AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003094

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003094 MtrunA17_Chr1g0181001 98.272 463 8 0 1 463 1 463 0.0 942
MsaG003094 MtrunA17_Chr8g0343641 39.370 127 72 3 318 443 527 649 8.14e-18 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003094 AT2G37025.2 50.000 114 56 1 321 433 271 384 1.07e-30 123
MsaG003094 AT2G37025.3 50.000 114 56 1 321 433 271 384 1.07e-30 123
MsaG003094 AT2G37025.1 50.000 114 56 1 321 433 271 384 1.07e-30 123
MsaG003094 AT1G72650.2 46.739 92 48 1 337 428 536 626 8.94e-20 92.8
MsaG003094 AT1G72650.1 46.739 92 48 1 337 428 530 620 9.09e-20 92.8
MsaG003094 AT1G17460.3 28.623 276 125 8 231 442 306 573 4.14e-18 87.4
MsaG003094 AT1G17460.1 28.623 276 125 8 231 442 327 594 4.15e-18 87.4
MsaG003094 AT1G17460.2 28.623 276 125 8 231 442 347 614 4.29e-18 87.4

Find 89 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATAGTACCTCTTTCTT+TGG 0.210015 1:+51716152 None:intergenic
AATGAAACATGATCATTTCT+AGG 0.222946 1:+51717731 None:intergenic
TACTCTTTGGCATTTCATAT+TGG 0.278595 1:+51718638 None:intergenic
GATTTAGATTGTGTACTATT+AGG 0.281326 1:+51716617 None:intergenic
GTGCAGTACAGGCTCTTAAA+AGG 0.298577 1:+51715110 None:intergenic
ACTCGGCTAGCCACACTAAA+AGG 0.320293 1:+51714835 None:intergenic
TTTGAATGACAAAGATGATT+TGG 0.323845 1:-51717205 MsaT003094.1:CDS
TCGGACTCTTCCGAGGAAAA+AGG 0.330555 1:+51715406 None:intergenic
TTGTTTCGTCGCTTTGGGTA+TGG 0.332970 1:+51714790 None:intergenic
CTCATCCAGAGATTTAATTT+CGG 0.364384 1:+51716595 None:intergenic
ATATACTGTTAGGTCCTTGA+TGG 0.365380 1:-51716970 MsaT003094.1:intron
CTTCCATTTCATCATCTTGA+AGG 0.382415 1:+51717774 None:intergenic
CTTGATGGATTCCTTGGAGA+TGG 0.383282 1:-51716955 MsaT003094.1:CDS
TAGAAATGATCATGTTTCAT+TGG 0.391808 1:-51717729 MsaT003094.1:CDS
TAGGTCCTTGATGGATTCCT+TGG 0.398304 1:-51716961 MsaT003094.1:CDS
TGTTTCGTCGCTTTGGGTAT+GGG 0.398644 1:+51714791 None:intergenic
TGCTTATGAAGACTCGCCTT+TGG 0.398646 1:-51716720 MsaT003094.1:CDS
TAAATCCGAAATTAAATCTC+TGG 0.403561 1:-51716600 MsaT003094.1:CDS
TGCATGTGGAGGGTATTTCT+TGG 0.407708 1:-51716878 MsaT003094.1:CDS
TACATGCAATCTACATTTGA+TGG 0.413497 1:+51716524 None:intergenic
ATTCCTTGGAGATGGATTCC+TGG 0.426741 1:-51716947 MsaT003094.1:CDS
TCTACATTTGATGGTTGAGT+TGG 0.429648 1:+51716533 None:intergenic
ATTGATGGCATATCTCAATA+TGG 0.429927 1:-51715295 MsaT003094.1:CDS
CTCCCTTCAAGATGATGAAA+TGG 0.431701 1:-51717777 MsaT003094.1:CDS
AGTCATTCTCCAGGATTTAG+TGG 0.434512 1:-51716680 MsaT003094.1:CDS
