AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24196

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24196.t1 MTR_4g097175 100.000 136 0 0 1 136 1 136 1.33e-96 274
MS.gene24196.t1 MTR_1g023630 100.000 136 0 0 1 136 1 136 1.33e-96 274
MS.gene24196.t1 MTR_8g061940 100.000 136 0 0 1 136 1 136 1.33e-96 274
MS.gene24196.t1 MTR_8g099430 99.265 136 1 0 1 136 1 136 4.84e-96 272
MS.gene24196.t1 MTR_4g097170 99.265 136 1 0 1 136 42 177 7.71e-95 271
MS.gene24196.t1 MTR_7g059070 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_5g029820 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_5g029770 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_4g065990 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_4g088150 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_2g035230 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_8g092720 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_8g063500 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_8g103245 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_8g092820 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene24196.t1 MTR_7g013610 97.059 136 4 0 1 136 100 235 2.63e-92 266
MS.gene24196.t1 MTR_2g082310 92.647 136 10 0 1 136 1 136 4.16e-90 257
MS.gene24196.t1 MTR_2g082340 92.647 136 10 0 1 136 1 136 4.16e-90 257
MS.gene24196.t1 MTR_2g082370 86.301 146 10 1 1 136 1 146 3.79e-84 243
MS.gene24196.t1 MTR_2g082400 85.294 136 18 2 1 135 1 135 1.39e-76 223
MS.gene24196.t1 MTR_7g013600 83.036 112 19 0 25 136 2 113 1.72e-62 187
MS.gene24196.t1 MTR_7g023830 67.164 134 43 1 1 134 1 133 3.79e-56 172
MS.gene24196.t1 MTR_1g023630 77.477 111 23 1 1 111 1 109 1.51e-54 167
MS.gene24196.t1 MTR_7g023880 60.150 133 39 3 3 134 18 137 2.40e-44 142
MS.gene24196.t1 MTR_5g024630 63.793 116 39 2 1 116 1 113 1.54e-42 136
MS.gene24196.t1 MTR_5g024530 65.455 110 15 2 19 128 68 154 6.25e-40 131
MS.gene24196.t1 MTR_0197s0100 96.970 66 2 0 1 66 1 66 1.84e-39 129
MS.gene24196.t1 MTR_8g027840 56.122 98 42 1 37 133 28 125 4.65e-31 108
MS.gene24196.t1 MTR_8g105150 59.783 92 3 2 37 127 11 69 1.24e-26 95.1
MS.gene24196.t1 MTR_8g092740 97.368 38 1 0 99 136 118 155 5.77e-20 80.5
MS.gene24196.t1 MTR_5g089120 68.085 47 15 0 82 128 6 52 1.58e-16 70.1
MS.gene24196.t1 MTR_5g024600 62.963 54 20 0 1 54 1 54 1.14e-15 66.6
MS.gene24196.t1 MTR_4g128040 72.973 37 10 0 79 115 20 56 6.10e-14 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.gene24196.t1 AT5G10980 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40040 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40040 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40040 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40030 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40030 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40030 100.000 136 0 0 1 136 1 136 1.39e-96 274
