AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040857

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040857.t1 MTR_1g033750 93.274 223 15 0 1 223 1 223 3.07e-154 427
MS.gene040857.t1 MTR_1g114640 68.037 219 67 2 4 222 5 220 4.68e-102 295
MS.gene040857.t1 MTR_1g114690 54.667 225 84 3 4 222 5 217 8.77e-79 236
MS.gene040857.t1 MTR_1g114690 53.982 226 86 3 4 223 5 218 4.56e-78 234
MS.gene040857.t1 MTR_1g114750 52.036 221 101 3 4 223 5 221 8.14e-75 226
MS.gene040857.t1 MTR_1g114640 69.048 168 49 2 4 171 5 169 1.41e-73 221
MS.gene040857.t1 MTR_1g114690 46.923 260 86 4 4 223 5 252 1.36e-70 216
MS.gene040857.t1 MTR_1g115130 50.230 217 78 3 7 223 8 194 4.20e-64 198
MS.gene040857.t1 MTR_8g100065 50.000 184 91 1 41 223 2 185 5.20e-60 187
MS.gene040857.t1 MTR_6g077990 46.569 204 101 2 20 223 4 199 3.08e-59 185
MS.gene040857.t1 MTR_6g077990 54.321 162 74 0 62 223 37 198 5.08e-59 185
MS.gene040857.t1 MTR_8g100065 55.215 163 72 1 62 223 45 207 5.20e-59 185
MS.gene040857.t1 MTR_6g077990 56.376 149 65 0 75 223 8 156 5.44e-56 176
MS.gene040857.t1 MTR_1g114690 46.602 206 80 5 4 203 5 186 7.47e-50 161
MS.gene040857.t1 MTR_1g114680 69.369 111 34 0 113 223 53 163 5.51e-46 151
MS.gene040857.t1 MTR_3g100750 40.645 155 91 1 66 220 102 255 6.10e-41 140
MS.gene040857.t1 MTR_7g083570 37.143 175 110 0 48 222 102 276 1.94e-40 140
MS.gene040857.t1 MTR_8g069110 37.989 179 100 2 52 220 90 267 8.77e-40 138
MS.gene040857.t1 MTR_6g077990 53.704 108 50 0 62 169 37 144 7.21e-36 124
MS.gene040857.t1 MTR_8g100065 47.244 127 66 1 42 167 3 129 2.42e-33 117
MS.gene040857.t1 MTR_8g100065 54.206 107 48 1 62 167 45 151 1.48e-32 115
MS.gene040857.t1 MTR_2g076350 33.755 237 132 7 1 222 1 227 4.63e-31 114
MS.gene040857.t1 MTR_5g015750 50.704 71 32 2 4 74 5 72 7.48e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040857.t1 AT5G08350 53.810 210 83 3 15 223 19 215 1.15e-73 223
MS.gene040857.t1 AT5G23370 52.232 224 89 5 5 223 6 216 7.49e-73 221
MS.gene040857.t1 AT5G23350 49.550 222 94 4 5 221 6 214 1.81e-71 217
MS.gene040857.t1 AT5G23360 51.546 194 91 2 30 222 16 207 1.13e-68 209
MS.gene040857.t1 AT4G01600 36.279 215 123 4 23 223 13 227 3.47e-42 143
MS.gene040857.t1 AT4G01600 38.674 181 103 2 51 223 8 188 1.64e-41 140
MS.gene040857.t1 AT5G13200 33.816 207 132 2 16 221 59 261 8.65e-41 140
