AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84795

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84795.t1 MTR_6g045327 92.342 222 15 2 1 221 1 221 1.40e-150 424
MS.gene84795.t1 MTR_4g021760 48.879 223 107 4 1 221 1 218 5.54e-60 191
MS.gene84795.t1 MTR_8g093040 49.774 221 96 4 1 221 1 206 8.95e-59 186
MS.gene84795.t1 MTR_4g021790 47.619 210 106 3 14 221 10 217 5.11e-56 179
MS.gene84795.t1 MTR_4g021845 44.843 223 115 4 1 221 1 217 2.58e-54 173
MS.gene84795.t1 MTR_1g032570 43.154 241 104 5 13 221 10 249 2.81e-54 183
MS.gene84795.t1 MTR_4g021855 46.667 210 108 3 14 221 10 217 1.51e-53 174
MS.gene84795.t1 MTR_8g079940 37.500 248 117 7 4 221 19 258 4.43e-44 155
MS.gene84795.t1 MTR_4g121020 37.975 237 117 4 13 221 30 264 1.19e-43 155
MS.gene84795.t1 MTR_4g121020 37.975 237 117 4 13 221 30 264 1.23e-43 155
MS.gene84795.t1 MTR_2g034960 38.298 235 117 4 13 221 28 260 2.01e-43 154
MS.gene84795.t1 MTR_3g086100 36.820 239 121 5 12 221 11 248 4.10e-43 152
MS.gene84795.t1 MTR_8g105600 40.435 230 113 4 14 221 9 236 2.01e-42 151
MS.gene84795.t1 MTR_4g131600 33.475 236 132 3 10 221 16 250 1.82e-37 137
MS.gene84795.t1 MTR_3g106220 34.711 242 124 5 13 221 7 247 1.85e-35 132
MS.gene84795.t1 MTR_5g055260 40.865 208 96 6 14 221 10 190 1.01e-34 124
MS.gene84795.t1 MTR_1g013170 35.146 239 123 5 13 221 4 240 2.41e-34 128
MS.gene84795.t1 MTR_0450s0040 33.019 212 133 2 18 221 8 218 4.39e-34 125
MS.gene84795.t1 MTR_3g102600 32.558 215 111 2 7 221 1 181 5.05e-34 120
MS.gene84795.t1 MTR_4g131580 32.051 234 132 3 14 221 17 249 1.32e-33 127
MS.gene84795.t1 MTR_3g102600 32.558 215 111 2 7 221 1 181 2.06e-33 120
MS.gene84795.t1 MTR_4g131570 30.435 253 143 4 1 221 1 252 3.08e-33 125
MS.gene84795.t1 MTR_1g032570 40.331 181 75 5 73 221 1 180 1.59e-32 124
MS.gene84795.t1 MTR_7g117705 32.353 238 131 4 13 221 4 240 1.05e-31 120
MS.gene84795.t1 MTR_6g016850 42.138 159 88 4 9 165 4 160 5.95e-31 112
MS.gene84795.t1 MTR_2g450070 29.688 256 141 4 4 221 8 262 1.12e-30 119
MS.gene84795.t1 MTR_2g450070 29.688 256 141 4 4 221 8 262 1.14e-30 119
MS.gene84795.t1 MTR_1g013180 31.200 250 142 3 1 221 143 391 3.93e-30 117
MS.gene84795.t1 MTR_3g102590 33.641 217 117 4 7 221 1 192 2.34e-29 108
MS.gene84795.t1 MTR_7g026400 36.269 193 105 3 44 221 17 206 3.13e-29 114
MS.gene84795.t1 MTR_3g102590 33.641 217 117 4 7 221 1 192 5.09e-29 109
MS.gene84795.t1 MTR_3g086100 35.955 178 84 5 73 221 1 177 1.47e-28 112
MS.gene84795.t1 MTR_4g023980 41.135 141 74 4 61 196 36 172 1.66e-27 103
MS.gene84795.t1 MTR_3g102600 31.325 166 80 2 56 221 1 132 2.46e-25 96.7
MS.gene84795.t1 MTR_3g102600 31.325 166 80 2 56 221 1 132 1.82e-24 95.9
MS.gene84795.t1 MTR_4g121020 35.256 156 73 2 93 221 6 160 6.22e-23 96.7
MS.gene84795.t1 MTR_5g014040 34.615 130 80 3 12 140 12 137 3.27e-13 68.6
MS.gene84795.t1 MTR_5g014040 34.615 130 80 3 12 140 12 137 3.38e-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.gene84795.t1 AT2G01760 37.551 245 116 5 13 221 6 249 6.99e-46 156
