AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42829

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42829.t1 MTR_2g093980 91.941 273 16 3 1 269 14 284 4.99e-162 451
MS.gene42829.t1 MTR_4g059780 65.019 263 80 4 14 269 46 303 1.18e-92 276
MS.gene42829.t1 MTR_2g017970 56.808 213 87 2 51 263 67 274 1.27e-76 234
MS.gene42829.t1 MTR_2g017960 55.607 214 90 2 51 264 67 275 1.34e-74 229
MS.gene42829.t1 MTR_4g059840 48.571 280 126 8 1 266 15 290 2.11e-74 229
MS.gene42829.t1 MTR_4g053380 51.867 241 103 5 16 244 34 273 3.63e-72 223
MS.gene42829.t1 MTR_8g087450 49.270 274 111 5 14 266 22 288 7.50e-72 222
MS.gene42829.t1 MTR_4g059790 56.716 201 74 4 38 225 53 253 2.48e-71 221
MS.gene42829.t1 MTR_2g093970 54.455 202 84 3 4 199 17 216 4.11e-66 207
MS.gene42829.t1 MTR_8g087460 54.008 237 92 7 8 237 55 281 6.13e-63 200
MS.gene42829.t1 MTR_2g017950 48.571 245 105 7 4 232 19 258 9.99e-63 199
MS.gene42829.t1 MTR_8g087470 54.008 237 92 7 8 237 55 281 1.01e-62 200
MS.gene42829.t1 MTR_4g059720 55.975 159 69 1 45 203 35 192 1.36e-57 184
MS.gene42829.t1 MTR_2g093990 61.074 149 57 1 52 200 41 188 6.38e-55 177
MS.gene42829.t1 MTR_7g101080 47.742 155 79 2 48 201 36 189 5.07e-43 147
MS.gene42829.t1 MTR_2g090765 34.842 221 133 2 43 263 29 238 4.52e-27 105
MS.gene42829.t1 MTR_5g098060 33.140 172 108 4 52 220 48 215 1.23e-17 80.5
MS.gene42829.t1 MTR_2g437700 29.870 154 101 3 52 201 195 345 1.94e-14 72.8
MS.gene42829.t1 MTR_7g075453 29.487 234 137 7 52 267 184 407 5.44e-13 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42829.t1 AT5G03170 51.220 164 78 2 48 209 32 195 9.73e-49 162
MS.gene42829.t1 AT5G60490 47.333 150 77 2 52 200 39 187 4.17e-43 147
MS.gene42829.t1 AT5G44130 38.624 189 103 4 52 238 36 213 1.47e-30 114
MS.gene42829.t1 AT2G20520 35.238 210 130 5 40 244 25 233 9.18e-29 110
MS.gene42829.t1 AT1G03870 34.010 197 115 5 52 242 39 226 2.20e-25 101
MS.gene42829.t1 AT3G46550 28.415 183 120 5 26 200 178 357 1.62e-13 70.1
MS.gene42829.t1 AT3G60900 28.866 194 128 4 37 227 175 361 4.23e-12 66.2

Find 49 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTCCTCTTGATTTCTT+TGG 0.151087 2.3:+7883791 MS.gene42829:CDS
TGCTTCCTCTTGATTTCTTT+GGG 0.217030 2.3:+7883792 MS.gene42829:CDS
ATGTTCAATGGAAGCTTTAA+AGG 0.264173 2.3:-7883659 None:intergenic
GTGGTTAATGCTACTGTTAC+TGG 0.308670 2.3:+7883719 MS.gene42829:CDS