CCCTGACATCTGTGGGAGTT+CGG 0.437149 1:+51715221 None:intergenic
TATACCTCTGAGTAGGCTTT+CGG 0.437182 1:+51716366 None:intergenic
ACCGAACTCCCACAGATGTC+AGG 0.442198 1:-51715222 MsaT003094.1:CDS
AATGATCATGTTTCATTGGA+TGG 0.447117 1:-51717725 MsaT003094.1:intron
CACTAAAAGGTAAGATCCGC+GGG 0.452158 1:+51714848 None:intergenic
GCATGTGGAGGGTATTTCTT+GGG 0.460808 1:-51716877 MsaT003094.1:intron
TTTCGGAATCTCTTCTCTCT+AGG 0.461041 1:+51716383 None:intergenic
TAGTGTGGCTAGCCGAGTGC+TGG 0.464765 1:-51714830 MsaT003094.1:CDS
ATGATACACATGGTGTCTTC+AGG 0.468776 1:-51716562 MsaT003094.1:CDS
AACAATGGTTATCCTTTAGC+TGG 0.469343 1:-51716464 MsaT003094.1:CDS
ACTTGCGCAAATATTCTTCC+CGG 0.477272 1:+51718664 None:intergenic
GGCTAGCCGAGTGCTGGAAT+TGG 0.480997 1:-51714824 MsaT003094.1:CDS
GAAGTGACAAAGTTGATTGA+TGG 0.483810 1:-51715310 MsaT003094.1:CDS
GCTGAATTTCTGTGCAGTAC+AGG 0.484370 1:+51715099 None:intergenic
CCGCTACTAGACTCGTCGCT+TGG 0.485164 1:+51716221 None:intergenic
CTACTGGTGTAAAACGTAAA+CGG 0.490582 1:-51716301 MsaT003094.1:CDS
CAAGAGAATATGCGATGGAC+CGG 0.494472 1:-51718683 None:intergenic
AATTCAGAAAGTCATTCTCC+AGG 0.495964 1:-51716689 MsaT003094.1:CDS
TATGGTCCATCTAGTAGTCT+TGG 0.496122 1:-51714745 MsaT003094.1:CDS
GAAGAAAGAATCAAAGGATG+TGG 0.504028 1:-51715342 MsaT003094.1:CDS
TGGTGTCAAATGTTCATCCT+CGG 0.505342 1:+51715387 None:intergenic
GGCATATCTCAATATGGAGT+TGG 0.506463 1:-51715289 MsaT003094.1:CDS
GAAATACCCTCCACATGCAT+TGG 0.510672 1:+51716882 None:intergenic
CTCAATATGGAGTTGGTCGA+TGG 0.518114 1:-51715282 MsaT003094.1:CDS
TTCCATTTCATCATCTTGAA+GGG 0.518648 1:+51717775 None:intergenic
AGATTCACCAGTGAAAACTA+TGG 0.522871 1:-51714763 MsaT003094.1:CDS
GTTGACATCAATGATCTTGA+AGG 0.524785 1:-51716919 MsaT003094.1:CDS
TGAAGACACCATGTGTATCA+TGG 0.526838 1:+51716564 None:intergenic
ATTTCATCATCTTGAAGGGA+GGG 0.528637 1:+51717779 None:intergenic
TAGTATATTGTCTTGTAAGA+AGG 0.534253 1:-51716441 MsaT003094.1:CDS
GTGCTACTTCCACTAAATCC+TGG 0.534846 1:+51716671 None:intergenic
GACAATATACTACCAGCTAA+AGG 0.542357 1:+51716452 None:intergenic
CAAGAAGCATCCAAAGAAAG+AGG 0.542469 1:-51716162 MsaT003094.1:intron
TTTAGTGGAAGTAGCACTGT+TGG 0.554801 1:-51716665 MsaT003094.1:CDS
CATTTCATCATCTTGAAGGG+AGG 0.558348 1:+51717778 None:intergenic
AAGATCGAAGAAAGAATCAA+AGG 0.561345 1:-51715348 MsaT003094.1:CDS
CGGAATCTCTTCTCTCTAGG+TGG 0.568097 1:+51716386 None:intergenic
CATTGATGTCAACATCATCC+AGG 0.573797 1:+51716929 None:intergenic
AGTGGAAGTAGCACTGTTGG+TGG 0.573972 1:-51716662 MsaT003094.1:CDS
