AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000194.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000194.01.T01 MTR_1g021760 96.842 95 3 0 23 117 111 205 1.71e-63 192
MsG0180000194.01.T01 MTR_3g078370 54.286 70 32 0 48 117 336 405 3.88e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000194.01.T01 AT1G74970 83.158 95 16 0 23 117 114 208 1.32e-54 169
MsG0180000194.01.T01 AT3G49080 52.857 70 33 0 48 117 361 430 1.10e-14 68.9

Find 56 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACTATCTGTAAAATTTC+TGG 0.180911 1:+2670704 MsG0180000193.01.T01:exon
TACTATGTTGAAGGTTTCTT+TGG 0.252502 1:+2670580 MsG0180000193.01.T01:exon
TCCATACTGGCAAAATAATA+AGG 0.283512 1:-2670514 None:intergenic
TTCGTATCCCAAAGTTAATA+AGG 0.290144 1:-2670138 None:intergenic
GAGGAAATAACATATATTTC+AGG 0.295972 1:-2670606 None:intergenic
TGTGGTTACGTTCAATTTAC+TGG 0.312861 1:+2669150 MsG0180000193.01.T01:intron
TTCACTGAGGCCTTTGTATT+CGG 0.318413 1:+2670474 MsG0180000193.01.T01:exon
AAACCTTCAACATAGTAAAA+AGG 0.337469 1:-2670574 None:intergenic
TTCCCTGTATCTCTGTAGTT+TGG 0.342025 1:+2670418 MsG0180000193.01.T01:exon
TAAGGTGCCCTTATTAACTT+TGG 0.349914 1:+2670130 MsG0180000193.01.T01:exon
GCTGAGGGTGGTGGCCTCTC+TGG 0.350070 1:+2670185 MsG0180000193.01.T01:exon
GCTATGGCTTCAATACATTA+AGG 0.364577 1:+2670112 MsG0180000193.01.T01:exon
GTTTCGGAACTATTGATTGT+AGG 0.392267 1:+2670450 MsG0180000193.01.T01:exon
TAACCAAACTACAGAGATAC+AGG 0.405060 1:-2670421 None:intergenic
AGTTTGGTTACTTTCAGTTT+CGG 0.405516 1:+2670434 MsG0180000193.01.T01:exon
TACATTTCCCAATTCCATAC+TGG 0.423204 1:-2670527 None:intergenic
TCGTATCCCAAAGTTAATAA+GGG 0.423632 1:-2670137 None:intergenic
ATCTGTAAAATTTCTGGAGA+TGG 0.437955 1:+2670710 MsG0180000193.01.T01:exon
AAGGTGCCCTTATTAACTTT+GGG 0.444377 1:+2670131 MsG0180000193.01.T01:exon
CTCAATATTCTAAACGTTGA+GGG 0.468618 1:+2670360 MsG0180000193.01.T01:exon
TGGCCTCTCTGGTCAAGCTC+AGG 0.474396 1:+2670196 MsG0180000193.01.T01:exon
CAAAATAATAAGGAAACAAA+GGG 0.488587 1:-2670504 None:intergenic
GTTGTACAGGAATATCTTCA+AGG 0.503982 1:+2670083 MsG0180000193.01.T01:intron
GCAAAATAATAAGGAAACAA+AGG 0.505814 1:-2670505 None:intergenic
CAAGCTCAGGCGATCACCCT+TGG 0.506389 1:+2670209 MsG0180000193.01.T01:exon
AGTATGGAATTGGGAAATGT+AGG 0.512865 1:+2670529 MsG0180000193.01.T01:exon
TACACACAATCAATTAAAAG+AGG 0.518003 1:-2670625 None:intergenic
CCTCAACGTTTAGAATATTG+AGG 0.522813 1:-2670359 None:intergenic
AGATACAGGGAAGAATGAAA+AGG 0.545154 1:-2670407 None:intergenic
AGAAGCCCTTGTTGTCTCAA+AGG 0.556232 1:-2670275 None:intergenic
CCTCAATATTCTAAACGTTG+AGG 0.561139 1:+2670359 MsG0180000193.01.T01:exon
TATTGCTCGTGCGTTGCTGA+AGG 0.576175 1:+2670232 MsG0180000193.01.T01:exon
GCTGTTGAGAGGAAGAAAGT+TGG 0.577966 1:+2670314 MsG0180000193.01.T01:exon
GACACTAACATGAACGCATG+TGG 0.582308 1:+2669132 MsG0180000193.01.T01:intron
ATCTTCAAGGAAATCCGCTA+TGG 0.582748 1:+2670096 MsG0180000193.01.T01:exon
TATAGTGTACACATGGTACA+AGG 0.587250 1:-2670742 None:intergenic
ATAATAAGGAAACAAAGGGC+AGG 0.589334 1:-2670500 None:intergenic
GTGTTTGTGAAAGCTGAGGG+TGG 0.596769 1:+2670173 MsG0180000193.01.T01:exon
TTTGTGAAAGCTGAGGGTGG+TGG 0.605348 1:+2670176 MsG0180000193.01.T01:exon
CATCTCAATACACTTGAACA+AGG 0.613434 1:-2670657 None:intergenic
GAGATTCTAGAGCTGTTGAG+AGG 0.623504 1:+2670303 MsG0180000193.01.T01:exon
ATTTCTGGAGATGGTTGCTG+TGG 0.624688 1:+2670719 MsG0180000193.01.T01:exon
TGATGTGTTTGTGAAAGCTG+AGG 0.626462 1:+2670169 MsG0180000193.01.T01:exon
AATATTCTAAACGTTGAGGG+TGG 0.633829 1:+2670363 MsG0180000193.01.T01:exon
AGAGTACCTTTGAGACAACA+AGG 0.639079 1:+2670269 MsG0180000193.01.T01:exon
GATGTGTTTGTGAAAGCTGA+GGG 0.645465 1:+2670170 MsG0180000193.01.T01:exon
GCAACGCACGAGCAATACCA+AGG 0.649038 1:-2670226 None:intergenic
TGCATGTTATAGTGTACACA+TGG 0.660660 1:-2670749 None:intergenic
GGGCAGGATTCCGAATACAA+AGG 0.665424 1:-2670484 None:intergenic
GCGTTGCTGAAGGTTAGTGA+AGG 0.671877 1:+2670242 MsG0180000193.01.T01:exon
AACCAAACTACAGAGATACA+GGG 0.685063 1:-2670420 None:intergenic
ATTGATTGTAGGTTTCACTG+AGG 0.707639 1:+2670461 MsG0180000193.01.T01:exon
CAACGCACGAGCAATACCAA+GGG 0.707901 1:-2670225 None:intergenic
GAGTACCTTTGAGACAACAA+GGG 0.708894 1:+2670270 MsG0180000193.01.T01:exon
TCGCCTGAGCTTGACCAGAG+AGG 0.719687 1:-2670199 None:intergenic
TTAATGTATTGAAGCCATAG+CGG 0.725178 1:-2670110 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTCATCCAAAAAATATA+AGG + Chr1:2669720-2669739 MsG0180000193.01.T01:intron 15.0%
!! AAGAAATCAAAGAAAATGTT+TGG - Chr1:2669978-2669997 None:intergenic 20.0%
!! CAAAATAATAAGGAAACAAA+GGG - Chr1:2670507-2670526 None:intergenic 20.0%
!!! TTGAAGATCCTTATATTTTT+TGG - Chr1:2669731-2669750 None:intergenic 20.0%
!!! TTTAGATTTTAATGTTGTAC+AGG + Chr1:2670070-2670089 MsG0180000193.01.T01:intron 20.0%
! AAACCTTCAACATAGTAAAA+AGG - Chr1:2670577-2670596 None:intergenic 25.0%
! ATGACAATCTAATGAAATAC+AGG - Chr1:2669186-2669205 None:intergenic 25.0%
! GAGGAAATAACATATATTTC+AGG - Chr1:2670609-2670628 None:intergenic 25.0%
! GCAAAATAATAAGGAAACAA+AGG - Chr1:2670508-2670527 None:intergenic 25.0%
! TACACACAATCAATTAAAAG+AGG - Chr1:2670628-2670647 None:intergenic 25.0%
! TCAACTATCTGTAAAATTTC+TGG + Chr1:2670704-2670723 MsG0180000193.01.T01:exon 25.0%
! TGATCATCCAAAAAAACATA+AGG + Chr1:2669342-2669361 MsG0180000193.01.T01:intron 25.0%
!! ACACTTATAATCTAAAGTCT+CGG - Chr1:2669506-2669525 None:intergenic 25.0%
!! ACATAGTAAAAAGGTGTATT+TGG - Chr1:2670568-2670587 None:intergenic 25.0%
!! CATAGTAAAAAGGTGTATTT+GGG - Chr1:2670567-2670586 None:intergenic 25.0%
AATTGAATTCATCCAATGAC+TGG - Chr1:2669776-2669795 None:intergenic 30.0%
CTCAATATTCTAAACGTTGA+GGG + Chr1:2670360-2670379 MsG0180000193.01.T01:exon 30.0%
CTTTAGATTATAAGTGTGTC+CGG + Chr1:2669509-2669528 MsG0180000193.01.T01:intron 30.0%
TACTATGTTGAAGGTTTCTT+TGG + Chr1:2670580-2670599 MsG0180000193.01.T01:exon 30.0%
TCCATACTGGCAAAATAATA+AGG - Chr1:2670517-2670536 None:intergenic 30.0%
TCGTATCCCAAAGTTAATAA+GGG - Chr1:2670140-2670159 None:intergenic 30.0%
TTAATGTATTGAAGCCATAG+CGG - Chr1:2670113-2670132 None:intergenic 30.0%
TTCGTATCCCAAAGTTAATA+AGG - Chr1:2670141-2670160 None:intergenic 30.0%
TTGGATGAATAACACTACAT+TGG - Chr1:2669712-2669731 None:intergenic 30.0%
TTGGATGATCAATACTACAT+TGG - Chr1:2669333-2669352 None:intergenic 30.0%
! ACACCTTTTTACTATGTTGA+AGG + Chr1:2670571-2670590 MsG0180000193.01.T01:exon 30.0%
! AGTTTGGTTACTTTCAGTTT+CGG + Chr1:2670434-2670453 MsG0180000193.01.T01:exon 30.0%
! ATCTGTAAAATTTCTGGAGA+TGG + Chr1:2670710-2670729 MsG0180000193.01.T01:exon 30.0%
! TAAAAAGGTGTATTTGGGTT+GGG - Chr1:2670562-2670581 None:intergenic 30.0%
! TATTTTGCCAGTATGGAATT+GGG + Chr1:2670520-2670539 MsG0180000193.01.T01:exon 30.0%
! TTTCTTTGATTTCTTTCCAC+TGG + Chr1:2669983-2670002 MsG0180000193.01.T01:intron 30.0%
!! TCCTTATTATTTTGCCAGTA+TGG + Chr1:2670513-2670532 MsG0180000193.01.T01:exon 30.0%
!! TTATTTTGCCAGTATGGAAT+TGG + Chr1:2670519-2670538 MsG0180000193.01.T01:exon 30.0%
!!! AGAAGCTCCTTATGTTTTTT+TGG - Chr1:2669352-2669371 None:intergenic 30.0%
AACCAAACTACAGAGATACA+GGG - Chr1:2670423-2670442 None:intergenic 35.0%
AATATTCTAAACGTTGAGGG+TGG + Chr1:2670363-2670382 MsG0180000193.01.T01:exon 35.0%
AGATACAGGGAAGAATGAAA+AGG - Chr1:2670410-2670429 None:intergenic 35.0%
AGCTTCTTACCAAACATAAG+TGG + Chr1:2669365-2669384 MsG0180000193.01.T01:intron 35.0%
AGGACTAATAAGAAAACCAG+TGG - Chr1:2670002-2670021 None:intergenic 35.0%
AGTATGGAATTGGGAAATGT+AGG + Chr1:2670529-2670548 MsG0180000193.01.T01:exon 35.0%
ATAATAAGGAAACAAAGGGC+AGG - Chr1:2670503-2670522 None:intergenic 35.0%
ATTGATTGTAGGTTTCACTG+AGG + Chr1:2670461-2670480 MsG0180000193.01.T01:exon 35.0%
CACTAACATTTGTCGTATAC+CGG - Chr1:2669531-2669550 None:intergenic 35.0%
CATCTCAATACACTTGAACA+AGG - Chr1:2670660-2670679 None:intergenic 35.0%
CCTCAATATTCTAAACGTTG+AGG + Chr1:2670359-2670378 MsG0180000193.01.T01:exon 35.0%
GCTATGGCTTCAATACATTA+AGG + Chr1:2670112-2670131 MsG0180000193.01.T01:exon 35.0%
GCTTCTTACCAAACATAAGT+GGG + Chr1:2669366-2669385 MsG0180000193.01.T01:intron 35.0%
GTTGTACAGGAATATCTTCA+AGG + Chr1:2670083-2670102 MsG0180000193.01.T01:intron 35.0%
TAACCAAACTACAGAGATAC+AGG - Chr1:2670424-2670443 None:intergenic 35.0%
TACATTTCCCAATTCCATAC+TGG - Chr1:2670530-2670549 None:intergenic 35.0%
TATAGTGTACACATGGTACA+AGG - Chr1:2670745-2670764 None:intergenic 35.0%
TCTCAGTTGTTAGAATCCAA+CGG + Chr1:2669818-2669837 MsG0180000193.01.T01:intron 35.0%
TGATGACAGATAGCAACATA+AGG - Chr1:2670022-2670041 None:intergenic 35.0%
TGCATGTTATAGTGTACACA+TGG - Chr1:2670752-2670771 None:intergenic 35.0%
TGTGGTTACGTTCAATTTAC+TGG + Chr1:2669150-2669169 MsG0180000193.01.T01:intron 35.0%
! AAGGTGCCCTTATTAACTTT+GGG + Chr1:2670131-2670150 MsG0180000193.01.T01:exon 35.0%
! CCTCAACGTTTAGAATATTG+AGG - Chr1:2670362-2670381 None:intergenic 35.0%
! GTAAAAAGGTGTATTTGGGT+TGG - Chr1:2670563-2670582 None:intergenic 35.0%
! GTTTCGGAACTATTGATTGT+AGG + Chr1:2670450-2670469 MsG0180000193.01.T01:exon 35.0%
! TAAGGTGCCCTTATTAACTT+TGG + Chr1:2670130-2670149 MsG0180000193.01.T01:exon 35.0%
!! GTTTGGATGAAGAGTTTTGA+AGG - Chr1:2669961-2669980 None:intergenic 35.0%
ATCTTCAAGGAAATCCGCTA+TGG + Chr1:2670096-2670115 MsG0180000193.01.T01:exon 40.0%
CTTACCAAACATAAGTGGGA+GGG + Chr1:2669370-2669389 MsG0180000193.01.T01:intron 40.0%
GATGTGTTTGTGAAAGCTGA+GGG + Chr1:2670170-2670189 MsG0180000193.01.T01:exon 40.0%
TCTTACCAAACATAAGTGGG+AGG + Chr1:2669369-2669388 MsG0180000193.01.T01:intron 40.0%
TGATGTGTTTGTGAAAGCTG+AGG + Chr1:2670169-2670188 MsG0180000193.01.T01:exon 40.0%
TTCACTGAGGCCTTTGTATT+CGG + Chr1:2670474-2670493 MsG0180000193.01.T01:exon 40.0%
TTCCCTGTATCTCTGTAGTT+TGG + Chr1:2670418-2670437 MsG0180000193.01.T01:exon 40.0%
! TGTGGTGACGTTCAATTTAC+AGG + Chr1:2669572-2669591 MsG0180000193.01.T01:intron 40.0%
!! AGAGTACCTTTGAGACAACA+AGG + Chr1:2670269-2670288 MsG0180000193.01.T01:exon 40.0%
!! ATCCAATGACTGGCTTTGAT+TGG - Chr1:2669766-2669785 None:intergenic 40.0%
!! GAGTACCTTTGAGACAACAA+GGG + Chr1:2670270-2670289 MsG0180000193.01.T01:exon 40.0%
!! TCCAATGACTGGCTTTGATT+GGG - Chr1:2669765-2669784 None:intergenic 40.0%
!!! AGTTTTGAAGGCAAAGTCGA+AGG - Chr1:2669949-2669968 None:intergenic 40.0%
GACACTAACACGAATGCATG+TGG + Chr1:2669554-2669573 MsG0180000193.01.T01:intron 45.0%
GACACTAACATGAACGCATG+TGG + Chr1:2669132-2669151 MsG0180000193.01.T01:intron 45.0%
GCTGTTGAGAGGAAGAAAGT+TGG + Chr1:2670314-2670333 MsG0180000193.01.T01:exon 45.0%
! AGAAGCCCTTGTTGTCTCAA+AGG - Chr1:2670278-2670297 None:intergenic 45.0%
! ATTTCTGGAGATGGTTGCTG+TGG + Chr1:2670719-2670738 MsG0180000193.01.T01:exon 45.0%
! GTCGAAGTGTCTGTGTTTCA+TGG + Chr1:2669596-2669615 MsG0180000193.01.T01:intron 45.0%
!! CCAATGACTGGCTTTGATTG+GGG - Chr1:2669764-2669783 None:intergenic 45.0%
!! GAGATTCTAGAGCTGTTGAG+AGG + Chr1:2670303-2670322 MsG0180000193.01.T01:exon 45.0%
!! AGAATAAAAAAATTAAATAA+TGG + Chr1:2669463-2669482 MsG0180000193.01.T01:intron 5.0%
ACCAAACATAAGTGGGAGGG+AGG + Chr1:2669373-2669392 MsG0180000193.01.T01:intron 50.0%
CAACGCACGAGCAATACCAA+GGG - Chr1:2670228-2670247 None:intergenic 50.0%
CCAAACATAAGTGGGAGGGA+GGG + Chr1:2669374-2669393 MsG0180000193.01.T01:intron 50.0%
CCCCAATCAAAGCCAGTCAT+TGG + Chr1:2669761-2669780 MsG0180000193.01.T01:intron 50.0%
GCGTTGCTGAAGGTTAGTGA+AGG + Chr1:2670242-2670261 MsG0180000193.01.T01:exon 50.0%
GGGCAGGATTCCGAATACAA+AGG - Chr1:2670487-2670506 None:intergenic 50.0%
GTGTTTGTGAAAGCTGAGGG+TGG + Chr1:2670173-2670192 MsG0180000193.01.T01:exon 50.0%
TACCTCTGCAGTTCAGAGGT+TGG - Chr1:2669844-2669863 None:intergenic 50.0%
TATTGCTCGTGCGTTGCTGA+AGG + Chr1:2670232-2670251 MsG0180000193.01.T01:exon 50.0%
