AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27843

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27843.t1 MTR_8g087450 97.544 285 7 0 1 285 1 285 0.0 556
MS.gene27843.t1 MTR_2g017960 71.530 281 67 4 1 278 1 271 2.05e-115 333
MS.gene27843.t1 MTR_2g017970 77.143 210 46 2 76 285 67 274 1.66e-109 318
MS.gene27843.t1 MTR_4g059840 55.932 236 89 6 58 283 53 283 9.13e-80 243
MS.gene27843.t1 MTR_4g053380 54.475 257 92 5 2 245 7 251 2.47e-78 239
MS.gene27843.t1 MTR_4g059790 60.199 201 70 3 58 248 53 253 7.53e-78 238
MS.gene27843.t1 MTR_2g093980 48.980 294 129 9 1 287 1 280 1.21e-75 233
MS.gene27843.t1 MTR_4g059780 49.815 271 115 5 21 284 45 301 9.44e-69 215
MS.gene27843.t1 MTR_2g093970 45.890 292 125 7 10 285 13 287 5.54e-68 213
MS.gene27843.t1 MTR_2g017950 43.345 293 139 8 6 285 12 290 2.52e-64 204
MS.gene27843.t1 MTR_8g087470 44.906 265 127 6 41 287 51 314 3.90e-62 199
MS.gene27843.t1 MTR_8g087460 46.360 261 119 7 45 285 53 312 9.76e-62 198
MS.gene27843.t1 MTR_4g059720 45.415 229 84 4 1 228 4 192 6.78e-57 183
MS.gene27843.t1 MTR_2g093990 46.117 206 101 3 77 279 41 239 6.89e-53 173
MS.gene27843.t1 MTR_7g101080 44.578 166 90 2 58 222 21 185 2.53e-41 143
MS.gene27843.t1 MTR_2g090765 35.565 239 132 4 50 286 29 247 1.62e-27 107
MS.gene27843.t1 MTR_5g098060 30.588 170 113 3 77 243 48 215 1.22e-15 75.5
MS.gene27843.t1 MTR_7g075453 31.746 189 113 4 68 250 175 353 3.45e-14 72.4
MS.gene27843.t1 MTR_2g437700 31.544 149 95 4 77 221 195 340 1.95e-12 67.4
MS.gene27843.t1 MTR_5g098420 30.270 185 114 5 55 235 177 350 6.58e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27843.t1 AT5G60490 54.795 146 64 2 77 221 39 183 5.96e-47 158
MS.gene27843.t1 AT5G03170 46.023 176 93 2 70 244 29 203 7.63e-45 152
MS.gene27843.t1 AT5G44130 40.437 183 103 3 77 257 36 214 1.27e-33 123
MS.gene27843.t1 AT2G20520 41.622 185 95 5 77 249 38 221 1.18e-29 112
MS.gene27843.t1 AT1G03870 38.830 188 109 4 77 263 39 221 2.67e-29 112
MS.gene27843.t1 AT2G04780 31.544 149 96 3 75 221 44 188 2.72e-13 68.6
MS.gene27843.t1 AT2G04780 31.544 149 96 3 75 221 44 188 2.72e-13 68.6
MS.gene27843.t1 AT3G46550 28.495 186 120 8 63 243 194 371 1.19e-12 68.2
MS.gene27843.t1 AT3G60900 28.488 172 117 3 70 240 183 349 3.00e-12 67.0

Find 49 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGCTGGAGCTTTAGCTTT+AGG 0.270473 4.3:+13451025 None:intergenic
TTCGAACTTGATACATATTC+AGG 0.279696 4.3:+13451250 None:intergenic
