AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0165470


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0165470 MtrunA17_Chr1g0153661 80.471 297 12 3 1 293 1 255 2.54e-158 441
Msa0165470 MtrunA17_Chr3g0133811 46.545 275 110 9 31 291 43 294 7.47e-34 125
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0165470 AT5G42750.1 37.580 314 152 12 10 284 17 325 1.24e-20 90.5

Find 42 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGAGAATAATTCTCTTAT+AGG 0.206112 1_4:-46076592 None:intergenic
GGAATTATGTGAAGATAATT+TGG 0.215579 1_4:-46076434 None:intergenic
GGGAAGAGGATTGTGAATTT+TGG 0.259584 1_4:-46076339 None:intergenic
TCTTGTTTATTTCTAGTTCT+AGG 0.261211 1_4:-46076928 None:intergenic
AAGGGAAGTGTGAGAAGATT+TGG 0.268332 1_4:-46076519 None:intergenic
TTATCATTAAGTTCAAATAA+AGG 0.298290 1_4:+46076730 Msa0165470:CDS
TTGGACTTATTGTTATTATG+AGG 0.316639 1_4:-46076415 None:intergenic
CTGAGAATAATTCTCTTATA+GGG 0.331590 1_4:-46076591 None:intergenic
TATCATTAAGTTCAAATAAA+GGG 0.343051 1_4:+46076731 Msa0165470:CDS
TCCTCCAAGTGATAGTAGTA+TGG 0.388873 1_4:+46077059 Msa0165470:CDS
AGTTCAAATAAAGGGACAAA+AGG 0.423209 1_4:+46076739 Msa0165470:CDS
AAAAGAACACCACTGTTTGA+TGG 0.436121 1_4:-46077018 None:intergenic
AACAAGAATTGATGAAAGGT+TGG 0.450874 1_4:+46076944 Msa0165470:CDS
CTATCACTTGGAGGAGGAAG+AGG 0.459530 1_4:-46077051 None:intergenic
TGGACTTATTGTTATTATGA+GGG 0.465498 1_4:-46076414 None:intergenic
TGAAGGAAAATTCATGAGAA+GGG 0.465614 1_4:-46076360 None:intergenic
TGGTGTGAACATGGTTGTGA+TGG 0.479025 1_4:-46076319 None:intergenic
AAATTCATGAGAAGGGGAAG+AGG 0.485413 1_4:-46076353 None:intergenic
GTTCAAATAAAGGGACAAAA+GGG 0.497754 1_4:+46076740 Msa0165470:CDS
ATGAGGGAATGTTGTGTTGA+AGG 0.505922 1_4:-46076398 None:intergenic
GAGCGAGGCGATATCGATGA+AGG 0.509000 1_4:-46076538 None:intergenic
GTGAAGGAAAATTCATGAGA+AGG 0.523242 1_4:-46076361 None:intergenic
TGGAAGAAAATATCATCAGC+TGG 0.551272 1_4:-46076478 None:intergenic
TCCATACTACTATCACTTGG+AGG 0.572168 1_4:-46077060 None:intergenic
TCGCTCCTCGACAAATTCCA+TGG 0.577145 1_4:+46076555 Msa0165470:CDS
GGAGAAGTTCTCATTGATGC+TGG 0.584601 1_4:-46076997 None:intergenic
AATAAACAAGAATTGATGAA+AGG 0.588793 1_4:+46076940 Msa0165470:CDS
TCTTCCATACTACTATCACT+TGG 0.596593 1_4:-46077063 None:intergenic
AGGGAGGGTGAAACTATCCA+TGG 0.597551 1_4:-46076572 None:intergenic
AAGTGTGAGAAGATTTGGAG+AGG 0.598817 1_4:-46076514 None:intergenic
TGATAAATCAAGTGCTGTGA+AGG 0.601297 1_4:-46076455 None:intergenic
AAAGGTTGGAGTATGAAACT+AGG 0.604735 1_4:+46076958 Msa0165470:CDS
AGAATAATTCTCTTATAGGG+AGG 0.614827 1_4:-46076588 None:intergenic
GAATAATTCTCTTATAGGGA+GGG 0.624482 1_4:-46076587 None:intergenic
GAAGGAAAATTCATGAGAAG+GGG 0.624850 1_4:-46076359 None:intergenic
ATACTACTATCACTTGGAGG+AGG 0.626202 1_4:-46077057 None:intergenic
AGCGAGGCGATATCGATGAA+GGG 0.633590 1_4:-46076537 None:intergenic
ATGGAATTTGTCGAGGAGCG+AGG 0.636228 1_4:-46076553 None:intergenic
ACTATCCATGGAATTTGTCG+AGG 0.659789 1_4:-46076560 None:intergenic
GGAGAGGAAGTAAATGACCA+TGG 0.661995 1_4:-46076498 None:intergenic
GGAGTTGTGTGAGATTGTGA+AGG 0.675634 1_4:-46076377 None:intergenic
AGAACTTCTCCATCAAACAG+TGG 0.700411 1_4:+46077009 Msa0165470:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAGAATCATCAAAAA+AGG + chr1_4:46076681-46076700 Msa0165470:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG - chr1_4:46076719-46076738 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG + chr1_4:46076730-46076749 Msa0165470:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG + chr1_4:46076731-46076750 Msa0165470:CDS 15.0%
!! AAATATAGAATCATCAAAAA+AGG + chr1_4:46076681-46076700 Msa0165470:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG - chr1_4:46076719-46076738 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG + chr1_4:46076730-46076749 Msa0165470:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG + chr1_4:46076731-46076750 Msa0165470:CDS 15.0%
!!! ATTTTCTCTCTTTTGAAAAA+TGG - chr1_4:46076865-46076884 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG + chr1_4:46076895-46076914 Msa0165470:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG + chr1_4:46076940-46076959 Msa0165470:CDS 20.0%