TCTTCAATATACCTCTGAGT+AGG 0.580112 1:+51716359 None:intergenic
GTTTAGCCAATTCCAGCACT+CGG 0.584124 1:+51714818 None:intergenic
GTGGAAGTAGCACTGTTGGT+GGG 0.586298 1:-51716661 MsaT003094.1:CDS
CAAAGATGATTTGGAACTAG+AGG 0.590374 1:-51717196 MsaT003094.1:intron
CATCTCCAAGGAATCCATCA+AGG 0.593123 1:+51716956 None:intergenic
AAGAGAATATGCGATGGACC+GGG 0.599053 1:-51718682 None:intergenic
TACAGTACCCTGACATCTGT+GGG 0.600151 1:+51715214 None:intergenic
TTCATCCTCGGACTCTTCCG+AGG 0.613472 1:+51715399 None:intergenic
ATCATCTTTGTCATTCAAAG+CGG 0.620385 1:+51717209 None:intergenic
CCGAACTCCCACAGATGTCA+GGG 0.622447 1:-51715221 MsaT003094.1:intron
GAAGACACCATGTGTATCAT+GGG 0.623115 1:+51716565 None:intergenic
TATGATTTATGCAGGACAAG+TGG 0.628551 1:-51715138 MsaT003094.1:intron
GTACAGTACCCTGACATCTG+TGG 0.628681 1:+51715213 None:intergenic
TTGGCAAAAGAAATTTACGT+AGG 0.641798 1:-51714726 MsaT003094.1:CDS
CATCCAGGAATCCATCTCCA+AGG 0.645479 1:+51716944 None:intergenic
ACACTAAAAGGTAAGATCCG+CGG 0.650416 1:+51714847 None:intergenic
CATCTGCATGAGTTGAACAA+TGG 0.658137 1:-51716479 MsaT003094.1:CDS
ACAGAAATTCAGCAAGAACG+AGG 0.709656 1:-51715089 MsaT003094.1:intron
ACAGTCACCCATGATACACA+TGG 0.714461 1:-51716572 MsaT003094.1:CDS
AAGGTTGAGATACTAGAACA+TGG 0.716208 1:-51716743 MsaT003094.1:CDS
CCAAGCGACGAGTCTAGTAG+CGG 0.719801 1:-51716221 MsaT003094.1:CDS
GATTCCGAAAGCCTACTCAG+AGG 0.733180 1:-51716370 MsaT003094.1:CDS
CTGGTGTAAAACGTAAACGG+CGG 0.772509 1:-51716298 MsaT003094.1:CDS
ACTAAAAGGTAAGATCCGCG+GGG 0.799147 1:+51714849 None:intergenic
AAAATGATGAGACTGCCCCG+CGG 0.836893 1:-51714864 MsaT003094.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 51714711 51718691 51714711 ID=MsaG003094
Chr1 mRNA 51714711 51718691 51714711 ID=MsaT003094.1;Parent=MsaG003094
Chr1 exon 51714711 51714893 51714711 ID=MsaT003094.1.exon8;Parent=MsaT003094.1
Chr1 CDS 51714711 51714893 51714711 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51715090 51715146 51715090 ID=MsaT003094.1.exon7;Parent=MsaT003094.1
Chr1 CDS 51715090 51715146 51715090 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51715222 51715449 51715222 ID=MsaT003094.1.exon6;Parent=MsaT003094.1
Chr1 CDS 51715222 51715449 51715222 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51716163 51716779 51716163 ID=MsaT003094.1.exon5;Parent=MsaT003094.1
Chr1 CDS 51716163 51716779 51716163 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51716878 51716980 51716878 ID=MsaT003094.1.exon4;Parent=MsaT003094.1
