AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27020.t1 MTR_1g023400 93.182 264 18 0 1 264 89 352 0.0 520
MS.gene27020.t1 MTR_1g022200 61.871 278 90 8 5 270 102 375 1.93e-106 313
MS.gene27020.t1 MTR_1g009110 46.209 277 129 9 1 265 111 379 1.75e-68 216
MS.gene27020.t1 MTR_4g080200 48.754 281 114 12 1 264 82 349 5.12e-68 214
MS.gene27020.t1 MTR_1g023430 69.014 142 38 2 132 270 40 178 1.03e-62 195
MS.gene27020.t1 MTR_1g037540 43.206 287 130 13 1 264 124 400 4.75e-55 182
MS.gene27020.t1 MTR_1g024125 73.214 112 29 1 137 247 38 149 2.26e-53 171
MS.gene27020.t1 MTR_1g022105 39.357 249 104 6 1 249 120 321 3.31e-49 165
MS.gene27020.t1 MTR_1g008000 35.231 281 112 15 3 265 41 269 1.23e-24 99.8
MS.gene27020.t1 MTR_0064s0160 25.784 287 173 13 2 263 148 419 5.67e-14 71.6
MS.gene27020.t1 MTR_2g021950 23.944 284 183 11 3 263 120 393 1.99e-11 63.9
MS.gene27020.t1 MTR_2g426090 25.939 293 176 14 1 264 96 376 3.06e-11 63.5
MS.gene27020.t1 MTR_1g061330 24.199 281 166 13 5 264 103 357 6.86e-11 62.4
MS.gene27020.t1 MTR_5g037680 26.293 232 144 10 5 226 126 340 8.73e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 77 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCCGTCATCTTGAGCATT+TGG 0.258740 1.3:+2017464 MS.gene27020:CDS
AATCAACATCAATTTGAAAT+TGG 0.285324 1.3:-2017642 None:intergenic
GCCCTCTGAGTTGGTGAAAC+TGG 0.301844 1.3:-2017348 None:intergenic
TGGTGTGTGGTCTTAGTAAA+AGG 0.318775 1.3:-2017211 None:intergenic
TAATTCCATCATAACTAGTA+TGG 0.350426 1.3:-2017126 None:intergenic
ATAGAATATTTGCAACAAAA+TGG 0.364437 1.3:-2017306 None:intergenic
GACTCATGCATGTATGGTTT+CGG 0.365854 1.3:+2017061 MS.gene27020:CDS
TCCCGTCATCTTGAGCATTT+GGG 0.381975 1.3:+2017465 MS.gene27020:CDS
TTGTTAACAGCGTTTATCAT+TGG 0.387639 1.3:+2017257 MS.gene27020:CDS
ATAATTTAAGTACCAACTCT+TGG 0.412072 1.3:+2017167 MS.gene27020:CDS
CATCTTGAGCATTTGGGTGA+TGG 0.434538 1.3:+2017471 MS.gene27020:CDS
GACAGCGACTCATGCATGTA+TGG 0.435390 1.3:+2017055 MS.gene27020:CDS
CGGTGGACCTCTCTAGTTGT+TGG 0.437420 1.3:-2017010 None:intergenic
CCTTGTCGACCTATCTAGCT+AGG 0.454046 1.3:+2017701 MS.gene27020:CDS
AACTTTGAAGTTGATGTTGT+TGG 0.457396 1.3:-2017095 None:intergenic
ATGATTATAGCAACTTTGCA+TGG 0.461665 1.3:+2017383 MS.gene27020:CDS