GAATTCTCTTTCTCAGCTTT+AGG 0.296501 4.3:+13450986 None:intergenic
TGCTATATATCATGTGAATA+AGG 0.305049 4.3:-13451074 MS.gene27843:CDS
CAGATTAATGTGACTGCATA+TGG 0.308276 4.3:-13451169 MS.gene27843:CDS
GGTGCTGGAGCAGGTGTTGA+AGG 0.331645 4.3:+13451565 None:intergenic
ATGCATGTTATTCAAGCTAA+TGG 0.337878 4.3:+13450913 None:intergenic
GAATAAGGTTCTTATTCCTT+TGG 0.338628 4.3:-13451059 MS.gene27843:CDS
TCTTGGTTTCCTGACGAATC+AGG 0.343060 4.3:+13451496 None:intergenic
AGCAGGTTACTTCAACTCCT+TGG 0.397163 4.3:-13451314 MS.gene27843:CDS
TGTGGTAATGCTGGGACTAA+TGG 0.407871 4.3:+13451535 None:intergenic
GATTAGTGTGTTGAATGATT+TGG 0.407894 4.3:+13451450 None:intergenic
TTAGAATCTTGATTATGTCT+TGG 0.417666 4.3:+13451479 None:intergenic
GCCTTAGCAAGAGCTGGTGC+TGG 0.431209 4.3:+13451010 None:intergenic
TCTGAAAAGGCACCATCATC+TGG 0.442423 4.3:+13451343 None:intergenic
GTGCTGGAGCAGGTGTTGAA+GGG 0.442970 4.3:+13451566 None:intergenic
AGAAGATAGAGGCAAGTAGT+AGG 0.446057 4.3:+13451677 None:intergenic
ATATCAGTGTTGGTTTCCCT+TGG 0.450067 4.3:-13450887 MS.gene27843:CDS
GGAGCAGGTGTTGAAGGGGT+TGG 0.451921 4.3:+13451571 None:intergenic
GCAGGTTACTTCAACTCCTT+GGG 0.455965 4.3:-13451313 MS.gene27843:CDS
AACAGTGTGAATATTTCAAC+TGG 0.459076 4.3:-13451145 MS.gene27843:CDS
GTAGGTGATTGTGGTAATGC+TGG 0.464029 4.3:+13451526 None:intergenic
GACGAATCAGGATTTGTTGT+AGG 0.471829 4.3:+13451508 None:intergenic
CATTAATCTGAAATCCTTGT+GGG 0.483229 4.3:+13451182 None:intergenic
ACCTGCTTTGAGTTCTGAAA+AGG 0.484192 4.3:+13451330 None:intergenic
TTAGGTGCCTTAGCAAGAGC+TGG 0.489973 4.3:+13451004 None:intergenic
GGATTTGTTGTAGGTGATTG+TGG 0.513333 4.3:+13451517 None:intergenic
ACAATTCTTGCACCAGATGA+TGG 0.514841 4.3:-13451355 MS.gene27843:CDS
ACAACAAATCCTGATTCGTC+AGG 0.522883 4.3:-13451505 MS.gene27843:CDS
AGTGGTGATTGAGAAGATAG+AGG 0.531658 4.3:+13451666 None:intergenic
TTTGTGTTGTCTTGAGCAAA+CGG 0.534377 4.3:+13451428 None:intergenic
TCCAGCACCAGCTCTTGCTA+AGG 0.542557 4.3:-13451011 MS.gene27843:CDS
AGCGTAAACGATTCCAGTGA+TGG 0.545525 4.3:+13451108 None:intergenic
TTACAAGCTGTGCATTGACT+TGG 0.551173 4.3:+13451398 None:intergenic
TGCTGGAGCAGGTGTTGAAG+GGG 0.559876 4.3:+13451567 None:intergenic
CATGCATGGAATATCAGTGT+TGG 0.573529 4.3:-13450897 MS.gene27843:CDS
ACATTAATCTGAAATCCTTG+TGG 0.574915 4.3:+13451181 None:intergenic
CTGCAAGCAGAGAAATTCCA+AGG 0.575775 4.3:+13450870 None:intergenic
AGCTGGTGATTGAGCTAAAG+TGG 0.578327 4.3:+13451648 None:intergenic