Chr1 CDS 51716878 51716980 51716878 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51717197 51717249 51717197 ID=MsaT003094.1.exon3;Parent=MsaT003094.1
Chr1 CDS 51717197 51717249 51717197 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51717726 51717825 51717726 ID=MsaT003094.1.exon2;Parent=MsaT003094.1
Chr1 CDS 51717726 51717825 51717726 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Chr1 exon 51718641 51718691 51718641 ID=MsaT003094.1.exon1;Parent=MsaT003094.1
Chr1 CDS 51718641 51718691 51718641 ID=cds.MsaT003094.1;Parent=MsaT003094.1
Gene Sequence

>MsaT003094.1

ATGGACCGGGAAGAATATTTGCGCAAGTGTTCCAATATGAAATGCCAAAGAGTTCAGCTTGATGAATCATATGTGCCCTCCCTTCAAGATGATGAAATGGAAGTTGAGCATTTGCTTGAAGAACCTAGAAATGATCATGTTTCATTGGATGGCACTTTAACTTCTCATACCGCTTTGAATGACAAAGATGATTTGGAACTAGAGGTCCTTGATGGATTCCTTGGAGATGGATTCCTGGATGATGTTGACATCAATGATCTTGAAGGAACTGATGTTTTCTCCAATGCATGTGGAGGGTATTTCTTGGATTTTGATTTGGCAAAGGTTGAGATACTAGAACATGGTGCTTATGAAGACTCGCCTTTGGAAAATTCAAATTCAGAAAGTCATTCTCCAGGATTTAGTGGAAGTAGCACTGTTGGTGGGATATCAGAATCAACAAAAGCACCTAATAGTACACAATCTAAATCCGAAATTAAATCTCTGGATGAGACAGTCACCCATGATACACATGGTGTCTTCAGGAACAATCCAACTCAACCATCAAATGTAGATTGCATGTACAACATTTCACTTGATATACAGCATCTGCATGAGTTGAACAATGGTTATCCTTTAGCTGGTAGTATATTGTCTTGTAAGAAGGAAAATGTTACTGTTGAACAATGTCAATCTGCTCCACCTAGAGAGAAGAGATTCCGAAAGCCTACTCAGAGGTATATTGAAGAATCTTCAAATTTGAAGTCAAAAGAAAAAGTATCAACTACTGGTGTAAAACGTAAACGGCGGACTGTGTCATTAAGCAATGAGTTCCATACAAAAACTAAAGAATTGAAAGATATTCCAAGCGACGAGTCTAGTAGCGGTAATAGTGATGTGACGCTTTCTGAGTTGCAACACTGCAAGAAGCATCCAAAGAAAGAGAAGCTTGAGTATGACTACGAGCCTTTTTCCTCGGAAGAGTCCGAGGATGAACATTTGACACCAAAAAGAGGCAGATCAAAAGATCGAAGAAAGAATCAAAGGATGTGGACAGTCTCTGAAGTGACAAAGTTGATTGATGGCATATCTCAATATGGAGTTGGTCGATGGACTGATATACAGAAGTTTTTGTTTTCTTCTGAAGGCTACCGAACTCCCACAGATGTCAGGGACAAGTGGCGTAACCTTTTAAGAGCCTGTACTGCACAGAAATTCAGCAAGAACGAGGATGAGCAAAATGATGAGACTGCCCCGCGGATCTTACCTTTTAGTGTGGCTAGCCGAGTGCTGGAATTGGCTAAACTTCACCCATACCCAAAGCGACGAAACAAAAAGAGATTCACCAGTGAAAACTATGGTCCATCTAGTAGTCTTGGCAAAAGAAATTTACGTAGGAAGAAGTGTACTTAG
Protein sequence

>MsaT003094.1

MDREEYLRKCSNMKCQRVQLDESYVPSLQDDEMEVEHLLEEPRNDHVSLDGTLTSHTALNDKDDLELEVLDGFLGDGFLDDVDINDLEGTDVFSNACGGYFLDFDLAKVEILEHGAYEDSPLENSNSESHSPGFSGSSTVGGISESTKAPNSTQSKSEIKSLDETVTHDTHGVFRNNPTQPSNVDCMYNISLDIQHLHELNNGYPLAGSILSCKKENVTVEQCQSAPPREKRFRKPTQRYIEESSNLKSKEKVSTTGVKRKRRTVSLSNEFHTKTKELKDIPSDESSSGNSDVTLSELQHCKKHPKKEKLEYDYEPFSSEESEDEHLTPKRGRSKDRRKNQRMWTVSEVTKLIDGISQYGVGRWTDIQKFLFSSEGYRTPTDVRDKWRNLLRACTAQKFSKNEDEQNDETAPRILPFSVASRVLELAKLHPYPKRRNKKRFTSENYGPSSSLGKRNLRRKKCT*