGAGGAGGAAGACGAAG+AGG 0.507090 5:+9328462 MsaT025513.1:CDS
GGAAGGGAAAGAGTGAGTTC+TGG 0.514086 5:-9327935 None:intergenic
TGAATACCATTTCTCTTGGT+AGG 0.515604 5:-9328017 None:intergenic
AGGTTTGGAAAATAAGAAGA+TGG 0.518980 5:+9328543 MsaT025513.1:CDS
TGAGTGAATACCATTTCTCT+TGG 0.519977 5:-9328021 None:intergenic
GATTGTTGATTCTATTGGAA+AGG 0.528242 5:+9328645 MsaT025513.1:CDS
AGACGAAGAGGAGGGAGTGA+TGG 0.530323 5:+9328474 MsaT025513.1:CDS
ATAGGATGCTTCTGAGAAAG+AGG 0.530581 5:-9328295 None:intergenic
TGAGGTTAATGGTTTCTTGG+TGG 0.535347 5:-9327988 None:intergenic
TCTTCAATGTCGTCATAAGA+TGG 0.539576 5:+9328138 MsaT025513.1:CDS
AATGGGTTGAGGTTTCTTTG+TGG 0.544865 5:-9327957 None:intergenic
AGAAACCTCAACCCATTCCA+TGG 0.546082 5:+9327963 MsaT025513.1:CDS
TCTCTTGGTAGGCTCTGATG+AGG 0.553443 5:-9328006 None:intergenic
TAAGAAGATGGAGATGATGA+AGG 0.556347 5:+9328555 MsaT025513.1:CDS
CGGCAGTCAATGGGAAGAAG+TGG 0.558439 5:+9328060 MsaT025513.1:CDS
GTTGAGGTTTCTTTGTGGGA+AGG 0.565690 5:-9327952 None:intergenic
CTTCTTCCCATTGACTGCCG+CGG 0.577676 5:-9328057 None:intergenic
AGAAGCGGCGGAGGAAGTAG+CGG 0.578291 5:-9328203 None:intergenic
CTGCTAGGTCTGTTAGGTCA+AGG 0.578720 5:+9328359 MsaT025513.1:CDS
GGTCTGACGGAGATAGGTAA+AGG 0.582332 5:-9328274 None:intergenic
CCGACGATAGCGACGGTGAG+AGG 0.582725 5:+9328320 MsaT025513.1:CDS
CCTCTCACCGTCGCTATCGT+CGG 0.588877 5:-9328320 None:intergenic
CGGAGGAAGTAGCGGTGAGG+CGG 0.592434 5:-9328195 None:intergenic
CTTCTGAGAAAGAGGTCTGA+CGG 0.593494 5:-9328287 None:intergenic
CGACGATAGCGACGGTGAGA+GGG 0.604292 5:+9328321 MsaT025513.1:CDS
AGTGAGTTCTGGTGAAGCGG+TGG 0.606604 5:-9327924 None:intergenic
CATGAGACGAAAATACTGCC+AGG 0.607104 5:-9328233 None:intergenic
AAGAGTGAGTTCTGGTGAAG+CGG 0.610541 5:-9327927 None:intergenic
CTGCCAGGATCGAGAAGAAG+CGG 0.618066 5:-9328218 None:intergenic
AGTTGAGAAGCTTTGCAGAG+AGG 0.619704 5:+9328515 MsaT025513.1:CDS
AGATGATGAAGGAAACAGAG+AGG 0.638850 5:+9328566 MsaT025513.1:CDS
CTCAAACGGGGCCCACTCCG+CGG 0.643190 5:+9328040 MsaT025513.1:CDS
TGATGAAACTGATGATGAAG+AGG 0.652723 5:+9328441 MsaT025513.1:CDS
TGATACTTGAATCTCAATGG+AGG 0.662965 5:+9328623 MsaT025513.1:CDS
CTCATGGATGATCTTGAACG+CGG 0.669974 5:+9328250 MsaT025513.1:CDS
CCAGGATCGAGAAGAAGCGG+CGG 0.670197 5:-9328215 None:intergenic
TGAAACTGATGATGAAGAGG+AGG 0.676552 5:+9328444 MsaT025513.1:CDS
CTTATGACGACATTGAAGAG+CGG 0.678566 5:-9328134 None:intergenic
CCTATCTCCGACGATAGCGA+CGG 0.688698 5:+9328313 MsaT025513.1:CDS
GTAATCGTAGCCGCAACGAG+CGG 0.705311 5:-9328095 None:intergenic
CGGCGGAGGAAGTAGCGGTG+AGG 0.707049 5:-9328198 None:intergenic
GATGGCGAAGAGTTTGACAG+CGG 0.738106 5:+9328492 MsaT025513.1:CDS
AAATGGTATTCACTCAAACG+GGG 0.751020 5:+9328028 MsaT025513.1:CDS
GTAGTCGTAGCCGCTCGTTG+CGG 0.770618 5:+9328085 MsaT025513.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 9327920 9328684 9327920 ID=MsaG025513
Chr5 mRNA 9327920 9328684 9327920 ID=MsaT025513.1;Parent=MsaG025513
Chr5 exon 9327920 9328684 9327920 ID=MsaT025513.1.exon1;Parent=MsaT025513.1
Chr5 CDS 9327920 9328684 9327920 ID=cds.MsaT025513.1;Parent=MsaT025513.1
Gene Sequence