ATTAGCTTGAATAACATGCA+TGG 0.579278 4.3:-13450911 MS.gene27843:CDS
TAGGTGATTGTGGTAATGCT+GGG 0.582717 4.3:+13451527 None:intergenic
GTTGTTGATACAACCATCAC+TGG 0.593007 4.3:-13451121 MS.gene27843:CDS
TTAGGCTTAACAAAATCCAA+AGG 0.601169 4.3:+13451043 None:intergenic
CTAGCTAGTGATAGCCCACA+AGG 0.607212 4.3:-13451196 MS.gene27843:CDS
TGATCAGACTCAGGCACACA+AGG 0.622744 4.3:-13450948 MS.gene27843:CDS
AGATGATGATGATCAGACTC+AGG 0.626792 4.3:-13450957 MS.gene27843:CDS
CACTAGCTAGTGTCAACACA+GGG 0.648522 4.3:+13451209 None:intergenic
TGCAAGCAGAGAAATTCCAA+GGG 0.658685 4.3:+13450871 None:intergenic
TCACTAGCTAGTGTCAACAC+AGG 0.685638 4.3:+13451208 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTATATATCATGTGAATA+AGG - chr4.3:13451494-13451513 MS.gene27843:CDS 25.0%
! TTAGAATCTTGATTATGTCT+TGG + chr4.3:13451092-13451111 None:intergenic 25.0%
AACAGTGTGAATATTTCAAC+TGG - chr4.3:13451423-13451442 MS.gene27843:CDS 30.0%
ATGCATGTTATTCAAGCTAA+TGG + chr4.3:13451658-13451677 None:intergenic 30.0%
CAGCTTGTAACTACAAAAAA+TGG - chr4.3:13451183-13451202 MS.gene27843:CDS 30.0%
CTTGTAACTACAAAAAATGG+AGG - chr4.3:13451186-13451205 MS.gene27843:CDS 30.0%
GAATAAGGTTCTTATTCCTT+TGG - chr4.3:13451509-13451528 MS.gene27843:CDS 30.0%
GATTAGTGTGTTGAATGATT+TGG + chr4.3:13451121-13451140 None:intergenic 30.0%
TTAGGCTTAACAAAATCCAA+AGG + chr4.3:13451528-13451547 None:intergenic 30.0%
TTCGAACTTGATACATATTC+AGG + chr4.3:13451321-13451340 None:intergenic 30.0%
! ACATTAATCTGAAATCCTTG+TGG + chr4.3:13451390-13451409 None:intergenic 30.0%
! ATTAGCTTGAATAACATGCA+TGG - chr4.3:13451657-13451676 MS.gene27843:CDS 30.0%
! CATTAATCTGAAATCCTTGT+GGG + chr4.3:13451389-13451408 None:intergenic 30.0%
CAGATTAATGTGACTGCATA+TGG - chr4.3:13451399-13451418 MS.gene27843:CDS 35.0%
GAATTCTCTTTCTCAGCTTT+AGG + chr4.3:13451585-13451604 None:intergenic 35.0%
TTTGTGTTGTCTTGAGCAAA+CGG + chr4.3:13451143-13451162 None:intergenic 35.0%
!! TTTTTGTTGTCTTTCTCCCA+AGG + chr4.3:13451274-13451293 None:intergenic 35.0%
ACAATTCTTGCACCAGATGA+TGG - chr4.3:13451213-13451232 MS.gene27843:CDS 40.0%
AGAAGATAGAGGCAAGTAGT+AGG + chr4.3:13450894-13450913 None:intergenic 40.0%
AGTGGTGATTGAGAAGATAG+AGG + chr4.3:13450905-13450924 None:intergenic 40.0%
CATGCATGGAATATCAGTGT+TGG - chr4.3:13451671-13451690 MS.gene27843:CDS 40.0%
GTTGTTGATACAACCATCAC+TGG - chr4.3:13451447-13451466 MS.gene27843:CDS 40.0%
TGCAAGCAGAGAAATTCCAA+GGG + chr4.3:13451700-13451719 None:intergenic 40.0%
