AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580025769.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580025769.01.T01 MTR_5g034230 95.968 248 10 0 1 248 1 248 1.96e-141 396
MsG0580025769.01.T01 MTR_8g064650 39.111 225 118 7 36 248 103 320 2.67e-36 131
MsG0580025769.01.T01 MTR_3g077890 30.488 246 112 9 32 248 70 285 4.10e-21 90.1
MsG0580025769.01.T01 MTR_4g105750 30.256 195 106 9 9 190 25 202 1.39e-14 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580025769.01.T01 AT1G70420 42.146 261 123 7 9 248 19 272 2.63e-48 160
MsG0580025769.01.T01 AT1G23710 36.054 294 133 10 1 248 11 295 1.41e-39 139
MsG0580025769.01.T01 AT3G27880 35.075 134 59 3 124 240 114 236 7.38e-13 66.6

Find 48 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACCTCTTAGCGAGGTTTC+TGG 0.215685 5:+23913852 MsG0580025769.01.T01:CDS
CCAAACAATTCTTGCCTATA+TGG 0.241815 5:-23914503 None:intergenic
CCATATAGGCAAGAATTGTT+TGG 0.312992 5:+23914503 MsG0580025769.01.T01:CDS
GGAAATCTTATTTGCCATAT+AGG 0.323222 5:+23914489 MsG0580025769.01.T01:CDS
CATATCGAAAATTCTCAATA+AGG 0.346868 5:-23914572 None:intergenic
GAAAATGGTGAAAGGTAAAA+AGG 0.359387 5:+23914397 MsG0580025769.01.T01:CDS
CATATAGGCAAGAATTGTTT+GGG 0.361904 5:+23914504 MsG0580025769.01.T01:CDS
GACGATTACGATAATGAATC+TGG 0.380124 5:+23914098 MsG0580025769.01.T01:CDS
GCGGAAATCGGTGAACCTTT+AGG 0.386454 5:-23914005 None:intergenic
CTTTGCTAGTACAAATGGAT+TGG 0.388215 5:+23914529 MsG0580025769.01.T01:CDS
AACACATCGTCAGCGGAAAT+CGG 0.392748 5:-23914017 None:intergenic
GCTGACGATGTGTTTGATAA+AGG 0.398323 5:+23914026 MsG0580025769.01.T01:CDS
TGCTGTAAAGAAAGTGAAAA+TGG 0.403149 5:+23914382 MsG0580025769.01.T01:CDS
GGGTTCTTTGCTAGTACAAA+TGG 0.406783 5:+23914524 MsG0580025769.01.T01:CDS
TTTGCTAGTACAAATGGATT+GGG 0.425121 5:+23914530 MsG0580025769.01.T01:CDS
AGCCACGAGTTCTGCGGCGG+TGG 0.451550 5:+23914175 MsG0580025769.01.T01:CDS
AAGGTAGAGAAAACGAGTTC+CGG 0.462931 5:+23914338 MsG0580025769.01.T01:CDS
TTCTCATGCGCCGACGGCGC+CGG 0.469285 5:-23914425 None:intergenic
ACGAGTTCTGCGGCGGTGGA+AGG 0.479410 5:+23914179 MsG0580025769.01.T01:CDS
TTTCCAGAAACCTCGCTAAG+AGG 0.489550 5:-23913855 None:intergenic
TGTGATGAGTAAAGCGAGGA+AGG 0.493698 5:+23914454 MsG0580025769.01.T01:CDS
AAAGGCGGCTCCGGCGCCGT+CGG 0.495359 5:+23914415 MsG0580025769.01.T01:CDS
CAACAGGATCATCAAACCTA+TGG 0.498516 5:+23914246 MsG0580025769.01.T01:CDS
CGAGGAAGGAAAGTGATAAA+CGG 0.500982 5:+23914468 MsG0580025769.01.T01:CDS
ATTCTTCGTCTCGCCGGCGC+CGG 0.505076 5:-23914357 None:intergenic
TCGGATCTCTTAACTTCCAT+AGG 0.509387 5:-23914262 None:intergenic