MS.gene24196.t1 AT4G40030 100.000 136 0 0 1 136 29 164 2.04e-96 275
MS.gene24196.t1 AT5G65360 97.059 136 4 0 1 136 1 136 3.84e-93 265
MS.gene24196.t1 AT5G10390 97.059 136 4 0 1 136 1 136 3.84e-93 265
MS.gene24196.t1 AT5G10400 97.059 136 4 0 1 136 1 136 3.84e-93 265
MS.gene24196.t1 AT3G27360 97.059 136 4 0 1 136 1 136 3.84e-93 265
MS.gene24196.t1 AT1G09200 97.059 136 4 0 1 136 1 136 3.84e-93 265
MS.gene24196.t1 AT1G75600 96.324 136 5 0 1 136 1 136 1.02e-92 264
MS.gene24196.t1 AT1G13370 94.853 136 7 0 1 136 1 136 2.16e-91 261
MS.gene24196.t1 AT5G65350 92.647 136 10 0 1 136 1 136 1.27e-88 254
MS.gene24196.t1 AT1G19890 90.511 137 12 1 1 136 1 137 1.89e-85 246
MS.gene24196.t1 AT5G12910 71.111 135 34 2 1 135 1 130 1.15e-65 196
MS.gene24196.t1 AT1G01370 54.867 113 48 2 24 134 63 174 3.24e-32 112
MS.gene24196.t1 AT1G01370 54.867 113 48 2 24 134 63 174 3.24e-32 112
MS.gene24196.t1 AT1G01370 54.867 113 48 2 24 134 63 174 3.24e-32 112
MS.gene24196.t1 AT1G01370 54.867 113 48 2 24 134 63 174 3.24e-32 112

Find 46 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATGCAGTTCTTGCACTTC+AGG 0.275497 1.2:+1447998 MS.gene24196:CDS
TACCGAAGAGCGACAGTTCC+AGG 0.284956 1.2:-1447541 None:intergenic
TCAAAAGCTCGGTACTCTTC+TGG 0.330386 1.2:-1447780 None:intergenic
CATTCGCGGTGAACGTGCTT+AGG 0.355234 1.2:+1448127 MS.gene24196:CDS
ACGAGCAAGCTGAATGTCCT+TGG 0.416100 1.2:-1448102 None:intergenic
TTGGTGGCGAGCTGCTTCCT+TGG 0.419011 1.2:-1447346 None:intergenic
GTGCAAGAACTGCATGGCTC+TGG 0.421979 1.2:-1447992 None:intergenic
TTACCTGGTTGGATTGTTTG+AGG 0.445449 1.2:+1448034 MS.gene24196:CDS
GGAAGCAGCTGAGGCTTACC+TGG 0.448380 1.2:+1448019 MS.gene24196:CDS
TCACGGACAAGACGCTGAAA+TGG 0.451915 1.2:-1447814 None:intergenic
CAGCTTGCTCGTCGCATTCG+CGG 0.459350 1.2:+1448113 MS.gene24196:CDS
TGAAATCTTGAGCAATTTCA+CGG 0.459574 1.2:-1447831 None:intergenic
CGACAGTTCCAGGGCGGTAT+CGG 0.460197 1.2:-1447531 None:intergenic
AGCATGAATTGCACACAGAT+TGG 0.461487 1.2:-1448060 None:intergenic
CGGTACTCTTCTGGTACTTA+CGG 0.466045 1.2:-1447771 None:intergenic
TGAAATTGCTCAAGATTTCA+AGG 0.466768 1.2:+1447834 MS.gene24196:CDS
AGGAAATCTGCTCCTACTAC+TGG 0.467062 1.2:+1447490 MS.gene24196:CDS
TCGCAAATCCACCGGTGGTA+AGG 0.474471 1.2:+1447321 MS.gene24196:CDS
GCCCTGGAACTGTCGCTCTT+CGG 0.475913 1.2:+1447539 MS.gene24196:CDS
TTCTTGACTCCTCCAGTAGT+AGG 0.487283 1.2:-1447502 None:intergenic
ATTCGCGGTGAACGTGCTTA+GGG 0.501136 1.2:+1448128 MS.gene24196:CDS
CGAGCAAGCTGAATGTCCTT+GGG 0.502974 1.2:-1448101 None:intergenic
GGATTTGCGAGCGGTTTGCT+TGG 0.506530 1.2:-1447308 None:intergenic
TGCACTTCAGGAAGCAGCTG+AGG 0.513447 1.2:+1448010 MS.gene24196:CDS
GCAGCTGAGGCTTACCTGGT+TGG 0.521313 1.2:+1448023 MS.gene24196:CDS