! ACAACAAATCCTGATTCGTC+AGG - chr4.3:13451063-13451082 MS.gene27843:CDS 40.0%
! AGATGATGATGATCAGACTC+AGG - chr4.3:13451611-13451630 MS.gene27843:CDS 40.0%
! TAGGTGATTGTGGTAATGCT+GGG + chr4.3:13451044-13451063 None:intergenic 40.0%
!! ACCTGCTTTGAGTTCTGAAA+AGG + chr4.3:13451241-13451260 None:intergenic 40.0%
!! ATATCAGTGTTGGTTTCCCT+TGG - chr4.3:13451681-13451700 MS.gene27843:CDS 40.0%
!! GACGAATCAGGATTTGTTGT+AGG + chr4.3:13451063-13451082 None:intergenic 40.0%
!! GGATTTGTTGTAGGTGATTG+TGG + chr4.3:13451054-13451073 None:intergenic 40.0%
!! TTACAAGCTGTGCATTGACT+TGG + chr4.3:13451173-13451192 None:intergenic 40.0%
!!! TTGAAGGGGTTGGTTTTGTA+GGG + chr4.3:13450990-13451009 None:intergenic 40.0%
!!! TTTGTAGGTGCTGGTTTTTC+TGG + chr4.3:13450961-13450980 None:intergenic 40.0%
AGCAGGTTACTTCAACTCCT+TGG - chr4.3:13451254-13451273 MS.gene27843:CDS 45.0%
AGCGTAAACGATTCCAGTGA+TGG + chr4.3:13451463-13451482 None:intergenic 45.0%
AGCTGGTGATTGAGCTAAAG+TGG + chr4.3:13450923-13450942 None:intergenic 45.0%
CACTAGCTAGTGTCAACACA+GGG + chr4.3:13451362-13451381 None:intergenic 45.0%
CTGCAAGCAGAGAAATTCCA+AGG + chr4.3:13451701-13451720 None:intergenic 45.0%
GCAGGTTACTTCAACTCCTT+GGG - chr4.3:13451255-13451274 MS.gene27843:CDS 45.0%
TCACTAGCTAGTGTCAACAC+AGG + chr4.3:13451363-13451382 None:intergenic 45.0%
TCTTGGTTTCCTGACGAATC+AGG + chr4.3:13451075-13451094 None:intergenic 45.0%
! GCCTTTTCAGAACTCAAAGC+AGG - chr4.3:13451237-13451256 MS.gene27843:CDS 45.0%
! GTAGGTGATTGTGGTAATGC+TGG + chr4.3:13451045-13451064 None:intergenic 45.0%
! TGTGGTAATGCTGGGACTAA+TGG + chr4.3:13451036-13451055 None:intergenic 45.0%
!! ACTAATGGTTTTGCTGGTGC+TGG + chr4.3:13451021-13451040 None:intergenic 45.0%
!! TCTGAAAAGGCACCATCATC+TGG + chr4.3:13451228-13451247 None:intergenic 45.0%
!!! GCTGGTTTTTCTGGTGCTTT+TGG + chr4.3:13450952-13450971 None:intergenic 45.0%
!!! GTTGAAGGGGTTGGTTTTGT+AGG + chr4.3:13450991-13451010 None:intergenic 45.0%
!!! TGAAGGGGTTGGTTTTGTAG+GGG + chr4.3:13450989-13451008 None:intergenic 45.0%
!!! TTTGTAGGGGCTGGTTTTGT+AGG + chr4.3:13450976-13450995 None:intergenic 45.0%
CTAGCTAGTGATAGCCCACA+AGG - chr4.3:13451372-13451391 MS.gene27843:CDS 50.0%
TGATCAGACTCAGGCACACA+AGG - chr4.3:13451620-13451639 MS.gene27843:CDS 50.0%
TTAGGTGCCTTAGCAAGAGC+TGG + chr4.3:13451567-13451586 None:intergenic 50.0%
!! GCTGGGACTAATGGTTTTGC+TGG + chr4.3:13451027-13451046 None:intergenic 50.0%