GCGGTGAAGAGTAATTCAAC+AGG 0.510549 5:+23914230 MsG0580025769.01.T01:CDS
CGAGTTCTGCGGCGGTGGAA+GGG 0.519054 5:+23914180 MsG0580025769.01.T01:CDS
TTCCACCGCCGCAGAACTCG+TGG 0.531134 5:-23914177 None:intergenic
AGCAACATTCTTCGTCTCGC+CGG 0.532365 5:-23914363 None:intergenic
TGAATCTGGAAACCGTTCGC+CGG 0.549557 5:+23914112 MsG0580025769.01.T01:CDS
GAGAAAACGAGTTCCGGCGC+CGG 0.566711 5:+23914344 MsG0580025769.01.T01:CDS
AAAATTTCTTTACCGGCGAA+CGG 0.570175 5:-23914124 None:intergenic
AAGAAAGTGAAAATGGTGAA+AGG 0.583207 5:+23914389 MsG0580025769.01.T01:CDS
TGGAAGGGACGTACTGCGAG+TGG 0.584129 5:+23914195 MsG0580025769.01.T01:CDS
TTCAGCTTCACCTCTTAGCG+AGG 0.586350 5:+23913845 MsG0580025769.01.T01:CDS
TAATGTTTCTCATGCGCCGA+CGG 0.590741 5:-23914431 None:intergenic
TCACTGTTACTTCTCAACTT+CGG 0.591865 5:-23914281 None:intergenic
AGATTCATTATCGTAATCGT+CGG 0.618554 5:-23914096 None:intergenic
GTGGCTGTCTTCGACGAAGA+CGG 0.621629 5:-23914158 None:intergenic
CAAATGGATTGGGAATGAGT+AGG 0.630616 5:+23914540 MsG0580025769.01.T01:CDS
GACAGCCACGAGTTCTGCGG+CGG 0.647643 5:+23914172 MsG0580025769.01.T01:CDS
GAAGACAGCCACGAGTTCTG+CGG 0.653644 5:+23914169 MsG0580025769.01.T01:CDS
CGAGTGGAATCCAACAAAAG+CGG 0.671451 5:+23914211 MsG0580025769.01.T01:CDS
TTTATCAAACACATCGTCAG+CGG 0.673861 5:-23914024 None:intergenic
ATTATGTGATGAGTAAAGCG+AGG 0.682546 5:+23914450 MsG0580025769.01.T01:CDS
AAGTTGAGAAGTAACAGTGA+CGG 0.682879 5:+23914284 MsG0580025769.01.T01:CDS
CGAAAACGAAGATAAACACG+AGG 0.714125 5:+23913932 MsG0580025769.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAAGTGAAAATGGTGAA+AGG + Chr5:23914389-23914408 MsG0580025769.01.T01:CDS 30.0%
AGATTCATTATCGTAATCGT+CGG - Chr5:23914099-23914118 None:intergenic 30.0%
CATATAGGCAAGAATTGTTT+GGG + Chr5:23914504-23914523 MsG0580025769.01.T01:CDS 30.0%
GAAAATGGTGAAAGGTAAAA+AGG + Chr5:23914397-23914416 MsG0580025769.01.T01:CDS 30.0%
TCGACGAAAAATTTCTTTAC+CGG - Chr5:23914134-23914153 None:intergenic 30.0%
TGACCGAAAAAAGGAAAAAT+CGG - Chr5:23914062-23914081 None:intergenic 30.0%
TGCTGTAAAGAAAGTGAAAA+TGG + Chr5:23914382-23914401 MsG0580025769.01.T01:CDS 30.0%
! GGAAATCTTATTTGCCATAT+AGG + Chr5:23914489-23914508 MsG0580025769.01.T01:CDS 30.0%
! TTTGCTAGTACAAATGGATT+GGG + Chr5:23914530-23914549 MsG0580025769.01.T01:CDS 30.0%
AAAATTTCTTTACCGGCGAA+CGG - Chr5:23914127-23914146 None:intergenic 35.0%
AAGTTGAGAAGTAACAGTGA+CGG + Chr5:23914284-23914303 MsG0580025769.01.T01:CDS 35.0%
AATGGTGAAAGGTAAAAAGG+CGG + Chr5:23914400-23914419 MsG0580025769.01.T01:CDS 35.0%
ATTATGTGATGAGTAAAGCG+AGG + Chr5:23914450-23914469 MsG0580025769.01.T01:CDS 35.0%
CCAAACAATTCTTGCCTATA+TGG - Chr5:23914506-23914525 None:intergenic 35.0%