GTGAACGGTGGTTACCTTGG+TGG 0.545269 1.2:-1447362 None:intergenic
CCACCGGTGGTAAGGCTCCA+AGG 0.549290 1.2:+1447329 MS.gene24196:CDS
CTTCCTTGGAGCCTTACCAC+CGG 0.553035 1.2:-1447332 None:intergenic
GGTTTGCTTGGTACGAGCCA+TGG 0.564383 1.2:-1447296 None:intergenic
AAACCTCACCGATACCGCCC+TGG 0.568091 1.2:+1447523 MS.gene24196:CDS
ACCGAAGAGCGACAGTTCCA+GGG 0.584614 1.2:-1447540 None:intergenic
CCTGAAGTGCAAGAACTGCA+TGG 0.601251 1.2:-1447998 None:intergenic
CCTTGGAGCCTTACCACCGG+TGG 0.612238 1.2:-1447329 None:intergenic
CAAACCGCTCGCAAATCCAC+CGG 0.613586 1.2:+1447313 MS.gene24196:CDS
AAATCTGCTCCTACTACTGG+AGG 0.621448 1.2:+1447493 MS.gene24196:CDS
AAGCTTGCGGATCAAAAGCT+CGG 0.627294 1.2:-1447791 None:intergenic
GAGGGTGACAATTATGCCCA+AGG 0.631876 1.2:+1448085 MS.gene24196:CDS
GTGTGCAATTCATGCTAAGA+GGG 0.636984 1.2:+1448067 MS.gene24196:CDS
GACGCTGAAATGGAAGCTTG+CGG 0.649029 1.2:-1447804 None:intergenic
GTTCCAGGGCGGTATCGGTG+AGG 0.654486 1.2:-1447526 None:intergenic
TGTGTGCAATTCATGCTAAG+AGG 0.657983 1.2:+1448066 MS.gene24196:CDS
ACCGCTCGCAAATCCACCGG+TGG 0.660143 1.2:+1447316 MS.gene24196:CDS
TGTCCTCAAACAATCCAACC+AGG 0.667495 1.2:-1448037 None:intergenic
ACCACCGGTGGATTTGCGAG+CGG 0.667602 1.2:-1447317 None:intergenic
AAGGAAGCAGCTCGCCACCA+AGG 0.670819 1.2:+1447348 MS.gene24196:CDS
GAAGAGCGACAGTTCCAGGG+CGG 0.776708 1.2:-1447537 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCATAATTTTTAGGAATT+TGG + chr1.2:1447685-1447704 MS.gene24196:intron 15.0%
!!! ATTTTGGATTCATAATTTTT+AGG + chr1.2:1447678-1447697 MS.gene24196:intron 15.0%
!!! TATGTTTTGAATTTGAATTT+TGG + chr1.2:1447662-1447681 MS.gene24196:intron 15.0%
!! ACAAATTAAATAAACCAAAG+AGG - chr1.2:1447908-1447927 None:intergenic 20.0%
!! TTTCTGTTTTCTTGATGTTA+GGG + chr1.2:1447406-1447425 MS.gene24196:intron 25.0%
!!! AATTTGGAGTTTTGTATTCT+CGG + chr1.2:1447701-1447720 MS.gene24196:intron 25.0%
!!! GATTGATTTCATCGATTTTT+TGG + chr1.2:1447456-1447475 MS.gene24196:intron 25.0%
AACCTAAAAATTAGGGGAAA+AGG - chr1.2:1447571-1447590 None:intergenic 30.0%
ACTCCGAAAACCTAAAAATT+AGG - chr1.2:1447579-1447598 None:intergenic 30.0%
CTCCGAAAACCTAAAAATTA+GGG - chr1.2:1447578-1447597 None:intergenic 30.0%
GAAAGAAGAAAAAACCGTTA+CGG - chr1.2:1447390-1447409 None:intergenic 30.0%
TCCGAAAACCTAAAAATTAG+GGG - chr1.2:1447577-1447596 None:intergenic 30.0%
TGAAATCTTGAGCAATTTCA+CGG - chr1.2:1447834-1447853 None:intergenic 30.0%
TGAAATTGCTCAAGATTTCA+AGG + chr1.2:1447834-1447853 MS.gene24196:CDS 30.0%
! CTTTCTGTTTTCTTGATGTT+AGG + chr1.2:1447405-1447424 MS.gene24196:intron 30.0%
! TTCCTTTTCCCCTAATTTTT+AGG + chr1.2:1447566-1447585 MS.gene24196:intron 30.0%
!! TTTGCTGTTGTTGTTATAGA+CGG + chr1.2:1447959-1447978 MS.gene24196:intron 30.0%
!!! TCCCCTAATTTTTAGGTTTT+CGG + chr1.2:1447573-1447592 MS.gene24196:intron 30.0%