!!! ATTTTCTCTCTTTTGAAAAA+TGG - chr1_4:46076865-46076884 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG + chr1_4:46076895-46076914 Msa0165470:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG + chr1_4:46076940-46076959 Msa0165470:CDS 20.0%
!! TGGACTTATTGTTATTATGA+GGG - chr1_4:46076417-46076436 None:intergenic 25.0%
!! TTGGACTTATTGTTATTATG+AGG - chr1_4:46076418-46076437 None:intergenic 25.0%
! GGAATTATGTGAAGATAATT+TGG - chr1_4:46076437-46076456 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG - chr1_4:46076594-46076613 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG - chr1_4:46076595-46076614 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG + chr1_4:46076834-46076853 Msa0165470:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG - chr1_4:46076931-46076950 None:intergenic 25.0%
!! TGGACTTATTGTTATTATGA+GGG - chr1_4:46076417-46076436 None:intergenic 25.0%
!! TTGGACTTATTGTTATTATG+AGG - chr1_4:46076418-46076437 None:intergenic 25.0%
! GGAATTATGTGAAGATAATT+TGG - chr1_4:46076437-46076456 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG - chr1_4:46076594-46076613 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG - chr1_4:46076595-46076614 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG + chr1_4:46076834-46076853 Msa0165470:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG - chr1_4:46076931-46076950 None:intergenic 25.0%
TGAAGGAAAATTCATGAGAA+GGG - chr1_4:46076363-46076382 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG - chr1_4:46076590-46076609 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG - chr1_4:46076591-46076610 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG + chr1_4:46076687-46076706 Msa0165470:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG + chr1_4:46076688-46076707 Msa0165470:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG + chr1_4:46076739-46076758 Msa0165470:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG + chr1_4:46076740-46076759 Msa0165470:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG + chr1_4:46076944-46076963 Msa0165470:CDS 30.0%
TGAAGGAAAATTCATGAGAA+GGG - chr1_4:46076363-46076382 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG - chr1_4:46076590-46076609 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG - chr1_4:46076591-46076610 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG + chr1_4:46076687-46076706 Msa0165470:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG + chr1_4:46076688-46076707 Msa0165470:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG + chr1_4:46076739-46076758 Msa0165470:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG + chr1_4:46076740-46076759 Msa0165470:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG + chr1_4:46076944-46076963 Msa0165470:CDS 30.0%
!! TGTGAATTTTGGTGTGAACA+TGG - chr1_4:46076331-46076350 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG - chr1_4:46076362-46076381 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG - chr1_4:46076364-46076383 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG - chr1_4:46076458-46076477 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG - chr1_4:46076481-46076500 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG + chr1_4:46076481-46076500 Msa0165470:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG + chr1_4:46076958-46076977 Msa0165470:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG - chr1_4:46077021-46077040 None:intergenic 35.0%
TCTTCCATACTACTATCACT+TGG - chr1_4:46077066-46077085 None:intergenic 35.0%
!! TGTGAATTTTGGTGTGAACA+TGG - chr1_4:46076331-46076350 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG - chr1_4:46076362-46076381 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG - chr1_4:46076364-46076383 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG - chr1_4:46076458-46076477 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG - chr1_4:46076481-46076500 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG + chr1_4:46076481-46076500 Msa0165470:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG + chr1_4:46076958-46076977 Msa0165470:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG - chr1_4:46077021-46077040 None:intergenic 35.0%