CCATATAGGCAAGAATTGTT+TGG + Chr5:23914503-23914522 MsG0580025769.01.T01:CDS 35.0%
CTTTGCTAGTACAAATGGAT+TGG + Chr5:23914529-23914548 MsG0580025769.01.T01:CDS 35.0%
GACGATTACGATAATGAATC+TGG + Chr5:23914098-23914117 MsG0580025769.01.T01:CDS 35.0%
TTTATCAAACACATCGTCAG+CGG - Chr5:23914027-23914046 None:intergenic 35.0%
! CGTCCGATTTTTCCTTTTTT+CGG + Chr5:23914056-23914075 MsG0580025769.01.T01:CDS 35.0%
! TCACTGTTACTTCTCAACTT+CGG - Chr5:23914284-23914303 None:intergenic 35.0%
!! TTTGTTTTCGCAGATCCTAA+AGG + Chr5:23913990-23914009 MsG0580025769.01.T01:CDS 35.0%
!!! GATTTTTCCTTTTTTCGGTC+AGG + Chr5:23914061-23914080 MsG0580025769.01.T01:CDS 35.0%
AAGGTAGAGAAAACGAGTTC+CGG + Chr5:23914338-23914357 MsG0580025769.01.T01:CDS 40.0%
CAACAGGATCATCAAACCTA+TGG + Chr5:23914246-23914265 MsG0580025769.01.T01:CDS 40.0%
CGAAAACGAAGATAAACACG+AGG + Chr5:23913932-23913951 MsG0580025769.01.T01:CDS 40.0%
CGAGGAAGGAAAGTGATAAA+CGG + Chr5:23914468-23914487 MsG0580025769.01.T01:CDS 40.0%
GCTGACGATGTGTTTGATAA+AGG + Chr5:23914026-23914045 MsG0580025769.01.T01:CDS 40.0%
GGGTTCTTTGCTAGTACAAA+TGG + Chr5:23914524-23914543 MsG0580025769.01.T01:CDS 40.0%
TCGGATCTCTTAACTTCCAT+AGG - Chr5:23914265-23914284 None:intergenic 40.0%
TGAAGATCCTGACCGAAAAA+AGG - Chr5:23914071-23914090 None:intergenic 40.0%
!! CAAATGGATTGGGAATGAGT+AGG + Chr5:23914540-23914559 MsG0580025769.01.T01:CDS 40.0%
!! TTACTCTTCACCGCTTTTGT+TGG - Chr5:23914224-23914243 None:intergenic 40.0%
AACACATCGTCAGCGGAAAT+CGG - Chr5:23914020-23914039 None:intergenic 45.0%
CGAGTGGAATCCAACAAAAG+CGG + Chr5:23914211-23914230 MsG0580025769.01.T01:CDS 45.0%
GCGGTGAAGAGTAATTCAAC+AGG + Chr5:23914230-23914249 MsG0580025769.01.T01:CDS 45.0%
TAATGTTTCTCATGCGCCGA+CGG - Chr5:23914434-23914453 None:intergenic 45.0%
TGTGATGAGTAAAGCGAGGA+AGG + Chr5:23914454-23914473 MsG0580025769.01.T01:CDS 45.0%
TTTCCAGAAACCTCGCTAAG+AGG - Chr5:23913858-23913877 None:intergenic 45.0%
!! CGCGTTCGTGTTTTTGAATC+CGG + Chr5:23914313-23914332 MsG0580025769.01.T01:CDS 45.0%
AGCAACATTCTTCGTCTCGC+CGG - Chr5:23914366-23914385 None:intergenic 50.0%
GAAAGGTAAAAAGGCGGCTC+CGG + Chr5:23914406-23914425 MsG0580025769.01.T01:CDS 50.0%
GCGGAAATCGGTGAACCTTT+AGG - Chr5:23914008-23914027 None:intergenic 50.0%
TCACCTCTTAGCGAGGTTTC+TGG + Chr5:23913852-23913871 MsG0580025769.01.T01:CDS 50.0%
TGAATCTGGAAACCGTTCGC+CGG + Chr5:23914112-23914131 MsG0580025769.01.T01:CDS 50.0%
TTCAGCTTCACCTCTTAGCG+AGG + Chr5:23913845-23913864 MsG0580025769.01.T01:CDS 50.0%
! CTCGTTTTCTCTACCTTCGC+CGG - Chr5:23914335-23914354 None:intergenic 50.0%