!!! TTTCATCGATTTTTTGGTTC+AGG + chr1.2:1447462-1447481 MS.gene24196:intron 30.0%
TGTGAAATCTTGTTCCTCTT+TGG + chr1.2:1447891-1447910 MS.gene24196:intron 35.0%
AGAAGAAAAAACCGTTACGG+CGG - chr1.2:1447387-1447406 None:intergenic 40.0%
AGCATGAATTGCACACAGAT+TGG - chr1.2:1448063-1448082 None:intergenic 40.0%
GTGTGCAATTCATGCTAAGA+GGG + chr1.2:1448067-1448086 MS.gene24196:CDS 40.0%
TGTGTGCAATTCATGCTAAG+AGG + chr1.2:1448066-1448085 MS.gene24196:CDS 40.0%
TTACCTGGTTGGATTGTTTG+AGG + chr1.2:1448034-1448053 MS.gene24196:CDS 40.0%
!!! ATTTTTTGGTTCAGGCTGCT+AGG + chr1.2:1447470-1447489 MS.gene24196:intron 40.0%
AAATCTGCTCCTACTACTGG+AGG + chr1.2:1447493-1447512 MS.gene24196:CDS 45.0%
AAGCTTGCGGATCAAAAGCT+CGG - chr1.2:1447794-1447813 None:intergenic 45.0%
AGGAAATCTGCTCCTACTAC+TGG + chr1.2:1447490-1447509 MS.gene24196:CDS 45.0%
CGGTACTCTTCTGGTACTTA+CGG - chr1.2:1447774-1447793 None:intergenic 45.0%
TCAAAAGCTCGGTACTCTTC+TGG - chr1.2:1447783-1447802 None:intergenic 45.0%
TGTCCTCAAACAATCCAACC+AGG - chr1.2:1448040-1448059 None:intergenic 45.0%
TTCTTGACTCCTCCAGTAGT+AGG - chr1.2:1447505-1447524 None:intergenic 45.0%
!!! TTTCTATTATTAATTTTTTT+AGG + chr1.2:1447606-1447625 MS.gene24196:intron 5.0%
AAAACCGTTACGGCGGTGAA+CGG - chr1.2:1447380-1447399 None:intergenic 50.0%
ACGAGCAAGCTGAATGTCCT+TGG - chr1.2:1448105-1448124 None:intergenic 50.0%
CCATGCAGTTCTTGCACTTC+AGG + chr1.2:1447998-1448017 MS.gene24196:CDS 50.0%
CCTGAAGTGCAAGAACTGCA+TGG - chr1.2:1448001-1448020 None:intergenic 50.0%
CGAGCAAGCTGAATGTCCTT+GGG - chr1.2:1448104-1448123 None:intergenic 50.0%
GACGCTGAAATGGAAGCTTG+CGG - chr1.2:1447807-1447826 None:intergenic 50.0%
GAGGGTGACAATTATGCCCA+AGG + chr1.2:1448085-1448104 MS.gene24196:CDS 50.0%
TCACGGACAAGACGCTGAAA+TGG - chr1.2:1447817-1447836 None:intergenic 50.0%
ACCGAAGAGCGACAGTTCCA+GGG - chr1.2:1447543-1447562 None:intergenic 55.0%
CAAACCGCTCGCAAATCCAC+CGG + chr1.2:1447313-1447332 MS.gene24196:CDS 55.0%
CTTCCTTGGAGCCTTACCAC+CGG - chr1.2:1447335-1447354 None:intergenic 55.0%
GTGAACGGTGGTTACCTTGG+TGG - chr1.2:1447365-1447384 None:intergenic 55.0%
GTGCAAGAACTGCATGGCTC+TGG - chr1.2:1447995-1448014 None:intergenic 55.0%
TACCGAAGAGCGACAGTTCC+AGG - chr1.2:1447544-1447563 None:intergenic 55.0%
TCGCAAATCCACCGGTGGTA+AGG + chr1.2:1447321-1447340 MS.gene24196:CDS 55.0%
TGCACTTCAGGAAGCAGCTG+AGG + chr1.2:1448010-1448029 MS.gene24196:CDS 55.0%
! GGATTTGCGAGCGGTTTGCT+TGG - chr1.2:1447311-1447330 None:intergenic 55.0%
AAACCTCACCGATACCGCCC+TGG + chr1.2:1447523-1447542 MS.gene24196:CDS 60.0%
AAGGAAGCAGCTCGCCACCA+AGG + chr1.2:1447348-1447367 MS.gene24196:CDS 60.0%
ACCACCGTTCACCGCCGTAA+CGG + chr1.2:1447373-1447392 MS.gene24196:intron 60.0%
CGACAGTTCCAGGGCGGTAT+CGG - chr1.2:1447534-1447553 None:intergenic 60.0%