MS.gene040857.t1 AT4G01600 36.019 211 124 5 23 223 13 222 3.39e-38 132
MS.gene040857.t1 AT1G28200 36.478 159 100 1 62 220 97 254 3.47e-37 130
MS.gene040857.t1 AT1G28200 36.478 159 100 1 62 220 97 254 3.47e-37 130
MS.gene040857.t1 AT2G22475 35.152 165 106 1 56 220 128 291 8.24e-37 130
MS.gene040857.t1 AT5G13200 32.026 153 99 2 16 167 59 207 1.64e-22 91.7
MS.gene040857.t1 AT4G40100 30.909 165 79 2 56 220 87 216 3.92e-22 90.9
MS.gene040857.t1 AT2G22475 31.304 115 78 1 56 170 128 241 1.23e-17 79.3

Find 36 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGCAATTTCAATGTACTTT+TGG 0.206367 1.2:+18477196 None:intergenic
GTTCTAATAAAGTGGCCTTT+TGG 0.325622 1.2:+18477468 None:intergenic
TTTCTTCAAGAGCTATTAGT+TGG 0.372608 1.2:-18478418 MS.gene040857:CDS
CTCACTAGGATGAACAATCT+TGG 0.396062 1.2:-18478126 MS.gene040857:CDS
ATTCACCTCAGCAGCATACT+TGG 0.404852 1.2:-18478389 MS.gene040857:CDS
AATTGACCCCTCACTACAAA+AGG 0.421103 1.2:+18477503 None:intergenic
CTTTATTAGAACACATTACA+AGG 0.441996 1.2:-18477457 MS.gene040857:intron
TGGGTGATAATTCATCAAAT+AGG 0.448132 1.2:-18478369 MS.gene040857:CDS
ATTAAAATCTCTTCTCCAAA+AGG 0.451579 1.2:-18477483 MS.gene040857:CDS
TCACTAGGATGAACAATCTT+GGG 0.454379 1.2:-18478125 MS.gene040857:CDS
CTTATTGTAGTAGTTGGACT+TGG 0.459996 1.2:+18478330 None:intergenic
GCTTGACTTATTGTAGTAGT+TGG 0.460001 1.2:+18478324 None:intergenic
TTATTCCACTTGGCAAGATA+AGG 0.462580 1.2:-18477254 MS.gene040857:CDS
TTTAAAATGCAGTGAAACTA+GGG 0.462654 1.2:-18477722 MS.gene040857:intron
GTGAAAGGAAAACTGAGGTT+AGG 0.467486 1.2:-18477681 MS.gene040857:CDS
GGAGCTAGAATTCTTCAAGT+TGG 0.475294 1.2:-18477660 MS.gene040857:CDS
TGTAATGTGTTCTAATAAAG+TGG 0.482439 1.2:+18477460 None:intergenic
TCAAGTTGGAGGAGTGGAAA+AGG 0.489991 1.2:-18477646 MS.gene040857:CDS
TGTTATCTATCAACAACAAT+GGG 0.501863 1.2:-18477567 MS.gene040857:CDS
GCTAGAATTCTTCAAGTTGG+AGG 0.512754 1.2:-18477657 MS.gene040857:CDS
ACAACAATGGGTCCTCTAGC+AGG 0.513963 1.2:-18477555 MS.gene040857:CDS
AAGTATGCTGCTGAGGTGAA+TGG 0.545777 1.2:+18478391 None:intergenic
TTGTAGGTCATTATTCCACT+TGG 0.560547 1.2:-18477264 MS.gene040857:intron
TTAGTGTAAAAGATGAAGAG+AGG 0.564160 1.2:-18477608 MS.gene040857:CDS
ATGTTATCTATCAACAACAA+TGG 0.566981 1.2:-18477568 MS.gene040857:CDS
AATTCTTCAAGTTGGAGGAG+TGG 0.572161 1.2:-18477652 MS.gene040857:CDS