TCTTCCATACTACTATCACT+TGG - chr1_4:46077066-46077085 None:intergenic 35.0%
! GGGAAGAGGATTGTGAATTT+TGG - chr1_4:46076342-46076361 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG - chr1_4:46076356-46076375 None:intergenic 40.0%
ATGAGGGAATGTTGTGTTGA+AGG - chr1_4:46076401-46076420 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG - chr1_4:46076517-46076536 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG - chr1_4:46076522-46076541 None:intergenic 40.0%
ACTATCCATGGAATTTGTCG+AGG - chr1_4:46076563-46076582 None:intergenic 40.0%
AGAACTTCTCCATCAAACAG+TGG + chr1_4:46077009-46077028 Msa0165470:CDS 40.0%
ATACTACTATCACTTGGAGG+AGG - chr1_4:46077060-46077079 None:intergenic 40.0%
TCCTCCAAGTGATAGTAGTA+TGG + chr1_4:46077059-46077078 Msa0165470:CDS 40.0%
TCCATACTACTATCACTTGG+AGG - chr1_4:46077063-46077082 None:intergenic 40.0%
! GGGAAGAGGATTGTGAATTT+TGG - chr1_4:46076342-46076361 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG - chr1_4:46076356-46076375 None:intergenic 40.0%
ATGAGGGAATGTTGTGTTGA+AGG - chr1_4:46076401-46076420 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG - chr1_4:46076517-46076536 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG - chr1_4:46076522-46076541 None:intergenic 40.0%
ACTATCCATGGAATTTGTCG+AGG - chr1_4:46076563-46076582 None:intergenic 40.0%
AGAACTTCTCCATCAAACAG+TGG + chr1_4:46077009-46077028 Msa0165470:CDS 40.0%
ATACTACTATCACTTGGAGG+AGG - chr1_4:46077060-46077079 None:intergenic 40.0%
TCCTCCAAGTGATAGTAGTA+TGG + chr1_4:46077059-46077078 Msa0165470:CDS 40.0%
TCCATACTACTATCACTTGG+AGG - chr1_4:46077063-46077082 None:intergenic 40.0%
TGGTGTGAACATGGTTGTGA+TGG - chr1_4:46076322-46076341 None:intergenic 45.0%
GGAGTTGTGTGAGATTGTGA+AGG - chr1_4:46076380-46076399 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG - chr1_4:46076501-46076520 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG - chr1_4:46076636-46076655 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG - chr1_4:46076637-46076656 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG - chr1_4:46077000-46077019 None:intergenic 45.0%
TGGTGTGAACATGGTTGTGA+TGG - chr1_4:46076322-46076341 None:intergenic 45.0%
GGAGTTGTGTGAGATTGTGA+AGG - chr1_4:46076380-46076399 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG - chr1_4:46076501-46076520 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG - chr1_4:46076636-46076655 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG - chr1_4:46076637-46076656 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG - chr1_4:46077000-46077019 None:intergenic 45.0%
AGCGAGGCGATATCGATGAA+GGG - chr1_4:46076540-46076559 None:intergenic 50.0%
ATGGAATTTGTCGAGGAGCG+AGG - chr1_4:46076556-46076575 None:intergenic 50.0%
TCGCTCCTCGACAAATTCCA+TGG + chr1_4:46076555-46076574 Msa0165470:CDS 50.0%
AGGGAGGGTGAAACTATCCA+TGG - chr1_4:46076575-46076594 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG - chr1_4:46076638-46076657 None:intergenic 50.0%
CTATCACTTGGAGGAGGAAG+AGG - chr1_4:46077054-46077073 None:intergenic 50.0%
AGCGAGGCGATATCGATGAA+GGG - chr1_4:46076540-46076559 None:intergenic 50.0%
ATGGAATTTGTCGAGGAGCG+AGG - chr1_4:46076556-46076575 None:intergenic 50.0%
TCGCTCCTCGACAAATTCCA+TGG + chr1_4:46076555-46076574 Msa0165470:CDS 50.0%
AGGGAGGGTGAAACTATCCA+TGG - chr1_4:46076575-46076594 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG - chr1_4:46076638-46076657 None:intergenic 50.0%
CTATCACTTGGAGGAGGAAG+AGG - chr1_4:46077054-46077073 None:intergenic 50.0%
GAGCGAGGCGATATCGATGA+AGG - chr1_4:46076541-46076560 None:intergenic 55.0%
GAGCGAGGCGATATCGATGA+AGG - chr1_4:46076541-46076560 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 46076280 46077161 46076280 ID=Msa0165470;Name=Msa0165470
chr1_4 mRNA 46076280 46077161 46076280 ID=Msa0165470-mRNA-1;Parent=Msa0165470;Name=Msa0165470-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|293
chr1_4 exon 46076280 46077161 46076280 ID=Msa0165470-mRNA-1:exon:13187;Parent=Msa0165470-mRNA-1
chr1_4 CDS 46076280 46077161 46076280 ID=Msa0165470-mRNA-1:cds;Parent=Msa0165470-mRNA-1
Gene Sequence