TCTGTCTCCAAGGTTTGTGT+TGG 0.467072 1.3:+2016948 MS.gene27020:CDS
AAACTCCATACTAGTTATGA+TGG 0.471735 1.3:+2017121 MS.gene27020:CDS
AAAGGAAGAGGATGTTCAGT+TGG 0.476611 1.3:-2017193 None:intergenic
GGTGGACCTCTCTAGTTGTT+GGG 0.479668 1.3:-2017009 None:intergenic
CAAATCCTTGGAGGAAAGGT+TGG 0.481459 1.3:+2017577 MS.gene27020:CDS
ACTTTGAAGTTGATGTTGTT+GGG 0.482647 1.3:-2017094 None:intergenic
CTATCTAGCTAGGGCACACT+AGG 0.484374 1.3:+2017711 MS.gene27020:CDS
AAGGAAGAGGATGTTCAGTT+GGG 0.484768 1.3:-2017192 None:intergenic
GCCGAGATCAAAGGTTCCCT+TGG 0.490016 1.3:+2017415 MS.gene27020:CDS
CTAGTGTGCCCTAGCTAGAT+AGG 0.491771 1.3:-2017710 None:intergenic
ACAAGAGTGCTATATCTAGA+AGG 0.495385 1.3:-2017238 None:intergenic
TGTTTCGTATGTGTGGCCTT+TGG 0.504996 1.3:+2017542 MS.gene27020:CDS
TATGAAACCAACACAAACCT+TGG 0.505418 1.3:-2016955 None:intergenic
GTTGATGTTGTTGGGATCAT+CGG 0.508372 1.3:-2017086 None:intergenic
GTCGACAAGGGAGCTATGCT+TGG 0.515430 1.3:-2017688 None:intergenic
ACCCAAATGCTCAAGATGAC+GGG 0.515580 1.3:-2017466 None:intergenic
AAGAATGGCGATCAAATCCT+TGG 0.518473 1.3:+2017565 MS.gene27020:CDS
GTTCTCCAACCTTTCCTCCA+AGG 0.525401 1.3:-2017582 None:intergenic
ATGTGTGGCCTTTGGAAGAA+TGG 0.525913 1.3:+2017550 MS.gene27020:CDS
TGATTATAGCAACTTTGCAT+GGG 0.536071 1.3:+2017384 MS.gene27020:CDS
TTCAGTTGGGGTCCAAGAGT+TGG 0.536792 1.3:-2017179 None:intergenic
ACCAAGGGAACCTTTGATCT+CGG 0.537068 1.3:-2017416 None:intergenic
CGATCAAATCCTTGGAGGAA+AGG 0.537340 1.3:+2017573 MS.gene27020:CDS
TTTGATCGCCATTCTTCCAA+AGG 0.545314 1.3:-2017558 None:intergenic
CACCCAAATGCTCAAGATGA+CGG 0.555873 1.3:-2017467 None:intergenic
CTCACATCATATGACTATCA+AGG 0.557817 1.3:+2017607 MS.gene27020:CDS
GATTGTGTTGCCGAGATCAA+AGG 0.560123 1.3:+2017406 MS.gene27020:CDS
TGGATTATAAGCAGTTCATA+CGG 0.560788 1.3:+2017277 MS.gene27020:CDS
TTTATAAGAATGGAATCATA+CGG 0.562387 1.3:+2016908 None:intergenic
GTGGTCTTAGTAAAAGGAAG+AGG 0.563530 1.3:-2017205 None:intergenic
GTCTTGATGAGTTGATTATG+TGG 0.567130 1.3:+2016984 MS.gene27020:CDS
GAATCATACGGTAGTTGCAA+TGG 0.573781 1.3:+2016920 MS.gene27020:CDS
TCGCTGTCAAGGCAGAGCCT+CGG 0.581840 1.3:-2017040 None:intergenic
TGCTATATCTAGAAGGACAT+TGG 0.583334 1.3:-2017231 None:intergenic
ACATGCATGAGTCGCTGTCA+AGG 0.587596 1.3:-2017051 None:intergenic