GACTTTGTCTTATCAGCTTT+CGG 0.319470 2.3:-7883860 None:intergenic
TCTGGTAATGTTGGGACTAA+TGG 0.353632 2.3:-7883320 None:intergenic
TTACCAGCCACTGTCTCAAC+AGG 0.354909 2.3:-7883632 None:intergenic
GTTGCTGTTGCTGCCGTGTT+GGG 0.357964 2.3:-7883233 None:intergenic
GTGAAATGAGTTGTGAGTTT+AGG 0.360618 2.3:-7883445 None:intergenic
CAAGCTTGCTATATATCGTT+TGG 0.363154 2.3:+7883760 MS.gene42829:CDS
TCTTGATTTCTTTGGGACTA+AGG 0.372078 2.3:+7883799 MS.gene42829:CDS
GGAACAACATTGAAGTCTAT+TGG 0.380617 2.3:+7883962 MS.gene42829:CDS
TTGTTGCAGTGGCAATGTTA+TGG 0.390462 2.3:+7883993 MS.gene42829:CDS
GCTATTGCTTCCGCAGCAAC+AGG 0.394680 2.3:-7883836 None:intergenic
TTTGGTGCCGGGGCATGTTT+CGG 0.395055 2.3:-7883272 None:intergenic
GATGTTGGTGATGCTGCTTT+TGG 0.401270 2.3:-7883290 None:intergenic
TGCTATATATCGTTTGGATA+AGG 0.401381 2.3:+7883766 MS.gene42829:CDS
TCTGGAGCAGTGAGTTTACT+TGG 0.406395 2.3:+7883932 MS.gene42829:CDS
TGTTGCTGTTGCTGCCGTGT+TGG 0.415192 2.3:-7883234 None:intergenic
GCAGCAACAGGAGCAGCAGC+AGG 0.428213 2.3:-7883824 None:intergenic
ACCAGTGTTAGTCTTTCAAC+TGG 0.433716 2.3:+7883695 MS.gene42829:CDS
GCTTTCTCACATCTCAAAGC+AGG 0.456572 2.3:+7883509 MS.gene42829:CDS
TGTTCAATGGAAGCTTTAAA+GGG 0.463949 2.3:-7883658 None:intergenic
CCATTGAACATCGAATCGTT+TGG 0.477903 2.3:+7883671 MS.gene42829:CDS
GCATGTTTCGGTGACGCTGC+TGG 0.495698 2.3:-7883260 None:intergenic
TCTGAGGTGTCTGGTAATGT+TGG 0.510374 2.3:-7883329 None:intergenic
TGTTAGTCTTTCAACTGGTG+TGG 0.520094 2.3:+7883700 MS.gene42829:CDS
TGTGAGAAAGCTGAGTCATC+CGG 0.520744 2.3:-7883497 None:intergenic
TGCTGCTGCTCCTGTTGCTG+CGG 0.526125 2.3:+7883826 MS.gene42829:CDS
CTGAGGTGTCTGGTAATGTT+GGG 0.532113 2.3:-7883328 None:intergenic
CCAAACGATTCGATGTTCAA+TGG 0.533393 2.3:-7883671 None:intergenic
CAACAAACTGTGGAAGAATG+TGG 0.559737 2.3:-7883580 None:intergenic
GTCGTCCGGGGTGGAATCTG+AGG 0.559966 2.3:-7883345 None:intergenic
GTCTTCTTCTGAAGAAGATG+AGG 0.569485 2.3:+7883880 MS.gene42829:CDS
AACCCTGTTGAGACAGTGGC+TGG 0.569511 2.3:+7883629 MS.gene42829:CDS
GGGGTGGAATCTGAGGTGTC+TGG 0.574659 2.3:-7883338 None:intergenic
CTTTCTCACATCTCAAAGCA+GGG 0.577178 2.3:+7883510 MS.gene42829:CDS
AGCGTCACCGAAACATGCCC+CGG 0.581778 2.3:+7883265 MS.gene42829:CDS
GTGAGTTTACTTGGAATGCA+AGG 0.589105 2.3:+7883941 MS.gene42829:CDS
CTCATTGTATTCTCCCAACA+CGG 0.596372 2.3:+7883220 MS.gene42829:CDS
TGAGGATGATACAACAACTC+AGG 0.597666 2.3:+7883898 MS.gene42829:CDS
ACCAGTTGAAAGACTAACAC+TGG 0.603639 2.3:-7883696 None:intergenic