MS.gene84795.t1 AT1G67710 38.298 235 114 6 17 221 10 243 1.04e-40 145
MS.gene84795.t1 AT2G01760 33.700 273 116 6 13 221 6 277 4.40e-40 142
MS.gene84795.t1 AT3G16857 33.206 262 125 6 8 221 27 286 1.89e-38 141
MS.gene84795.t1 AT3G16857 33.206 262 125 6 8 221 27 286 2.14e-38 141
MS.gene84795.t1 AT4G31920 35.021 237 133 7 1 221 1 232 1.04e-33 127
MS.gene84795.t1 AT2G25180 32.114 246 140 4 1 221 1 244 1.89e-33 126
MS.gene84795.t1 AT3G16857 31.797 217 100 4 52 221 1 216 1.20e-30 119
MS.gene84795.t1 AT5G49240 30.000 250 144 6 3 223 27 274 5.49e-30 113
MS.gene84795.t1 AT5G58080 32.618 233 131 5 13 221 13 243 7.17e-30 116
MS.gene84795.t1 AT2G01760 36.264 182 79 5 76 221 4 184 1.11e-28 110
MS.gene84795.t1 AT1G67710 37.430 179 81 6 73 221 1 178 4.25e-27 107
MS.gene84795.t1 AT3G62670 31.092 238 130 9 12 221 34 265 2.28e-25 102
MS.gene84795.t1 AT1G49190 27.888 251 146 8 4 221 20 268 8.75e-24 98.2
MS.gene84795.t1 AT1G67710 38.365 159 67 6 93 221 12 169 3.26e-21 91.3
MS.gene84795.t1 AT5G07210 26.154 260 132 7 18 221 16 271 8.23e-15 73.2
MS.gene84795.t1 AT1G49190 28.676 136 96 1 4 139 20 154 2.94e-13 68.6
MS.gene84795.t1 AT5G07210 27.556 225 103 7 53 221 59 279 4.63e-13 68.2
MS.gene84795.t1 AT5G59570 37.931 87 53 1 135 221 105 190 9.88e-12 63.5
MS.gene84795.t1 AT5G59570 37.931 87 53 1 135 221 105 190 9.88e-12 63.5
MS.gene84795.t1 AT2G27070 50.909 55 26 1 167 221 221 274 4.05e-11 62.4
MS.gene84795.t1 AT2G40970 50.980 51 25 0 171 221 104 154 5.24e-11 60.8
MS.gene84795.t1 AT5G05090 50.980 51 25 0 171 221 80 130 9.58e-11 60.5
MS.gene84795.t1 AT3G46640 50.980 51 25 0 171 221 143 193 9.85e-11 60.8

Find 36 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAGGGCTGTGAATCAATT+TGG 0.229550 6.3:+49403091 MS.gene84795:CDS
CAATGCATCAAGAATTTCTA+AGG 0.275756 6.3:+49403074 MS.gene84795:CDS
GCATATTGCTAGCCATTTAC+AGG 0.279083 6.3:+49403271 MS.gene84795:CDS
CCCGTTTGCAATAGCCTTCA+TGG 0.290834 6.3:-49402849 None:intergenic
TAAACCCTCTAAGAATTGTT+GGG 0.362447 6.3:-49402167 None:intergenic
ACTTCCCCAACAATTCTTAG+AGG 0.375785 6.3:+49402162 MS.gene84795:CDS
TGACAGGAATATTGATTTGT+TGG 0.378211 6.3:-49402519 None:intergenic
GATCAAATTCATGTTGATAA+TGG 0.381612 6.3:+49402968 MS.gene84795:CDS
TGATTTGTTGGGTAATTTGT+TGG 0.402510 6.3:-49402507 None:intergenic
TTAAACCCTCTAAGAATTGT+TGG 0.417447 6.3:-49402168 None:intergenic
GCCATCGTTGAAAAGTCAAT+TGG 0.430946 6.3:+49402229 MS.gene84795:CDS
GACAGGAATATTGATTTGTT+GGG 0.435755 6.3:-49402518 None:intergenic
TGTGCAGTGATGGGTGTTGA+TGG 0.436154 6.3:+49402812 MS.gene84795:intron
AATTTGTTGGAGAAAATCAT+AGG 0.440238 6.3:-49402494 None:intergenic
CCATGAAGGCTATTGCAAAC+GGG 0.441100 6.3:+49402849 MS.gene84795:CDS
TCCATGAAGGCTATTGCAAA+CGG 0.446848 6.3:+49402848 MS.gene84795:CDS
AACGATGGCATTGTGGATAG+TGG 0.451069 6.3:-49402215 None:intergenic