TTCACCTCAGCAGCATACTT+GGG 0.589074 1.2:-18478388 MS.gene040857:CDS
GAGCAAATTCAGTTCTCACT+AGG 0.589590 1.2:-18478140 MS.gene040857:CDS
AAAATAACTGATACAGTGAA+AGG 0.595974 1.2:-18477696 MS.gene040857:CDS
AAAGTACATTGAAATTGCTA+CGG 0.602017 1.2:-18477193 MS.gene040857:CDS
ACAAACCTTATCTTGCCAAG+TGG 0.607201 1.2:+18477249 None:intergenic
ATCACCCAAGTATGCTGCTG+AGG 0.611603 1.2:+18478384 None:intergenic
GTACATTGAAATTGCTACGG+TGG 0.620058 1.2:-18477190 MS.gene040857:CDS
GCAACTGGACTCAAAGAACA+TGG 0.622654 1.2:-18478084 MS.gene040857:intron
ATGAAGAGTAAGCCTGCTAG+AGG 0.652380 1.2:+18477543 None:intergenic
ATACAGTGAAAGGAAAACTG+AGG 0.714258 1.2:-18477686 MS.gene040857:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAATAACATTATAAATG+AGG + chr1.2:18477794-18477813 None:intergenic 10.0%
!! GAAGATTAAATTTAAATTAA+AGG + chr1.2:18477261-18477280 None:intergenic 10.0%
!! AAAAAAAAAAAATGTCTAAG+AGG + chr1.2:18477694-18477713 None:intergenic 15.0%
!!! AAGTTTTTCTTTATATTTCT+TGG + chr1.2:18477300-18477319 None:intergenic 15.0%
!!! ATTTTTTTTTTTTCATCTAG+AGG - chr1.2:18477701-18477720 MS.gene040857:CDS 15.0%
!!! TTTTTTTTTTTTCATCTAGA+GGG - chr1.2:18477702-18477721 MS.gene040857:CDS 15.0%
!! TTAAAAATCATATGAAGCAA+AGG + chr1.2:18478222-18478241 None:intergenic 20.0%
!!! ATTTTCTTTAACCCTATTAT+TGG - chr1.2:18477604-18477623 MS.gene040857:CDS 20.0%
! AAAATAACTGATACAGTGAA+AGG - chr1.2:18477838-18477857 MS.gene040857:intron 25.0%
! AAAGTACATTGAAATTGCTA+CGG - chr1.2:18478341-18478360 MS.gene040857:CDS 25.0%
! ATGTTATCTATCAACAACAA+TGG - chr1.2:18477966-18477985 MS.gene040857:intron 25.0%
! ATTAAAATCTCTTCTCCAAA+AGG - chr1.2:18478051-18478070 MS.gene040857:intron 25.0%
! CTTTATTAGAACACATTACA+AGG - chr1.2:18478077-18478096 MS.gene040857:intron 25.0%
! GATAAATCTCACCAATAATA+GGG + chr1.2:18477618-18477637 None:intergenic 25.0%
! TGTAATGTGTTCTAATAAAG+TGG + chr1.2:18478077-18478096 None:intergenic 25.0%
! TGTAATTTATCTATCCTTGT+AGG - chr1.2:18478254-18478273 MS.gene040857:intron 25.0%
! TGTTATCTATCAACAACAAT+GGG - chr1.2:18477967-18477986 MS.gene040857:intron 25.0%
!! AGCAATTTCAATGTACTTTT+GGG + chr1.2:18478340-18478359 None:intergenic 25.0%
!! TAGCAATTTCAATGTACTTT+TGG + chr1.2:18478341-18478360 None:intergenic 25.0%
!! TTTAAAATGCAGTGAAACTA+GGG - chr1.2:18477812-18477831 MS.gene040857:intron 25.0%