!! CGTGTTTTTGAATCCGGCGA+AGG + Chr5:23914319-23914338 MsG0580025769.01.T01:CDS 50.0%
GAAGACAGCCACGAGTTCTG+CGG + Chr5:23914169-23914188 MsG0580025769.01.T01:CDS 55.0%
GTGGCTGTCTTCGACGAAGA+CGG - Chr5:23914161-23914180 None:intergenic 55.0%
GAGAAAACGAGTTCCGGCGC+CGG + Chr5:23914344-23914363 MsG0580025769.01.T01:CDS 60.0%
TGGAAGGGACGTACTGCGAG+TGG + Chr5:23914195-23914214 MsG0580025769.01.T01:CDS 60.0%
ACGAGTTCTGCGGCGGTGGA+AGG + Chr5:23914179-23914198 MsG0580025769.01.T01:CDS 65.0%
ATTCTTCGTCTCGCCGGCGC+CGG - Chr5:23914360-23914379 None:intergenic 65.0%
CGAGTTCTGCGGCGGTGGAA+GGG + Chr5:23914180-23914199 MsG0580025769.01.T01:CDS 65.0%
GACAGCCACGAGTTCTGCGG+CGG + Chr5:23914172-23914191 MsG0580025769.01.T01:CDS 65.0%
TTCCACCGCCGCAGAACTCG+TGG - Chr5:23914180-23914199 None:intergenic 65.0%
AGCCACGAGTTCTGCGGCGG+TGG + Chr5:23914175-23914194 MsG0580025769.01.T01:CDS 70.0%
! TTCTCATGCGCCGACGGCGC+CGG - Chr5:23914428-23914447 None:intergenic 70.0%
AAAGGCGGCTCCGGCGCCGT+CGG + Chr5:23914415-23914434 MsG0580025769.01.T01:CDS 75.0%
Chromosome Type Strat End Strand Name
Chr5 gene 23913834 23914580 23913834 ID=MsG0580025769.01;Name=MsG0580025769.01
Chr5 mRNA 23913834 23914580 23913834 ID=MsG0580025769.01.T01;Parent=MsG0580025769.01;Name=MsG0580025769.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|248
Chr5 exon 23913834 23914580 23913834 ID=MsG0580025769.01.T01:exon:24313;Parent=MsG0580025769.01.T01
Chr5 CDS 23913834 23914580 23913834 ID=MsG0580025769.01.T01:cds;Parent=MsG0580025769.01.T01
Gene Sequence

>MsG0580025769.01.T01

ATGCAAACTGTTTCAGCTTCACCTCTTAGCGAGGTTTCTGGAAAATTCGAGAACGATTTCTTCTCAAAGCTTAAAATTGAAGACGAGAAAATCGAAAACGAAAACGAAGATAAACACGAGGTAGAAGAAGAAGATGAAGATGATGATGAGTTTACATTTGTTTTCGCAGATCCTAAAGGTTCACCGATTTCCGCTGACGATGTGTTTGATAAAGGTCAGATTCGTCCGATTTTTCCTTTTTTCGGTCAGGATCTTCATTTCACCGACGATTACGATAATGAATCTGGAAACCGTTCGCCGGTAAAGAAATTTTTCGTCGAATCACCGTCTTCGTCGAAGACAGCCACGAGTTCTGCGGCGGTGGAAGGGACGTACTGCGAGTGGAATCCAACAAAAGCGGTGAAGAGTAATTCAACAGGATCATCAAACCTATGGAAGTTAAGAGATCCGAAGTTGAGAAGTAACAGTGACGGAAAAGACGCGTTCGTGTTTTTGAATCCGGCGAAGGTAGAGAAAACGAGTTCCGGCGCCGGCGAGACGAAGAATGTTGCTGTAAAGAAAGTGAAAATGGTGAAAGGTAAAAAGGCGGCTCCGGCGCCGTCGGCGCATGAGAAACATTATGTGATGAGTAAAGCGAGGAAGGAAAGTGATAAACGGAAATCTTATTTGCCATATAGGCAAGAATTGTTTGGGTTCTTTGCTAGTACAAATGGATTGGGAATGAGTAGGAATGTTCATCCTTATTGA

Protein sequence

>MsG0580025769.01.T01

MQTVSASPLSEVSGKFENDFFSKLKIEDEKIENENEDKHEVEEEDEDDDEFTFVFADPKGSPISADDVFDKGQIRPIFPFFGQDLHFTDDYDNESGNRSPVKKFFVESPSSSKTATSSAAVEGTYCEWNPTKAVKSNSTGSSNLWKLRDPKLRSNSDGKDAFVFLNPAKVEKTSSGAGETKNVAVKKVKMVKGKKAAPAPSAHEKHYVMSKARKESDKRKSYLPYRQELFGFFASTNGLGMSRNVHPY*