CGGATTAACAATCTTAGCAC+CGG 0.603845 2.3:+7883478 MS.gene42829:CDS
TAGTAACCCTGTTGAGACAG+TGG 0.611903 2.3:+7883625 MS.gene42829:CDS
TTAGTCCCAAAGAAATCAAG+AGG 0.616533 2.3:-7883797 None:intergenic
TACCAGCCACTGTCTCAACA+GGG 0.663127 2.3:-7883631 None:intergenic
TTATTGCTATCAACAAACTG+TGG 0.684733 2.3:-7883590 None:intergenic
CGTGTTGGGAGAATACAATG+AGG 0.742075 2.3:-7883219 None:intergenic
AGACACCTCAGATTCCACCC+CGG 0.745070 2.3:+7883340 MS.gene42829:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CATAACAAAAATCCTCAAAA+AGG + chr2.3:7883367-7883386 MS.gene42829:CDS 25.0%
ACTCAGGATAAAAAAAGTTC+TGG + chr2.3:7883914-7883933 MS.gene42829:CDS 30.0%
TGCTATATATCGTTTGGATA+AGG + chr2.3:7883766-7883785 MS.gene42829:CDS 30.0%
TTATTGCTATCAACAAACTG+TGG - chr2.3:7883593-7883612 None:intergenic 30.0%
! ATGTTCAATGGAAGCTTTAA+AGG - chr2.3:7883662-7883681 None:intergenic 30.0%
!! TGTTCAATGGAAGCTTTAAA+GGG - chr2.3:7883661-7883680 None:intergenic 30.0%
!!! TTTGTGTTGTTTTTAGGAGA+CGG - chr2.3:7883415-7883434 None:intergenic 30.0%
CAACTCATTTCACCAAAAAG+CGG + chr2.3:7883455-7883474 MS.gene42829:CDS 35.0%
CCTAAAAACAACACAAATCG+TGG + chr2.3:7883418-7883437 MS.gene42829:CDS 35.0%
GACTTTGTCTTATCAGCTTT+CGG - chr2.3:7883863-7883882 None:intergenic 35.0%
GGAACAACATTGAAGTCTAT+TGG + chr2.3:7883962-7883981 MS.gene42829:CDS 35.0%
GTGAAATGAGTTGTGAGTTT+AGG - chr2.3:7883448-7883467 None:intergenic 35.0%
TGCTTCCTCTTGATTTCTTT+GGG + chr2.3:7883792-7883811 MS.gene42829:CDS 35.0%
TTAGTCCCAAAGAAATCAAG+AGG - chr2.3:7883800-7883819 None:intergenic 35.0%
TTGCTTCCTCTTGATTTCTT+TGG + chr2.3:7883791-7883810 MS.gene42829:CDS 35.0%
! TGAATGTTTTCGCCTTTTTG+AGG - chr2.3:7883382-7883401 None:intergenic 35.0%
!! AGGATTTTTGTTATGTCGTC+CGG - chr2.3:7883362-7883381 None:intergenic 35.0%
!! CAAGCTTGCTATATATCGTT+TGG + chr2.3:7883760-7883779 MS.gene42829:CDS 35.0%
!! TCTTGATTTCTTTGGGACTA+AGG + chr2.3:7883799-7883818 MS.gene42829:CDS 35.0%
!!! ACTAATGGTTTTGTCGATGT+TGG - chr2.3:7883308-7883327 None:intergenic 35.0%
!!! CCACGATTTGTGTTGTTTTT+AGG - chr2.3:7883421-7883440 None:intergenic 35.0%
!!! TTGTGTTGTTTTTAGGAGAC+GGG - chr2.3:7883414-7883433 None:intergenic 35.0%
ACCAGTTGAAAGACTAACAC+TGG - chr2.3:7883699-7883718 None:intergenic 40.0%
CAACAAACTGTGGAAGAATG+TGG - chr2.3:7883583-7883602 None:intergenic 40.0%
CCAAACGATTCGATGTTCAA+TGG - chr2.3:7883674-7883693 None:intergenic 40.0%
CCATTGAACATCGAATCGTT+TGG + chr2.3:7883671-7883690 MS.gene42829:CDS 40.0%
CGGATTAACAATCTTAGCAC+CGG + chr2.3:7883478-7883497 MS.gene42829:CDS 40.0%
CTCATTGTATTCTCCCAACA+CGG + chr2.3:7883220-7883239 MS.gene42829:CDS 40.0%
CTTTCTCACATCTCAAAGCA+GGG + chr2.3:7883510-7883529 MS.gene42829:CDS 40.0%
GTGAGTTTACTTGGAATGCA+AGG + chr2.3:7883941-7883960 MS.gene42829:CDS 40.0%
GTGGTTAATGCTACTGTTAC+TGG + chr2.3:7883719-7883738 MS.gene42829:CDS 40.0%
TGAGGATGATACAACAACTC+AGG + chr2.3:7883898-7883917 MS.gene42829:CDS 40.0%
TTGTTGCAGTGGCAATGTTA+TGG + chr2.3:7883993-7884012 MS.gene42829:CDS 40.0%
! GTCTTCTTCTGAAGAAGATG+AGG + chr2.3:7883880-7883899 MS.gene42829:CDS 40.0%
! TCTGGTAATGTTGGGACTAA+TGG - chr2.3:7883323-7883342 None:intergenic 40.0%
!! ACCAGTGTTAGTCTTTCAAC+TGG + chr2.3:7883695-7883714 MS.gene42829:CDS 40.0%
!! GATTTTTGTTATGTCGTCCG+GGG - chr2.3:7883360-7883379 None:intergenic 40.0%
!! GGATTTTTGTTATGTCGTCC+GGG - chr2.3:7883361-7883380 None:intergenic 40.0%
!! TGTTAGTCTTTCAACTGGTG+TGG + chr2.3:7883700-7883719 MS.gene42829:CDS 40.0%
!!! ATTGTTAATCCGCCGCTTTT+TGG - chr2.3:7883470-7883489 None:intergenic 40.0%
!!! TTGTTTTTAGGAGACGGGTT+AGG - chr2.3:7883409-7883428 None:intergenic 40.0%
CGTGTTGGGAGAATACAATG+AGG - chr2.3:7883222-7883241 None:intergenic 45.0%
CTCATTTCACCAAAAAGCGG+CGG + chr2.3:7883458-7883477 MS.gene42829:CDS 45.0%
GCTTTCTCACATCTCAAAGC+AGG + chr2.3:7883509-7883528 MS.gene42829:CDS 45.0%
TAGTAACCCTGTTGAGACAG+TGG + chr2.3:7883625-7883644 MS.gene42829:CDS 45.0%
TGTGAGAAAGCTGAGTCATC+CGG - chr2.3:7883500-7883519 None:intergenic 45.0%
! CTGAGGTGTCTGGTAATGTT+GGG - chr2.3:7883331-7883350 None:intergenic 45.0%
! TCTGAGGTGTCTGGTAATGT+TGG - chr2.3:7883332-7883351 None:intergenic 45.0%
! TCTGGAGCAGTGAGTTTACT+TGG + chr2.3:7883932-7883951 MS.gene42829:CDS 45.0%
! TGGAGTAGCTTTTGTTGCAG+TGG + chr2.3:7883982-7884001 MS.gene42829:CDS 45.0%
!!! GATGTTGGTGATGCTGCTTT+TGG - chr2.3:7883293-7883312 None:intergenic 45.0%
TACCAGCCACTGTCTCAACA+GGG - chr2.3:7883634-7883653 None:intergenic 50.0%
TTACCAGCCACTGTCTCAAC+AGG - chr2.3:7883635-7883654 None:intergenic 50.0%
!! TTTTGTTATGTCGTCCGGGG+TGG - chr2.3:7883357-7883376 None:intergenic 50.0%
AACCCTGTTGAGACAGTGGC+TGG + chr2.3:7883629-7883648 MS.gene42829:CDS 55.0%
AGACACCTCAGATTCCACCC+CGG + chr2.3:7883340-7883359 MS.gene42829:CDS 55.0%
GCTATTGCTTCCGCAGCAAC+AGG - chr2.3:7883839-7883858 None:intergenic 55.0%