!!! AATCGTTATTTTTTCTCTTC+AGG - chr1.2:18477369-18477388 MS.gene040857:intron 25.0%
!!! GATTTTGAGTTTTGGTTTAT+GGG - chr1.2:18478369-18478388 MS.gene040857:CDS 25.0%
!!! TGATTTTGAGTTTTGGTTTA+TGG - chr1.2:18478368-18478387 MS.gene040857:CDS 25.0%
!!! TTTTAAAATGCAGTGAAACT+AGG - chr1.2:18477811-18477830 MS.gene040857:intron 25.0%
GGATAAATCTCACCAATAAT+AGG + chr1.2:18477619-18477638 None:intergenic 30.0%
TAACATTATAAATGAGGTCG+AGG + chr1.2:18477788-18477807 None:intergenic 30.0%
TGGGTGATAATTCATCAAAT+AGG - chr1.2:18477165-18477184 MS.gene040857:CDS 30.0%
TTAGTGTAAAAGATGAAGAG+AGG - chr1.2:18477926-18477945 MS.gene040857:intron 30.0%
TTTCTTCAAGAGCTATTAGT+TGG - chr1.2:18477116-18477135 MS.gene040857:CDS 30.0%
! AAAATTGCCTTTTGTAGTGA+GGG - chr1.2:18478024-18478043 MS.gene040857:intron 30.0%
! TAAAATTGCCTTTTGTAGTG+AGG - chr1.2:18478023-18478042 MS.gene040857:intron 30.0%
!! ATTTCAATGTACTTTTGGGT+AGG + chr1.2:18478336-18478355 None:intergenic 30.0%
AAGTGGAATAATGACCTACA+AGG + chr1.2:18478271-18478290 None:intergenic 35.0%
AGGAGAGACTTCACTAAAAA+TGG + chr1.2:18477674-18477693 None:intergenic 35.0%
ATACAGTGAAAGGAAAACTG+AGG - chr1.2:18477848-18477867 MS.gene040857:intron 35.0%
ATAGCCGTTAAGTACATGTT+TGG - chr1.2:18478129-18478148 MS.gene040857:CDS 35.0%
CAAAGGATTTAGTATCTGCA+TGG + chr1.2:18478205-18478224 None:intergenic 35.0%
CGATCCAAACATGTACTTAA+CGG + chr1.2:18478136-18478155 None:intergenic 35.0%
CTTATTGTAGTAGTTGGACT+TGG + chr1.2:18477207-18477226 None:intergenic 35.0%
GATTTAGTATCTGCATGGAT+TGG + chr1.2:18478200-18478219 None:intergenic 35.0%
GCTTGACTTATTGTAGTAGT+TGG + chr1.2:18477213-18477232 None:intergenic 35.0%
TCACTAGGATGAACAATCTT+GGG - chr1.2:18477409-18477428 MS.gene040857:intron 35.0%
TTATTCCACTTGGCAAGATA+AGG - chr1.2:18478280-18478299 MS.gene040857:intron 35.0%
TTGTAGGTCATTATTCCACT+TGG - chr1.2:18478270-18478289 MS.gene040857:intron 35.0%
! AAAGCTGACAATTTTGCAAC+TGG - chr1.2:18477435-18477454 MS.gene040857:intron 35.0%
! AAATTGCCTTTTGTAGTGAG+GGG - chr1.2:18478025-18478044 MS.gene040857:intron 35.0%
! ACAAGAGCATATGAGAAGAA+CGG + chr1.2:18477331-18477350 None:intergenic 35.0%
! GTTCTAATAAAGTGGCCTTT+TGG + chr1.2:18478069-18478088 None:intergenic 35.0%
AATTGACCCCTCACTACAAA+AGG + chr1.2:18478034-18478053 None:intergenic 40.0%
ACAAACCTTATCTTGCCAAG+TGG + chr1.2:18478288-18478307 None:intergenic 40.0%