>MsaT025513.1

ATGGCCACCGCTTCACCAGAACTCACTCTTTCCCTTCCCACAAAGAAACCTCAACCCATTCCATGGACCCACCAAGAAACCATTAACCTCATCAGAGCCTACCAAGAGAAATGGTATTCACTCAAACGGGGCCCACTCCGCGGCAGTCAATGGGAAGAAGTGGCTGTAGTCGTAGCCGCTCGTTGCGGCTACGATTACAACCACCCTTCCAAAACCGCTCTTCAATGTCGTCATAAGATGGAAAAACTCCGTCAACGCCACCGATCTGAAAAACACCGCCTCACCGCTACTTCCTCCGCCGCTTCTTCTCGATCCTGGCAGTATTTTCGTCTCATGGATGATCTTGAACGCGGTCCTTTACCTATCTCCGTCAGACCTCTTTCTCAGAAGCATCCTATCTCCGACGATAGCGACGGTGAGAGGGTGAAAAAGCACAGTGCTGCTAGGTCTGTTAGGTCAAGGAGTATTCATACTGTTCTTAACCAGAAACCAACAGTAACAAGACAACAACAACAACAACGTGATGAAACTGATGATGAAGAGGAGGAGGAGGAAGACGAAGAGGAGGGAGTGATGGCGAAGAGTTTGACAGCGGAGTTGAGAAGCTTTGCAGAGAGGATTGTAGGTTTGGAAAATAAGAAGATGGAGATGATGAAGGAAACAGAGAGGTTTAGATTAGAGATGGAGAATAAGAGGATTCGTATGATACTTGAATCTCAATGGAGGATTGTTGATTCTATTGGAAAGGCATTTGGGTCTTCTTAG
Protein sequence

>MsaT025513.1

MATASPELTLSLPTKKPQPIPWTHQETINLIRAYQEKWYSLKRGPLRGSQWEEVAVVVAARCGYDYNHPSKTALQCRHKMEKLRQRHRSEKHRLTATSSAASSRSWQYFRLMDDLERGPLPISVRPLSQKHPISDDSDGERVKKHSAARSVRSRSIHTVLNQKPTVTRQQQQQRDETDDEEEEEEDEEEGVMAKSLTAELRSFAERIVGLENKKMEMMKETERFRLEMENKRIRMILESQWRIVDSIGKAFGSS*