CTATAATCATATGAGAAGGT+TGG 0.594270 1.3:-2017370 None:intergenic
AGAAGGTTGGCCCTCTGAGT+TGG 0.594377 1.3:-2017357 None:intergenic
AATGGCGATCAAATCCTTGG+AGG 0.596817 1.3:+2017568 MS.gene27020:CDS
GGCAGAGCCTCGGAGGAACA+CGG 0.598335 1.3:-2017030 None:intergenic
CTTGTCGACCTATCTAGCTA+GGG 0.600363 1.3:+2017702 MS.gene27020:CDS
ACCAGTTTCACCAACTCAGA+GGG 0.601175 1.3:+2017347 MS.gene27020:CDS
TACGAAACATTGACACAAGT+GGG 0.601347 1.3:-2017528 None:intergenic
GTTGCTATAATCATATGAGA+AGG 0.609576 1.3:-2017374 None:intergenic
GTGTCAATGTTTCGTATGTG+TGG 0.615188 1.3:+2017535 MS.gene27020:CDS
TACAATGCACAACATAACCA+AGG 0.616377 1.3:-2017432 None:intergenic
CTGTCAAGGCAGAGCCTCGG+AGG 0.616821 1.3:-2017037 None:intergenic
ATACGAAACATTGACACAAG+TGG 0.622567 1.3:-2017529 None:intergenic
CCTAGCTAGATAGGTCGACA+AGG 0.638285 1.3:-2017701 None:intergenic
ACAATGCACAACATAACCAA+GGG 0.652154 1.3:-2017431 None:intergenic
AGGTCCACCGTGTTCCTCCG+AGG 0.662733 1.3:+2017023 MS.gene27020:CDS
AACCAGTTTCACCAACTCAG+AGG 0.670970 1.3:+2017346 MS.gene27020:CDS
GGGTGATGGATCAAAGTGGA+TGG 0.671155 1.3:+2017485 MS.gene27020:CDS
TGATGGAATTATGAGATCAG+CGG 0.673695 1.3:+2017138 MS.gene27020:CDS
GTGGAACCCAACAACTAGAG+AGG 0.673963 1.3:+2017003 MS.gene27020:CDS
AGGAAGAGGATGTTCAGTTG+GGG 0.674344 1.3:-2017191 None:intergenic
TGATAGTCATATGATGTGAG+CGG 0.685126 1.3:-2017604 None:intergenic
GTTGGTGAAACTGGTTGTTG+CGG 0.693105 1.3:-2017339 None:intergenic
TCTAGAAGGACATTGGTGTG+TGG 0.699232 1.3:-2017224 None:intergenic
CTAGCTAGATAGGTCGACAA+GGG 0.718320 1.3:-2017700 None:intergenic
ATTTGGGTGATGGATCAAAG+TGG 0.755177 1.3:+2017481 MS.gene27020:CDS
AGAGCCTCGGAGGAACACGG+TGG 0.797176 1.3:-2017027 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAATATTTGCAACAAAA+TGG - chr1.3:2017309-2017328 None:intergenic 20.0%
!!! AATCAACATCAATTTGAAAT+TGG - chr1.3:2017645-2017664 None:intergenic 20.0%
! ATAATTTAAGTACCAACTCT+TGG + chr1.3:2017167-2017186 MS.gene27020:CDS 25.0%
! TAATTCCATCATAACTAGTA+TGG - chr1.3:2017129-2017148 None:intergenic 25.0%
AAACTCCATACTAGTTATGA+TGG + chr1.3:2017121-2017140 MS.gene27020:CDS 30.0%
ATGATTATAGCAACTTTGCA+TGG + chr1.3:2017383-2017402 MS.gene27020:CDS 30.0%
CTATAATCATATGAGAAGGT+TGG - chr1.3:2017373-2017392 None:intergenic 30.0%