CTCACTAGGATGAACAATCT+TGG - chr1.2:18477408-18477427 MS.gene040857:intron 40.0%
GAGCAAATTCAGTTCTCACT+AGG - chr1.2:18477394-18477413 MS.gene040857:intron 40.0%
GGAGCTAGAATTCTTCAAGT+TGG - chr1.2:18477874-18477893 MS.gene040857:intron 40.0%
GTACATTGAAATTGCTACGG+TGG - chr1.2:18478344-18478363 MS.gene040857:CDS 40.0%
GTATCGCATAGGCAATGTTT+CGG + chr1.2:18477735-18477754 None:intergenic 40.0%
GTGAAAGGAAAACTGAGGTT+AGG - chr1.2:18477853-18477872 MS.gene040857:intron 40.0%
GTTAATTCCTCGCTAGTCAT+AGG + chr1.2:18477652-18477671 None:intergenic 40.0%
TATCGCATAGGCAATGTTTC+GGG + chr1.2:18477734-18477753 None:intergenic 40.0%
!! AATTCTTCAAGTTGGAGGAG+TGG - chr1.2:18477882-18477901 MS.gene040857:intron 40.0%
!! GCTAGAATTCTTCAAGTTGG+AGG - chr1.2:18477877-18477896 MS.gene040857:intron 40.0%
!! TTAGTATCTGCATGGATTGG+CGG + chr1.2:18478197-18478216 None:intergenic 40.0%
!!! CGGTGGATGATTTTGAGTTT+TGG - chr1.2:18478361-18478380 MS.gene040857:CDS 40.0%
AAGTATGCTGCTGAGGTGAA+TGG + chr1.2:18477146-18477165 None:intergenic 45.0%
ATGAAGAGTAAGCCTGCTAG+AGG + chr1.2:18477994-18478013 None:intergenic 45.0%
ATTCACCTCAGCAGCATACT+TGG - chr1.2:18477145-18477164 MS.gene040857:CDS 45.0%
GCAACTGGACTCAAAGAACA+TGG - chr1.2:18477450-18477469 MS.gene040857:intron 45.0%
TCGCTAGTCATAGGCAACAT+CGG + chr1.2:18477643-18477662 None:intergenic 45.0%
TTCACCTCAGCAGCATACTT+GGG - chr1.2:18477146-18477165 MS.gene040857:CDS 45.0%
! TCCTTTGACTCGTATCGCAT+AGG + chr1.2:18477746-18477765 None:intergenic 45.0%
!! TCAAGTTGGAGGAGTGGAAA+AGG - chr1.2:18477888-18477907 MS.gene040857:intron 45.0%
!! AAATTAATTATATTAGTATA+TGG + chr1.2:18477498-18477517 None:intergenic 5.0%
ACAACAATGGGTCCTCTAGC+AGG - chr1.2:18477979-18477998 MS.gene040857:intron 50.0%
ATCACCCAAGTATGCTGCTG+AGG + chr1.2:18477153-18477172 None:intergenic 50.0%
CTAGTCATAGGCAACATCGG+TGG + chr1.2:18477640-18477659 None:intergenic 50.0%
GATGTTGCCTATGACTAGCG+AGG - chr1.2:18477642-18477661 MS.gene040857:CDS 50.0%
GCCTATGCGATACGAGTCAA+AGG - chr1.2:18477742-18477761 MS.gene040857:intron 50.0%
!! GCATGGATTGGCGGTGAGTT+TGG + chr1.2:18478188-18478207 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 18477107 18478449 18477107 ID=MS.gene040857
chr1.2 mRNA 18477107 18478449 18477107 ID=MS.gene040857.t1;Parent=MS.gene040857
chr1.2 exon 18478308 18478449 18478308 ID=MS.gene040857.t1.exon1;Parent=MS.gene040857.t1
chr1.2 CDS 18478308 18478449 18478308 ID=cds.MS.gene040857.t1;Parent=MS.gene040857.t1
chr1.2 exon 18478085 18478165 18478085 ID=MS.gene040857.t1.exon2;Parent=MS.gene040857.t1
chr1.2 CDS 18478085 18478165 18478085 ID=cds.MS.gene040857.t1;Parent=MS.gene040857.t1
chr1.2 exon 18477458 18477732 18477458 ID=MS.gene040857.t1.exon3;Parent=MS.gene040857.t1
chr1.2 CDS 18477458 18477732 18477458 ID=cds.MS.gene040857.t1;Parent=MS.gene040857.t1
chr1.2 exon 18477107 18477280 18477107 ID=MS.gene040857.t1.exon4;Parent=MS.gene040857.t1
chr1.2 CDS 18477107 18477280 18477107 ID=cds.MS.gene040857.t1;Parent=MS.gene040857.t1
Gene Sequence

>MS.gene040857

ATGGCTTATTTTCTTCAAGAGCTATTAGTTGGATTTCCATTCACCTCAGCAGCATACTTGGGTGATAATTCATCAAATAGGTACTTAATAAATTCTTCCAAGTCCAACTACTACAATAAGTCAAGCACAAATTCAAATCAAAGTAAGACATCCTTTAATTTAAATTTAATCTTCATTGATCAAGTTTTTACCAAGAAATATAAAGAAAAACTTTATTTGATCCGTTCTTCTCATATGCTCTTGTTGTATTCACAATATTGAAAATCGTTATTTTTTCTCTTCAGGTAGAGCAAATTCAGTTCTCACTAGGATGAACAATCTTGGGAGAAAAGCTGACAATTTTGCAACTGGACTCAAAGAACATGGTATATACATATACTCATCGAAACCATATACTAATATAATTAATTTGCACATGTCTAAATAATTTACTAAATTTTAGAACTTGAACTTGTATATTAGTATTTCTCAACAATATAATATACAATAAATTTGTAATTTTCTTTAACCCTATTATTGGTGAGATTTATCCACCGATGTTGCCTATGACTAGCGAGGAATTAACCATTTTTAGTGAAGTCTCTCCTCTTAGACATTTTTTTTTTTTCATCTAGAGGGCTTAAACCCGAAACATTGCCTATGCGATACGAGTCAAAGGATTCTAGTCTAGAATCGAGACCTCGACCTCATTTATAATGTTATTTTTTTAAAATGCAGTGAAACTAGGGCAAAAAATAACTGATACAGTGAAAGGAAAACTGAGGTTAGGAGCTAGAATTCTTCAAGTTGGAGGAGTGGAAAAGGTGTTCATGCAACTTTTTAGTGTAAAAGATGAAGAGAGGCTACTAAAAGCATCTCAATGTTATCTATCAACAACAATGGGTCCTCTAGCAGGCTTACTCTTCATATCAACTAATAAAATTGCCTTTTGTAGTGAGGGGTCAATTAAAATCTCTTCTCCAAAAGGCCACTTTATTAGAACACATTACAAGGTAATAATACACATATTGATTTGTACAAAAATAGCCGTTAAGTACATGTTTGGATCGATAGTGAGTTTGACTAAATCGTGATTTCTCCAAACTCACCGCCAATCCATGCAGATACTAAATCCTTTGCTTCATATGATTTTTAATCTCATAAACATTGTAATTTATCTATCCTTGTAGGTCATTATTCCACTTGGCAAGATAAGGTTTGTTAATCAAAGTGAGCATGTGAAGAAGCCTACCCAAAAGTACATTGAAATTGCTACGGTGGATGATTTTGAGTTTTGGTTTATGGGTTTCTTAAATCATCAGCAAGCTTTCAAATATTTGAAGCAAGCTATCTCTCAATCTTAG
Protein sequence

>MS.gene040857.t1

MAYFLQELLVGFPFTSAAYLGDNSSNRYLINSSKSNYYNKSSTNSNQSRANSVLTRMNNLGRKADNFATGLKEHVKLGQKITDTVKGKLRLGARILQVGGVEKVFMQLFSVKDEERLLKASQCYLSTTMGPLAGLLFISTNKIAFCSEGSIKISSPKGHFIRTHYKVIIPLGKIRFVNQSEHVKKPTQKYIEIATVDDFEFWFMGFLNHQQAFKYLKQAISQS