>Msa0165470

ATGGAAAAACAAATTGAAGTAGAAAATCAACAACAAAAACCATCACAACCATGTTCACACCAAAATTCACAATCCTCTTCCCCTTCTCATGAATTTTCCTTCACAATCTCACACAACTCCTTCAACACAACATTCCCTCATAATAACAATAAGTCCAAATTATCTTCACATAATTCCTTCACAGCACTTGATTTATCACCAGCTGATGATATTTTCTTCCATGGTCATTTACTTCCTCTCCAAATCTTCTCACACTTCCCTTCATCGATATCGCCTCGCTCCTCGACAAATTCCATGGATAGTTTCACCCTCCCTATAAGAGAATTATTCTCAGAAGATGATGATGAAAATCTCCCCACAAAAGACAGTAGCAGCAGCAGCAACAGCAACAATAGCAGCAAAAATATAGAATCATCAAAAAAGGTAGAGGGTAAGTCCAAGTTTTCATTTTTATCATTAAGTTCAAATAAAGGGACAAAAGGGTGTATTAAAGAGAAAGAAGATAAAGTGAAGAATAAGAAGAAGCTGAGATTTGATTTTGATGTGTTACATGCAGTGAAAAAGTACTTAAGAAAGGTGAAGCCATTTTTCAAAAGAGAGAAAATTAGAGAACATAAAAAGTCTTATTCTTATTCAGGAAATGTAACACCTAGAACTAGAAATAAACAAGAATTGATGAAAGGTTGGAGTATGAAACTAGGACAATATTATTCAGCACCAGCATCAATGAGAACTTCTCCATCAAACAGTGGTGTTCTTTTTGCTACTACACCTCTTCCTCCTCCAAGTGATAGTAGTATGGAAGAGTTACAAGCTGCTATTCAATCTGCAATTGCTCATTGCAAAAATTCATATTCAAAAGAAGAGAAGCTCAATTGCTGA

Protein sequence

>Msa0165470

MEKQIEVENQQQKPSQPCSHQNSQSSSPSHEFSFTISHNSFNTTFPHNNNKSKLSSHNSFTALDLSPADDIFFHGHLLPLQIFSHFPSSISPRSSTNSMDSFTLPIRELFSEDDDENLPTKDSSSSSNSNNSSKNIESSKKVEGKSKFSFLSLSSNKGTKGCIKEKEDKVKNKKKLRFDFDVLHAVKKYLRKVKPFFKREKIREHKKSYSYSGNVTPRTRNKQELMKGWSMKLGQYYSAPASMRTSPSNSGVLFATTPLPPPSDSSMEELQAAIQSAIAHCKNSYSKEEKLNC*