GTTGCTATAATCATATGAGA+AGG - chr1.3:2017377-2017396 None:intergenic 30.0%
TGATTATAGCAACTTTGCAT+GGG + chr1.3:2017384-2017403 MS.gene27020:CDS 30.0%
TGGATTATAAGCAGTTCATA+CGG + chr1.3:2017277-2017296 MS.gene27020:CDS 30.0%
TTGTTAACAGCGTTTATCAT+TGG + chr1.3:2017257-2017276 MS.gene27020:CDS 30.0%
!! AACTTTGAAGTTGATGTTGT+TGG - chr1.3:2017098-2017117 None:intergenic 30.0%
!! ACTTTGAAGTTGATGTTGTT+GGG - chr1.3:2017097-2017116 None:intergenic 30.0%
ACAATGCACAACATAACCAA+GGG - chr1.3:2017434-2017453 None:intergenic 35.0%
ATACGAAACATTGACACAAG+TGG - chr1.3:2017532-2017551 None:intergenic 35.0%
CTCACATCATATGACTATCA+AGG + chr1.3:2017607-2017626 MS.gene27020:CDS 35.0%
TACAATGCACAACATAACCA+AGG - chr1.3:2017435-2017454 None:intergenic 35.0%
TACGAAACATTGACACAAGT+GGG - chr1.3:2017531-2017550 None:intergenic 35.0%
TATGAAACCAACACAAACCT+TGG - chr1.3:2016958-2016977 None:intergenic 35.0%
TGATAGTCATATGATGTGAG+CGG - chr1.3:2017607-2017626 None:intergenic 35.0%
TGATGGAATTATGAGATCAG+CGG + chr1.3:2017138-2017157 MS.gene27020:CDS 35.0%
TGCTATATCTAGAAGGACAT+TGG - chr1.3:2017234-2017253 None:intergenic 35.0%
!! ACAAGAGTGCTATATCTAGA+AGG - chr1.3:2017241-2017260 None:intergenic 35.0%
!! GTCTTGATGAGTTGATTATG+TGG + chr1.3:2016984-2017003 MS.gene27020:CDS 35.0%
AAAGGAAGAGGATGTTCAGT+TGG - chr1.3:2017196-2017215 None:intergenic 40.0%
AAGAATGGCGATCAAATCCT+TGG + chr1.3:2017565-2017584 MS.gene27020:CDS 40.0%
AAGGAAGAGGATGTTCAGTT+GGG - chr1.3:2017195-2017214 None:intergenic 40.0%
GAATCATACGGTAGTTGCAA+TGG + chr1.3:2016920-2016939 MS.gene27020:CDS 40.0%
GACTCATGCATGTATGGTTT+CGG + chr1.3:2017061-2017080 MS.gene27020:CDS 40.0%
GTGTCAATGTTTCGTATGTG+TGG + chr1.3:2017535-2017554 MS.gene27020:CDS 40.0%
GTTGATGTTGTTGGGATCAT+CGG - chr1.3:2017089-2017108 None:intergenic 40.0%
TTTGATCGCCATTCTTCCAA+AGG - chr1.3:2017561-2017580 None:intergenic 40.0%
! GTGGTCTTAGTAAAAGGAAG+AGG - chr1.3:2017208-2017227 None:intergenic 40.0%
! TGGCACAAAAAGTGCAACAT+TGG + chr1.3:2017505-2017524 MS.gene27020:CDS 40.0%
! TGGTGTGTGGTCTTAGTAAA+AGG - chr1.3:2017214-2017233 None:intergenic 40.0%
!! ATTTGGGTGATGGATCAAAG+TGG + chr1.3:2017481-2017500 MS.gene27020:CDS 40.0%
AACCAGTTTCACCAACTCAG+AGG + chr1.3:2017346-2017365 MS.gene27020:CDS 45.0%