GAAGAGCGACAGTTCCAGGG+CGG - chr1.2:1447540-1447559 None:intergenic 60.0%
GCAGCTGAGGCTTACCTGGT+TGG + chr1.2:1448023-1448042 MS.gene24196:CDS 60.0%
GCCCTGGAACTGTCGCTCTT+CGG + chr1.2:1447539-1447558 MS.gene24196:CDS 60.0%
GCGGTGAACGGTGGTTACCT+TGG - chr1.2:1447368-1447387 None:intergenic 60.0%
GGAAGCAGCTGAGGCTTACC+TGG + chr1.2:1448019-1448038 MS.gene24196:CDS 60.0%
! ACCACCGGTGGATTTGCGAG+CGG - chr1.2:1447320-1447339 None:intergenic 60.0%
! CAGCTTGCTCGTCGCATTCG+CGG + chr1.2:1448113-1448132 MS.gene24196:CDS 60.0%
!! TTGGTGGCGAGCTGCTTCCT+TGG - chr1.2:1447349-1447368 None:intergenic 60.0%
ACCGCTCGCAAATCCACCGG+TGG + chr1.2:1447316-1447335 MS.gene24196:CDS 65.0%
ACCGTTACGGCGGTGAACGG+TGG - chr1.2:1447377-1447396 None:intergenic 65.0%
CCACCGGTGGTAAGGCTCCA+AGG + chr1.2:1447329-1447348 MS.gene24196:CDS 65.0%
CCTTGGAGCCTTACCACCGG+TGG - chr1.2:1447332-1447351 None:intergenic 65.0%
!! GTTCCAGGGCGGTATCGGTG+AGG - chr1.2:1447529-1447548 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 1447298 1448148 1447298 ID=MS.gene24196
chr1.2 mRNA 1447298 1448148 1447298 ID=MS.gene24196.t1;Parent=MS.gene24196
chr1.2 exon 1447298 1447369 1447298 ID=MS.gene24196.t1.exon1;Parent=MS.gene24196.t1
chr1.2 CDS 1447298 1447369 1447298 ID=cds.MS.gene24196.t1;Parent=MS.gene24196.t1
chr1.2 exon 1447484 1447560 1447484 ID=MS.gene24196.t1.exon2;Parent=MS.gene24196.t1
chr1.2 CDS 1447484 1447560 1447484 ID=cds.MS.gene24196.t1;Parent=MS.gene24196.t1
chr1.2 exon 1447765 1447855 1447765 ID=MS.gene24196.t1.exon3;Parent=MS.gene24196.t1
chr1.2 CDS 1447765 1447855 1447765 ID=cds.MS.gene24196.t1;Parent=MS.gene24196.t1
chr1.2 exon 1447978 1448148 1447978 ID=MS.gene24196.t1.exon4;Parent=MS.gene24196.t1
chr1.2 CDS 1447978 1448148 1447978 ID=cds.MS.gene24196.t1;Parent=MS.gene24196.t1
Gene Sequence

>MS.gene24196

ATGGCTCGTACCAAGCAAACCGCTCGCAAATCCACCGGTGGTAAGGCTCCAAGGAAGCAGCTCGCCACCAAGGTAACCACCGTTCACCGCCGTAACGGTTTTTTCTTCTTTCTGTTTTCTTGATGTTAGGGTTTCGTTTTCTTCAATTCGAATTTTTTGATTGATTTCATCGATTTTTTGGTTCAGGCTGCTAGGAAATCTGCTCCTACTACTGGAGGAGTCAAGAAACCTCACCGATACCGCCCTGGAACTGTCGCTCTTCGGTAATTTCCTTTTCCCCTAATTTTTAGGTTTTCGGAGTTTTGCAGTTTCTATTATTAATTTTTTTAGGTTTTCGTTGTGTTTTGAATATTCGATTGAATTTTATGTTTTGAATTTGAATTTTGGATTCATAATTTTTAGGAATTTGGAGTTTTGTATTCTCGGTTTATGATTTTTAGTTAATTTTCAATTGATGTGATTTACAGTGAGATCCGTAAGTACCAGAAGAGTACCGAGCTTTTGATCCGCAAGCTTCCATTTCAGCGTCTTGTCCGTGAAATTGCTCAAGATTTCAAGGTAAATATTGTTACTTAGTTTCATAATTGATTTTGTGTGAAATCTTGTTCCTCTTTGGTTTATTTAATTTGTAATTGTTGTTTTTGATATTTTTCTGATTAATTTTGCTGTTGTTGTTATAGACGGATTTGAGATTCCAGAGCCATGCAGTTCTTGCACTTCAGGAAGCAGCTGAGGCTTACCTGGTTGGATTGTTTGAGGACACCAATCTGTGTGCAATTCATGCTAAGAGGGTGACAATTATGCCCAAGGACATTCAGCTTGCTCGTCGCATTCGCGGTGAACGTGCTTAG
Protein sequence

>MS.gene24196.t1

MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA