AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27789

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27789.t1 MTR_1g017090 95.726 117 4 1 37 152 155 271 2.17e-76 229
MS.gene27789.t1 MTR_5g014890 62.295 122 35 3 37 153 148 263 4.84e-45 149
MS.gene27789.t1 MTR_4g097600 74.444 90 21 1 37 126 152 239 2.36e-42 142
MS.gene27789.t1 MTR_1g054285 71.429 91 24 1 37 127 179 267 2.24e-41 140
MS.gene27789.t1 MTR_7g093430 71.429 91 24 1 37 127 185 273 3.41e-41 139
MS.gene27789.t1 MTR_2g061030 56.349 126 50 3 4 126 189 312 1.74e-39 136
MS.gene27789.t1 MTR_4g100550 57.522 113 38 3 37 148 145 248 4.26e-38 131
MS.gene27789.t1 MTR_5g013010 54.701 117 43 3 37 152 161 268 3.20e-37 129
MS.gene27789.t1 MTR_8g006705 67.416 89 26 2 37 124 171 257 6.33e-36 126
MS.gene27789.t1 MTR_3g103590 59.350 123 40 3 37 152 170 289 1.05e-33 120
MS.gene27789.t1 MTR_4g084750 54.455 101 41 2 29 124 81 181 7.42e-29 105
MS.gene27789.t1 MTR_2g038625 56.989 93 39 1 38 130 108 199 3.73e-26 99.0
MS.gene27789.t1 MTR_2g038580 56.989 93 39 1 38 130 108 199 3.73e-26 99.0
MS.gene27789.t1 MTR_4g126900 57.303 89 36 2 38 124 114 202 3.18e-24 94.0
MS.gene27789.t1 MTR_7g010020 50.000 70 28 1 37 99 105 174 2.74e-12 62.8
MS.gene27789.t1 MTR_6g007647 52.381 63 30 0 37 99 92 154 3.17e-12 62.8
MS.gene27789.t1 MTR_6g007647 52.381 63 30 0 37 99 58 120 3.23e-12 62.4
MS.gene27789.t1 MTR_5g039000 47.619 63 33 0 37 99 102 164 1.26e-11 61.2
MS.gene27789.t1 MTR_3g086790 36.441 118 65 2 37 147 85 199 1.83e-11 60.8
MS.gene27789.t1 MTR_3g080100 47.143 70 30 1 37 99 45 114 4.37e-11 58.9
MS.gene27789.t1 MTR_6g011610 50.725 69 27 1 37 98 121 189 5.21e-11 59.3
MS.gene27789.t1 MTR_8g468210 44.444 63 35 0 37 99 102 164 5.97e-11 59.3
MS.gene27789.t1 MTR_3g080100 47.143 70 30 1 37 99 84 153 6.69e-11 58.9
MS.gene27789.t1 MTR_6g011610 50.725 69 27 1 37 98 102 170 8.78e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27789.t1 AT4G37790 73.333 90 22 1 37 126 151 238 2.74e-42 142
MS.gene27789.t1 AT5G06710 65.049 103 31 2 37 139 215 312 1.42e-41 141
MS.gene27789.t1 AT2G22800 71.111 90 24 1 37 126 138 225 3.06e-39 134
MS.gene27789.t1 AT4G16780 56.637 113 39 3 37 148 154 257 1.32e-36 127
MS.gene27789.t1 AT5G47370 45.625 160 61 5 4 151 111 256 8.92e-35 122
MS.gene27789.t1 AT2G44910 64.835 91 29 2 37 126 188 276 1.57e-34 123
MS.gene27789.t1 AT3G60390 65.909 88 29 1 37 124 187 273 1.57e-34 122
MS.gene27789.t1 AT4G17460 60.870 92 35 1 37 128 160 250 9.91e-32 114
MS.gene27789.t1 AT2G01430 51.515 99 43 3 29 126 155 249 7.71e-25 96.7
MS.gene27789.t1 AT1G70920 48.000 100 39 2 37 134 64 152 1.26e-22 88.6
MS.gene27789.t1 AT1G70920 38.095 147 65 4 1 134 49 182 1.77e-22 89.0
MS.gene27789.t1 AT1G26960 41.111 90 49 2 38 127 97 182 1.43e-12 63.5
MS.gene27789.t1 AT5G15150 39.048 105 55 2 37 134 140 242 6.16e-11 59.7

Find 27 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGGAATCTTCATATAAA+AGG 0.190194 1.2:-5705300 None:intergenic
CCCTCAACAACATTGCTTAC+TGG 0.286571 1.2:+5705386 MS.gene27789:CDS
GTGAGCCTAAGTTTCTTCCT+TGG 0.317530 1.2:-5703729 None:intergenic
AAAACAACAATCAGAAGTTT+TGG 0.327778 1.2:+5703752 MS.gene27789:CDS
TGAGCCTAAGTTTCTTCCTT+GGG 0.367322 1.2:-5703728 None:intergenic
TAGAGGTGTGGTTTCAAAAT+CGG 0.417824 1.2:+5704577 MS.gene27789:CDS
AGCAAATAAGCTGAATCTGC+AGG 0.462898 1.2:+5704545 MS.gene27789:CDS
CCTTCGTGCGAGACAATTTG+TGG 0.481936 1.2:+5705341 MS.gene27789:CDS
AAGCAATGTTGTTGAGGGTA+AGG 0.487754 1.2:-5705381 None:intergenic
GCTGGAATCTTCATATAAAA+GGG 0.492378 1.2:-5705299 None:intergenic
GGTTTCAAAATCGGAGAGCC+AGG 0.511878 1.2:+5704586 MS.gene27789:CDS
GGAGAACAAGAAGTTGCAAA+AGG 0.515455 1.2:+5705235 MS.gene27789:CDS
CCAGTAAGCAATGTTGTTGA+GGG 0.519543 1.2:-5705386 None:intergenic
CACAAATTGTCTCGCACGAA+GGG 0.524067 1.2:-5705340 None:intergenic
AGAGCATTCTACTCTTAATC+CGG 0.524461 1.2:+5703788 MS.gene27789:CDS
GCCAGTAAGCAATGTTGTTG+AGG 0.532003 1.2:-5705387 None:intergenic
CAGAACAAAGCTGAAACAAA+CGG 0.533275 1.2:+5705166 MS.gene27789:intron
GTAGCCCAAGGAAGAAACTT+AGG 0.555898 1.2:+5703724 MS.gene27789:CDS
TGTCTCGCACGAAGGGCAGA+TGG 0.584824 1.2:-5705333 None:intergenic
ATTTGTGGTGGCAACAACAA+TGG 0.596806 1.2:+5705356 MS.gene27789:CDS
CAGATGGTAAGTGTTGCTGC+TGG 0.599263 1.2:-5705317 None:intergenic
TCTGCAGGCTAGACAAGTAG+AGG 0.619659 1.2:+5704560 MS.gene27789:CDS
TTGATAAAGATGGTAGCCCA+AGG 0.634722 1.2:+5703712 None:intergenic
TCGTGCGAGACAATTTGTGG+TGG 0.644683 1.2:+5705344 MS.gene27789:CDS
GTGTTGCGAATCTCTAACAG+AGG 0.648660 1.2:+5705214 MS.gene27789:CDS
CCACAAATTGTCTCGCACGA+AGG 0.651452 1.2:-5705341 None:intergenic
AGGCTAGACAAGTAGAGGTG+TGG 0.674713 1.2:+5704565 MS.gene27789:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAAAAATTAAATTCTA+AGG - chr1.2:5704404-5704423 None:intergenic 10.0%
!! AAACAAAGAAGTAAAATATA+TGG - chr1.2:5704815-5704834 None:intergenic 15.0%
!! AAGTTTATAAAAATTGTTTC+AGG - chr1.2:5704309-5704328 None:intergenic 15.0%
!!! ACAATTTTTATAAACTTGTA+CGG + chr1.2:5704312-5704331 MS.gene27789:intron 15.0%
!!! ATTTTATTAGAATTAGATCT+TGG + chr1.2:5704099-5704118 MS.gene27789:intron 15.0%
!! AAATTTGTAATACATTGGAT+TGG - chr1.2:5704447-5704466 None:intergenic 20.0%
!! AGTTTCAAAATTTATTCTCT+TGG + chr1.2:5704180-5704199 MS.gene27789:intron 20.0%
!! ATATAATTTCACAAAATCTG+AGG - chr1.2:5705111-5705130 None:intergenic 20.0%
!! ATGAGAATATTGATGAATTA+AGG - chr1.2:5703816-5703835 None:intergenic 20.0%
!! CTACAAAATTTGTAATACAT+TGG - chr1.2:5704452-5704471 None:intergenic 20.0%
!! TTTCAGGAAATTATTTATTC+TGG - chr1.2:5704293-5704312 None:intergenic 20.0%
!!! ACTTCTTTGTTTTTTTTTAC+TGG + chr1.2:5704823-5704842 MS.gene27789:intron 20.0%
!!! CATTTTTTTAGAAATGTTTC+TGG + chr1.2:5704361-5704380 MS.gene27789:intron 20.0%
!!! GAAACATTTCTAAAAAAATG+AGG - chr1.2:5704361-5704380 None:intergenic 20.0%
!!! TCATTTCCATAAAAACTTTT+TGG + chr1.2:5705421-5705440 MS.gene27789:CDS 20.0%
! ACAAAAAATGTTAACAGCTA+GGG + chr1.2:5705017-5705036 MS.gene27789:intron 25.0%
! AGACGTTTAAAAAGTTTAGA+AGG - chr1.2:5705058-5705077 None:intergenic 25.0%
! ATATATATTGTTAGAGCGAA+AGG + chr1.2:5704926-5704945 MS.gene27789:intron 25.0%
! ATATTGATGAATTAAGGTAC+CGG - chr1.2:5703810-5703829 None:intergenic 25.0%
! CATCAATATTCTCATATCTT+TGG + chr1.2:5703821-5703840 MS.gene27789:intron 25.0%
!! AAAACAACAATCAGAAGTTT+TGG + chr1.2:5703752-5703771 MS.gene27789:CDS 25.0%
!! AATATCAAAACAAAAGTACG+TGG - chr1.2:5703876-5703895 None:intergenic 25.0%
AAAAGTTTAGAAGGAGGTTT+AGG - chr1.2:5705049-5705068 None:intergenic 30.0%
AAAGTTTAGAAGGAGGTTTA+GGG - chr1.2:5705048-5705067 None:intergenic 30.0%
ATCATCATGACAATTGCTAA+TGG - chr1.2:5704693-5704712 None:intergenic 30.0%
CACAAAAAATGTTAACAGCT+AGG + chr1.2:5705016-5705035 MS.gene27789:intron 30.0%
CGTTTAAAAAGTTTAGAAGG+AGG - chr1.2:5705055-5705074 None:intergenic 30.0%
GCTGGAATCTTCATATAAAA+GGG - chr1.2:5705302-5705321 None:intergenic 30.0%
GGTAAAATCTTGATATTCCT+AGG + chr1.2:5704242-5704261 MS.gene27789:intron 30.0%
TATGAAGCAAACTCAATCTA+AGG - chr1.2:5704161-5704180 None:intergenic 30.0%
TGCTGGAATCTTCATATAAA+AGG - chr1.2:5705303-5705322 None:intergenic 30.0%
TTAGAATTAGATCTTGGTCT+TGG + chr1.2:5704105-5704124 MS.gene27789:intron 30.0%
TTCACAAAATCTGAGGAATA+AGG - chr1.2:5705104-5705123 None:intergenic 30.0%
! AAAACAAAAGTACGTGGTAT+AGG - chr1.2:5703870-5703889 None:intergenic 30.0%
! ATTTTACCAAACACTTTGGT+GGG - chr1.2:5704230-5704249 None:intergenic 30.0%
! CAAGATTTTACCAAACACTT+TGG - chr1.2:5704234-5704253 None:intergenic 30.0%
! TCTCTTGGATTACATTTTCT+AGG + chr1.2:5704195-5704214 MS.gene27789:intron 30.0%
AAGGTAAAGTATGCGATCAA+AGG - chr1.2:5705085-5705104 None:intergenic 35.0%
AGGTAAAGTATGCGATCAAA+GGG - chr1.2:5705084-5705103 None:intergenic 35.0%
CAGAACAAAGCTGAAACAAA+CGG + chr1.2:5705166-5705185 MS.gene27789:intron 35.0%
CGATACTATCTTAAAACGCA+CGG - chr1.2:5704624-5704643 None:intergenic 35.0%
CTTGATATTCCTAGGAAAGT+TGG + chr1.2:5704250-5704269 MS.gene27789:intron 35.0%
! AGAGCATTCTACTCTTAATC+CGG + chr1.2:5703788-5703807 MS.gene27789:CDS 35.0%
! ATATTCCTAGGAAAGTTGGT+AGG + chr1.2:5704254-5704273 MS.gene27789:intron 35.0%
! ATTATTCCCACCAAAGTGTT+TGG + chr1.2:5704221-5704240 MS.gene27789:intron 35.0%
! GATTTTACCAAACACTTTGG+TGG - chr1.2:5704231-5704250 None:intergenic 35.0%
! TAGAGGTGTGGTTTCAAAAT+CGG + chr1.2:5704577-5704596 MS.gene27789:CDS 35.0%
! TCTAAGGTGTGTTTGTTTCA+AGG - chr1.2:5704388-5704407 None:intergenic 35.0%
!! ACAACAATCAGAAGTTTTGG+AGG + chr1.2:5703755-5703774 MS.gene27789:CDS 35.0%
AAGCAATGTTGTTGAGGGTA+AGG - chr1.2:5705384-5705403 None:intergenic 40.0%
AGCAAATAAGCTGAATCTGC+AGG + chr1.2:5704545-5704564 MS.gene27789:CDS 40.0%
AGGAGAAAACTTAGATGGCA+CGG + chr1.2:5704946-5704965 MS.gene27789:intron 40.0%
ATTTGTGGTGGCAACAACAA+TGG + chr1.2:5705356-5705375 MS.gene27789:CDS 40.0%
CCAGTAAGCAATGTTGTTGA+GGG - chr1.2:5705389-5705408 None:intergenic 40.0%
GCGAAAGGAGAAAACTTAGA+TGG + chr1.2:5704941-5704960 MS.gene27789:intron 40.0%
GGAGAACAAGAAGTTGCAAA+AGG + chr1.2:5705235-5705254 MS.gene27789:CDS 40.0%
TATTCTCTACGTGCGCAATA+TGG - chr1.2:5704983-5705002 None:intergenic 40.0%
TGAGCCTAAGTTTCTTCCTT+GGG - chr1.2:5703731-5703750 None:intergenic 40.0%
! CACGCACAGTATTTTTCTCA+TGG + chr1.2:5704001-5704020 MS.gene27789:intron 40.0%
! TGGTCTTGGTTGATTGTGTT+TGG + chr1.2:5704119-5704138 MS.gene27789:intron 40.0%
ACACACCTACCAACTTTCCT+AGG - chr1.2:5704262-5704281 None:intergenic 45.0%
CACAAATTGTCTCGCACGAA+GGG - chr1.2:5705343-5705362 None:intergenic 45.0%
CCCTCAACAACATTGCTTAC+TGG + chr1.2:5705386-5705405 MS.gene27789:CDS 45.0%
GCCAGTAAGCAATGTTGTTG+AGG - chr1.2:5705390-5705409 None:intergenic 45.0%
GTAGCCCAAGGAAGAAACTT+AGG + chr1.2:5703724-5703743 MS.gene27789:CDS 45.0%
GTGAGCCTAAGTTTCTTCCT+TGG - chr1.2:5703732-5703751 None:intergenic 45.0%
GTGTTGCGAATCTCTAACAG+AGG + chr1.2:5705214-5705233 MS.gene27789:CDS 45.0%
AGGCTAGACAAGTAGAGGTG+TGG + chr1.2:5704565-5704584 MS.gene27789:CDS 50.0%
CCACAAATTGTCTCGCACGA+AGG - chr1.2:5705344-5705363 None:intergenic 50.0%
CCTTCGTGCGAGACAATTTG+TGG + chr1.2:5705341-5705360 MS.gene27789:CDS 50.0%
GCACGGAGCAGTAAATTACC+TGG - chr1.2:5704607-5704626 None:intergenic 50.0%
GGTTTCAAAATCGGAGAGCC+AGG + chr1.2:5704586-5704605 MS.gene27789:CDS 50.0%
TCGTGCGAGACAATTTGTGG+TGG + chr1.2:5705344-5705363 MS.gene27789:CDS 50.0%
TCTGCAGGCTAGACAAGTAG+AGG + chr1.2:5704560-5704579 MS.gene27789:CDS 50.0%
! CAGATGGTAAGTGTTGCTGC+TGG - chr1.2:5705320-5705339 None:intergenic 50.0%
TGTCTCGCACGAAGGGCAGA+TGG - chr1.2:5705336-5705355 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 5703721 5705448 5703721 ID=MS.gene27789
chr1.2 mRNA 5703721 5705448 5703721 ID=MS.gene27789.t1;Parent=MS.gene27789
chr1.2 exon 5703721 5703809 5703721 ID=MS.gene27789.t1.exon1;Parent=MS.gene27789.t1
chr1.2 CDS 5703721 5703809 5703721 ID=cds.MS.gene27789.t1;Parent=MS.gene27789.t1
chr1.2 exon 5704509 5704607 5704509 ID=MS.gene27789.t1.exon2;Parent=MS.gene27789.t1
chr1.2 CDS 5704509 5704607 5704509 ID=cds.MS.gene27789.t1;Parent=MS.gene27789.t1
chr1.2 exon 5705169 5705448 5705169 ID=MS.gene27789.t1.exon3;Parent=MS.gene27789.t1
chr1.2 CDS 5705169 5705448 5705169 ID=cds.MS.gene27789.t1;Parent=MS.gene27789.t1
Gene Sequence

>MS.gene27789

ATGGTAGCCCAAGGAAGAAACTTAGGCTCACAAAACAACAATCAGAAGTTTTGGAGGAAAACTTCAAAGAGCATTCTACTCTTAATCCGGTACCTTAATTCATCAATATTCTCATATCTTTGGTTGCTTTAAATAATTCTTTTGCTCCTATACCACGTACTTTTGTTTTGATATTTTTATTTTAGTACTAATAACTATTTTATATATATAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAGACACACACGCACAGTATTTTTCTCATGGCACACTAATTGTGTGTAGCATATAGTAAATGAAGAATATGATATCATTTTAAACGAGTTTTCTCGATGATATTTGATTTTATTAGAATTAGATCTTGGTCTTGGTTGATTGTGTTTGGTCTAAAACTGAGAAGACCTTAGATTGAGTTTGCTTCATAGTTTCAAAATTTATTCTCTTGGATTACATTTTCTAGGAATATTATTCCCACCAAAGTGTTTGGTAAAATCTTGATATTCCTAGGAAAGTTGGTAGGTGTGTTTTATTTTCCAGAATAAATAATTTCCTGAAACAATTTTTATAAACTTGTACGGAATATAATAATATTAAATTCTAACCTCATTTTTTTAGAAATGTTTCTGGACCTTGAAACAAACACACCTTAGAATTTAATTTTTTTTCTAATTTGTGCAATTGCTACATCCAATCCAATGTATTACAAATTTTGTAGCATGAGTATATGTTGCTTTGTTATTATTAATAAAAAGAAAATCTCATTTTCTTCAGAAGCAAAAGCAAGCATTAGCAAATAAGCTGAATCTGCAGGCTAGACAAGTAGAGGTGTGGTTTCAAAATCGGAGAGCCAGGTAATTTACTGCTCCGTGCGTTTTAAGATAGTATCGTTTAAAGTTCTTTTATATAGATTAAAAAATTTACAAAACTGTTTATCCATTAGCAATTGTCATGATGATGCATAACAAAATATAATGTCTTGAGACTTATGTACACACAAAAAGTTGTGATAAAATTGAAATAATGAAATTATACTATTGATGTTACATTAAAAAGTACCATATATTTTACTTCTTTGTTTTTTTTTACTGGATCGCACATACTTTACTTTATTGCTTCTTTAATAGATAAATGTTACTTTTTTTAATAATAAATAAATGTTACTTGTTAGTATATATATTGTTAGAGCGAAAGGAGAAAACTTAGATGGCACGGATCTCAACTCTCCATATTGCGCACGTAGAGAATACTCGATTTACACACACAAAAAATGTTAACAGCTAGGGTCAAACCCTAAACCTCCTTCTAAACTTTTTAAACGTCTCGACCCTTTGATCGCATACTTTACCTTATTCCTCAGATTTTGTGAAATTATATTTCTTGCATATACTAATGATTACTATATACATGTTCAGAACAAAGCTGAAACAAACGGAATCTGATTGTGAAATACTGAAGAAGTGTTGCGAATCTCTAACAGAGGAGAACAAGAAGTTGCAAAAGGAGCTACAAGAACTAAAGTCAATGCAAACAGTAGCAGCAGCACCCTTTTATATGAAGATTCCAGCAGCAACACTTACCATCTGCCCTTCGTGCGAGACAATTTGTGGTGGCAACAACAATGGCTCCTTACCCTCAACAACATTGCTTACTGGCTCAAAGAATCATCATTTCCATAAAAACTTTTTGGTTTGA
Protein sequence

>MS.gene27789.t1

MVAQGRNLGSQNNNQKFWRKTSKSILLLIRKSHFLQKQKQALANKLNLQARQVEVWFQNRRARTKLKQTESDCEILKKCCESLTEENKKLQKELQELKSMQTVAAAPFYMKIPAATLTICPSCETICGGNNNGSLPSTTLLTGSKNHHFHKNFLV