TTTGTGAAAGCTGAGGGTGG+TGG + Chr1:2670176-2670195 MsG0180000193.01.T01:exon 50.0%
!!! TGGGAGGGAGGGTTTTAGAA+AGG + Chr1:2669385-2669404 MsG0180000193.01.T01:intron 50.0%
CAGCTACCTCTGCAGTTCAG+AGG - Chr1:2669848-2669867 None:intergenic 55.0%
CCCTCCCTCCCACTTATGTT+TGG - Chr1:2669377-2669396 None:intergenic 55.0%
CTGAACTGCAGAGGTAGCTG+AGG + Chr1:2669848-2669867 MsG0180000193.01.T01:intron 55.0%
GCAACGCACGAGCAATACCA+AGG - Chr1:2670229-2670248 None:intergenic 55.0%
! GGCTTTGATTGGGGCAGAAG+AGG - Chr1:2669755-2669774 None:intergenic 55.0%
CAAGCTCAGGCGATCACCCT+TGG + Chr1:2670209-2670228 MsG0180000193.01.T01:exon 60.0%
GGCCAACCTCTGAACTGCAG+AGG + Chr1:2669839-2669858 MsG0180000193.01.T01:intron 60.0%
TCGCCTGAGCTTGACCAGAG+AGG - Chr1:2670202-2670221 None:intergenic 60.0%
TGGCCTCTCTGGTCAAGCTC+AGG + Chr1:2670196-2670215 MsG0180000193.01.T01:exon 60.0%
! GCAGTTCAGAGGTTGGCCGT+TGG - Chr1:2669837-2669856 None:intergenic 60.0%
! GCTGAGGGTGGTGGCCTCTC+TGG + Chr1:2670185-2670204 MsG0180000193.01.T01:exon 70.0%
Chromosome Type Strat End Strand Name
Chr1 gene 2669120 2670781 2669120 ID=MsG0180000194.01;Name=MsG0180000194.01
Chr1 mRNA 2669120 2670781 2669120 ID=MsG0180000194.01.T01;Parent=MsG0180000194.01;Name=MsG0180000194.01.T01;_AED=0.49;_eAED=0.54;_QI=0|0|0.5|1|1|1|2|402|117
Chr1 exon 2670092 2670781 2670092 ID=MsG0180000194.01.T01:exon:6508;Parent=MsG0180000194.01.T01
Chr1 exon 2669120 2669185 2669120 ID=MsG0180000194.01.T01:exon:6507;Parent=MsG0180000194.01.T01
Chr1 CDS 2669120 2669185 2669120 ID=MsG0180000194.01.T01:cds;Parent=MsG0180000194.01.T01
Chr1 CDS 2670092 2670379 2670092 ID=MsG0180000194.01.T01:cds;Parent=MsG0180000194.01.T01
Chr1 three_prime_UTR 2670380 2670781 2670380 ID=MsG0180000194.01.T01:three_prime_utr;Parent=MsG0180000194.01.T01
Gene Sequence

>MsG0180000194.01.T01

ATGTTAGTCTTTGACACTAACATGAACGCATGTGGTTACGTTCAATTTACTGGTGTCAAAGTGCCTGAATATCTTCAAGGAAATCCGCTATGGCTTCAATACATTAAGGTGCCCTTATTAACTTTGGGATACGAAACTAGTTATGATGTGTTTGTGAAAGCTGAGGGTGGTGGCCTCTCTGGTCAAGCTCAGGCGATCACCCTTGGTATTGCTCGTGCGTTGCTGAAGGTTAGTGAAGGTCATAGAGTACCTTTGAGACAACAAGGGCTTCTGACTAGAGATTCTAGAGCTGTTGAGAGGAAGAAAGTTGGTCTCAAGAAAGCTCGTAAAGCTCCTCAATATTCTAAACGTTGA

Protein sequence

>MsG0180000194.01.T01

MLVFDTNMNACGYVQFTGVKVPEYLQGNPLWLQYIKVPLLTLGYETSYDVFVKAEGGGLSGQAQAITLGIARALLKVSEGHRVPLRQQGLLTRDSRAVERKKVGLKKARKAPQYSKR*