!! GGTGCTGGAGCTTTAGCTTT+AGG + chr4.3:13451546-13451565 None:intergenic 50.0%
TCCAGCACCAGCTCTTGCTA+AGG - chr4.3:13451557-13451576 MS.gene27843:CDS 55.0%
!! GTGCTGGAGCAGGTGTTGAA+GGG + chr4.3:13451005-13451024 None:intergenic 55.0%
!! TGCTGGAGCAGGTGTTGAAG+GGG + chr4.3:13451004-13451023 None:intergenic 55.0%
GCCTTAGCAAGAGCTGGTGC+TGG + chr4.3:13451561-13451580 None:intergenic 60.0%
!! GGAGCAGGTGTTGAAGGGGT+TGG + chr4.3:13451000-13451019 None:intergenic 60.0%
!! GGTGCTGGAGCAGGTGTTGA+AGG + chr4.3:13451006-13451025 None:intergenic 60.0%
!! GGTTTTGCTGGTGCTGGAGC+AGG + chr4.3:13451015-13451034 None:intergenic 60.0%
!!! GGGGCTGGTTTTGTAGGTGC+TGG + chr4.3:13450970-13450989 None:intergenic 60.0%
!!! GGGGTTGGTTTTGTAGGGGC+TGG + chr4.3:13450985-13451004 None:intergenic 60.0%
!!! GGTGCTTTTGGTGCTGCAGC+TGG + chr4.3:13450940-13450959 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 13450865 13451725 13450865 ID=MS.gene27843
chr4.3 mRNA 13450865 13451725 13450865 ID=MS.gene27843.t1;Parent=MS.gene27843
chr4.3 exon 13450865 13451725 13450865 ID=MS.gene27843.t1.exon1;Parent=MS.gene27843.t1
chr4.3 CDS 13450865 13451725 13450865 ID=cds.MS.gene27843.t1;Parent=MS.gene27843.t1
Gene Sequence

>MS.gene27843

ATGAATCAAATTTTCTTGTTCTCACTCCTACTACTTGCCTCTATCTTCTCAATCACCACTTTAGCTCAATCACCAGCTGCAGCACCAAAAGCACCAGAAAAACCAGCACCTACAAAACCAGCCCCTACAAAACCAACCCCTTCAACACCTGCTCCAGCACCAGCAAAACCATTAGTCCCAGCATTACCACAATCACCTACAACAAATCCTGATTCGTCAGGAAACCAAGACATAATCAAGATTCTAAGAAAAGCCAAATCATTCAACACACTAATCCGTTTGCTCAAGACAACACAAATCATCAACCAAGTCAATGCACAGCTTGTAACTACAAAAAATGGAGGCTTGACAATTCTTGCACCAGATGATGGTGCCTTTTCAGAACTCAAAGCAGGTTACTTCAACTCCTTGGGAGAAAGACAACAAAAAGAATTGATTCAGTATCATGTTCTTCCTGAATATGTATCAAGTTCGAACTTTGATTCTCTCAGCAACCCTGTGTTGACACTAGCTAGTGATAGCCCACAAGGATTTCAGATTAATGTGACTGCATATGGAAACAGTGTGAATATTTCAACTGGCGTTGTTGATACAACCATCACTGGAATCGTTTACGCTGATAAAACACTTGCTATATATCATGTGAATAAGGTTCTTATTCCTTTGGATTTTGTTAAGCCTAAAGCTAAAGCTCCAGCACCAGCTCTTGCTAAGGCACCTAAAGCTGAGAAAGAGAATTCATCTGCAGATGATGATGATCAGACTCAGGCACACAAGGATAGTTCTGATGCCATTAGCTTGAATAACATGCATGGAATATCAGTGTTGGTTTCCCTTGGAATTTCTCTGCTTGCAGTTGCA
Protein sequence

>MS.gene27843.t1

MNQIFLFSLLLLASIFSITTLAQSPAAAPKAPEKPAPTKPAPTKPTPSTPAPAPAKPLVPALPQSPTTNPDSSGNQDIIKILRKAKSFNTLIRLLKTTQIINQVNAQLVTTKNGGLTILAPDDGAFSELKAGYFNSLGERQQKELIQYHVLPEYVSSSNFDSLSNPVLTLASDSPQGFQINVTAYGNSVNISTGVVDTTITGIVYADKTLAIYHVNKVLIPLDFVKPKAKAPAPALAKAPKAEKENSSADDDDQTQAHKDSSDAISLNNMHGISVLVSLGISLLAVA