AATGGCGATCAAATCCTTGG+AGG + chr1.3:2017568-2017587 MS.gene27020:CDS 45.0%
ACCAAGGGAACCTTTGATCT+CGG - chr1.3:2017419-2017438 None:intergenic 45.0%
ACCAGTTTCACCAACTCAGA+GGG + chr1.3:2017347-2017366 MS.gene27020:CDS 45.0%
ACCCAAATGCTCAAGATGAC+GGG - chr1.3:2017469-2017488 None:intergenic 45.0%
AGGAAGAGGATGTTCAGTTG+GGG - chr1.3:2017194-2017213 None:intergenic 45.0%
CAAATCCTTGGAGGAAAGGT+TGG + chr1.3:2017577-2017596 MS.gene27020:CDS 45.0%
CACCCAAATGCTCAAGATGA+CGG - chr1.3:2017470-2017489 None:intergenic 45.0%
CATCTTGAGCATTTGGGTGA+TGG + chr1.3:2017471-2017490 MS.gene27020:CDS 45.0%
CGATCAAATCCTTGGAGGAA+AGG + chr1.3:2017573-2017592 MS.gene27020:CDS 45.0%
CTAGCTAGATAGGTCGACAA+GGG - chr1.3:2017703-2017722 None:intergenic 45.0%
CTTGTCGACCTATCTAGCTA+GGG + chr1.3:2017702-2017721 MS.gene27020:CDS 45.0%
GATTGTGTTGCCGAGATCAA+AGG + chr1.3:2017406-2017425 MS.gene27020:CDS 45.0%
TCCCGTCATCTTGAGCATTT+GGG + chr1.3:2017465-2017484 MS.gene27020:CDS 45.0%
TCTAGAAGGACATTGGTGTG+TGG - chr1.3:2017227-2017246 None:intergenic 45.0%
TCTGTCTCCAAGGTTTGTGT+TGG + chr1.3:2016948-2016967 MS.gene27020:CDS 45.0%
TGTTTCGTATGTGTGGCCTT+TGG + chr1.3:2017542-2017561 MS.gene27020:CDS 45.0%
! AATGGCGTTTTCTGTCTCCA+AGG + chr1.3:2016938-2016957 MS.gene27020:CDS 45.0%
! ATGTGTGGCCTTTGGAAGAA+TGG + chr1.3:2017550-2017569 MS.gene27020:CDS 45.0%
! GTTGGTGAAACTGGTTGTTG+CGG - chr1.3:2017342-2017361 None:intergenic 45.0%
ACATGCATGAGTCGCTGTCA+AGG - chr1.3:2017054-2017073 None:intergenic 50.0%
CCTAGCTAGATAGGTCGACA+AGG - chr1.3:2017704-2017723 None:intergenic 50.0%
CCTTGTCGACCTATCTAGCT+AGG + chr1.3:2017701-2017720 MS.gene27020:CDS 50.0%
CTAGTGTGCCCTAGCTAGAT+AGG - chr1.3:2017713-2017732 None:intergenic 50.0%
CTCCCGTCATCTTGAGCATT+TGG + chr1.3:2017464-2017483 MS.gene27020:CDS 50.0%
GACAGCGACTCATGCATGTA+TGG + chr1.3:2017055-2017074 MS.gene27020:CDS 50.0%
GGTGGACCTCTCTAGTTGTT+GGG - chr1.3:2017012-2017031 None:intergenic 50.0%
GTGGAACCCAACAACTAGAG+AGG + chr1.3:2017003-2017022 MS.gene27020:CDS 50.0%
GTTCTCCAACCTTTCCTCCA+AGG - chr1.3:2017585-2017604 None:intergenic 50.0%
TTCAGTTGGGGTCCAAGAGT+TGG - chr1.3:2017182-2017201 None:intergenic 50.0%
!! GGGTGATGGATCAAAGTGGA+TGG + chr1.3:2017485-2017504 MS.gene27020:CDS 50.0%