! GTTGCTGTTGCTGCCGTGTT+GGG - chr2.3:7883236-7883255 None:intergenic 55.0%
! TGTTGCTGTTGCTGCCGTGT+TGG - chr2.3:7883237-7883256 None:intergenic 55.0%
!! TTTGGTGCCGGGGCATGTTT+CGG - chr2.3:7883275-7883294 None:intergenic 55.0%
!!! GGTGATGCTGCTTTTGGTGC+CGG - chr2.3:7883287-7883306 None:intergenic 55.0%
!!! GTGATGCTGCTTTTGGTGCC+GGG - chr2.3:7883286-7883305 None:intergenic 55.0%
!!! TGATGCTGCTTTTGGTGCCG+GGG - chr2.3:7883285-7883304 None:intergenic 55.0%
AGCGTCACCGAAACATGCCC+CGG + chr2.3:7883265-7883284 MS.gene42829:CDS 60.0%
GCATGTTTCGGTGACGCTGC+TGG - chr2.3:7883263-7883282 None:intergenic 60.0%
TGCTGCTGCTCCTGTTGCTG+CGG + chr2.3:7883826-7883845 MS.gene42829:CDS 60.0%
! GGGGTGGAATCTGAGGTGTC+TGG - chr2.3:7883341-7883360 None:intergenic 60.0%
GCAGCAACAGGAGCAGCAGC+AGG - chr2.3:7883827-7883846 None:intergenic 65.0%
GTCGTCCGGGGTGGAATCTG+AGG - chr2.3:7883348-7883367 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 7883212 7884021 7883212 ID=MS.gene42829
chr2.3 mRNA 7883212 7884021 7883212 ID=MS.gene42829.t1;Parent=MS.gene42829
chr2.3 exon 7883212 7884021 7883212 ID=MS.gene42829.t1.exon1;Parent=MS.gene42829.t1
chr2.3 CDS 7883212 7884021 7883212 ID=cds.MS.gene42829.t1;Parent=MS.gene42829.t1
Gene Sequence

>MS.gene42829

ATGTTCTCCTCATTGTATTCTCCCAACACGGCAGCAACAGCAACAGCACCAGCAGCGTCACCGAAACATGCCCCGGCACCAAAAGCAGCATCACCAACATCGACAAAACCATTAGTCCCAACATTACCAGACACCTCAGATTCCACCCCGGACGACATAACAAAAATCCTCAAAAAGGCGAAAACATTCACAATCCTAACCCGTCTCCTAAAAACAACACAAATCGTGGACAACCTAAACTCACAACTCATTTCACCAAAAAGCGGCGGATTAACAATCTTAGCACCGGATGACTCAGCTTTCTCACATCTCAAAGCAGGGTTCTTCAATTCGCTAAACGAAAACAAAAAAATCGAACTATTACAATTCCACATTCTTCCACAGTTTGTTGATAGCAATAACTTTGATTCTCTTAGTAACCCTGTTGAGACAGTGGCTGGTAAAGACCCTTTAAAGCTTCCATTGAACATCGAATCGTTTGGTACCAGTGTTAGTCTTTCAACTGGTGTGGTTAATGCTACTGTTACTGGTGTAGTCTATCAAGATAACAAGCTTGCTATATATCGTTTGGATAAGGTTTTGCTTCCTCTTGATTTCTTTGGGACTAAGGCACCTGCTGCTGCTCCTGTTGCTGCGGAAGCAATAGCACCGAAAGCTGATAAGACAAAGTCTTCTTCTGAAGAAGATGAGGATGATACAACAACTCAGGATAAAAAAAGTTCTGGAGCAGTGAGTTTACTTGGAATGCAAGGAACAACATTGAAGTCTATTGGAGTAGCTTTTGTTGCAGTGGCAATGTTATGGAGTTGA
Protein sequence

>MS.gene42829.t1

MFSSLYSPNTAATATAPAASPKHAPAPKAASPTSTKPLVPTLPDTSDSTPDDITKILKKAKTFTILTRLLKTTQIVDNLNSQLISPKSGGLTILAPDDSAFSHLKAGFFNSLNENKKIELLQFHILPQFVDSNNFDSLSNPVETVAGKDPLKLPLNIESFGTSVSLSTGVVNATVTGVVYQDNKLAIYRLDKVLLPLDFFGTKAPAAAPVAAEAIAPKADKTKSSSEEDEDDTTTQDKKSSGAVSLLGMQGTTLKSIGVAFVAVAMLWS