CGGTGGACCTCTCTAGTTGT+TGG - chr1.3:2017013-2017032 None:intergenic 55.0%
GCCGAGATCAAAGGTTCCCT+TGG + chr1.3:2017415-2017434 MS.gene27020:CDS 55.0%
GTCGACAAGGGAGCTATGCT+TGG - chr1.3:2017691-2017710 None:intergenic 55.0%
! AGAAGGTTGGCCCTCTGAGT+TGG - chr1.3:2017360-2017379 None:intergenic 55.0%
!! GCCCTCTGAGTTGGTGAAAC+TGG - chr1.3:2017351-2017370 None:intergenic 55.0%
TCGCTGTCAAGGCAGAGCCT+CGG - chr1.3:2017043-2017062 None:intergenic 60.0%
AGAGCCTCGGAGGAACACGG+TGG - chr1.3:2017030-2017049 None:intergenic 65.0%
AGGTCCACCGTGTTCCTCCG+AGG + chr1.3:2017023-2017042 MS.gene27020:CDS 65.0%
CTGTCAAGGCAGAGCCTCGG+AGG - chr1.3:2017040-2017059 None:intergenic 65.0%
GGCAGAGCCTCGGAGGAACA+CGG - chr1.3:2017033-2017052 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 2016917 2017732 2016917 ID=MS.gene27020
chr1.3 mRNA 2016917 2017732 2016917 ID=MS.gene27020.t1;Parent=MS.gene27020
chr1.3 exon 2016917 2017732 2016917 ID=MS.gene27020.t1.exon1;Parent=MS.gene27020.t1
chr1.3 CDS 2016917 2017732 2016917 ID=cds.MS.gene27020.t1;Parent=MS.gene27020.t1
Gene Sequence

>MS.gene27020

ATGGAATCATACGGTAGTTGCAATGGCGTTTTCTGTCTCCAAGGTTTGTGTTGGTTTCATAAGAGTTGTCTTGATGAGTTGATTATGTGGAACCCAACAACTAGAGAGGTCCACCGTGTTCCTCCGAGGCTCTGCCTTGACAGCGACTCATGCATGTATGGTTTCGGTGCCGATGATCCCAACAACATCAACTTCAAAGTTGTGAAACTCCATACTAGTTATGATGGAATTATGAGATCAGCGGAAGTTTATAATTTAAGTACCAACTCTTGGACCCCAACTGAACATCCTCTTCCTTTTACTAAGACCACACACCAATGTCCTTCTAGATATAGCACTCTTGTTAACAGCGTTTATCATTGGATTATAAGCAGTTCATACGGCAATCGCCATTTTGTTGCAAATATTCTATGCTTTGACTTCCGCAACAACCAGTTTCACCAACTCAGAGGGCCAACCTTCTCATATGATTATAGCAACTTTGCATGGGATTGTGTTGCCGAGATCAAAGGTTCCCTTGGTTATGTTGTGCATTGTAACTTCAATGCTCCCGTCATCTTGAGCATTTGGGTGATGGATCAAAGTGGATGGCACAAAAAGTGCAACATTGGCCCACTTGTGTCAATGTTTCGTATGTGTGGCCTTTGGAAGAATGGCGATCAAATCCTTGGAGGAAAGGTTGGAGAACCGCTCACATCATATGACTATCAAGGTAACTCACTTGACCAATTTCAAATTGATGTTGATTATATTAAACTTCATGAGTATGTGCCAAGCATAGCTCCCTTGTCGACCTATCTAGCTAGGGCACACTAG
Protein sequence

>MS.gene27020.t1

MESYGSCNGVFCLQGLCWFHKSCLDELIMWNPTTREVHRVPPRLCLDSDSCMYGFGADDPNNINFKVVKLHTSYDGIMRSAEVYNLSTNSWTPTEHPLPFTKTTHQCPSRYSTLVNSVYHWIISSSYGNRHFVANILCFDFRNNQFHQLRGPTFSYDYSNFAWDCVAEIKGSLGYVVHCNFNAPVILSIWVMDQSGWHKKCNIGPLVSMFRMCGLWKNGDQILGGKVGEPLTSYDYQGNSLDQFQIDVDYIKLHEYVPSIAPLSTYLARAH