ATTCATGTGATGAATGTTCC+TGG 0.451107 6.3:+49403236 MS.gene84795:CDS
TTGCTTGAGACCATGTTAAA+CGG 0.467130 6.3:-49403054 None:intergenic
GGCAAAGAATCTTACTATCA+AGG 0.473824 6.3:-49403114 None:intergenic
AATGGCTCTTTCAACTGAGA+TGG 0.494149 6.3:+49402135 None:intergenic
TCATGTTGATGTGGTTGAAA+AGG 0.515561 6.3:+49403003 MS.gene84795:CDS
TATATATTCTTACTAATGAC+AGG 0.521693 6.3:-49402535 None:intergenic
CGTTGAAAAGTCAATTGGAT+GGG 0.523926 6.3:+49402234 MS.gene84795:CDS
CTTCCCCAACAATTCTTAGA+GGG 0.553790 6.3:+49402163 MS.gene84795:CDS
ACATGTGCAAACACGTTCCA+AGG 0.562980 6.3:+49402921 MS.gene84795:CDS
TTGATTAGGTCATCACTCAA+AGG 0.569533 6.3:-49402896 None:intergenic
TCGTTGAAAAGTCAATTGGA+TGG 0.580260 6.3:+49402233 MS.gene84795:CDS
ATCAACAAGTGCATCCATGA+AGG 0.588196 6.3:+49402835 MS.gene84795:CDS
TCAATTGGATGGGATTACAA+AGG 0.596849 6.3:+49402244 MS.gene84795:CDS
AAACCCTCTAAGAATTGTTG+GGG 0.603847 6.3:-49402166 None:intergenic
AAAAGAAGCATTAGAGCATG+TGG 0.613637 6.3:-49402395 None:intergenic
AATGCATCAAGAATTTCTAA+GGG 0.619626 6.3:+49403075 MS.gene84795:CDS
AAAAGAATCTCATGTTGATG+TGG 0.621750 6.3:+49402994 MS.gene84795:CDS
CATGAAGGCTATTGCAAACG+GGG 0.626135 6.3:+49402850 MS.gene84795:CDS
ATATGCTCTCTTGTCAAACC+AGG 0.644357 6.3:-49403254 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAGAAAAAAAAAAG+TGG - chr6.3:49403138-49403157 None:intergenic 15.0%
!!! ATCACATGAATAATTTTTTT+TGG - chr6.3:49403227-49403246 None:intergenic 15.0%
!!! GTTTGTTTTTTAGATTAATT+TGG + chr6.3:49403293-49403312 MS.gene84795:intron 15.0%
!! TATATATTCTTACTAATGAC+AGG - chr6.3:49402538-49402557 None:intergenic 20.0%
! AATGCATCAAGAATTTCTAA+GGG + chr6.3:49403075-49403094 MS.gene84795:CDS 25.0%
! CTAAAAAACAAACCTGTAAA+TGG - chr6.3:49403286-49403305 None:intergenic 25.0%
!! GATCAAATTCATGTTGATAA+TGG + chr6.3:49402968-49402987 MS.gene84795:CDS 25.0%
!!! AATGTCTGTTTTTGCTTTAT+TGG + chr6.3:49402652-49402671 MS.gene84795:intron 25.0%
!!! AATTTGTTGGAGAAAATCAT+AGG - chr6.3:49402497-49402516 None:intergenic 25.0%
!!! GTTTTGCATCTGAAATATAA+GGG - chr6.3:49403205-49403224 None:intergenic 25.0%
!!! TTAAACGGTTCTTTTTTGTT+GGG - chr6.3:49403042-49403061 None:intergenic 25.0%
AAAAGAATCTCATGTTGATG+TGG + chr6.3:49402994-49403013 MS.gene84795:CDS 30.0%
CAAAAAAGAACCGTTTAACA+TGG + chr6.3:49403044-49403063 MS.gene84795:CDS 30.0%
CAATGCATCAAGAATTTCTA+AGG + chr6.3:49403074-49403093 MS.gene84795:CDS 30.0%
! GTTTCATTCAAAGTTTTCCT+TGG - chr6.3:49402941-49402960 None:intergenic 30.0%
! TAAACCCTCTAAGAATTGTT+GGG - chr6.3:49402170-49402189 None:intergenic 30.0%
! TTAAACCCTCTAAGAATTGT+TGG - chr6.3:49402171-49402190 None:intergenic 30.0%
!! GACAGGAATATTGATTTGTT+GGG - chr6.3:49402521-49402540 None:intergenic 30.0%
!! GGTTTTGCATCTGAAATATA+AGG - chr6.3:49403206-49403225 None:intergenic 30.0%
!! GTTTGCACATGTTTTTGATT+AGG - chr6.3:49402913-49402932 None:intergenic 30.0%
!! TGACAGGAATATTGATTTGT+TGG - chr6.3:49402522-49402541 None:intergenic 30.0%
!! TGATTTGTTGGGTAATTTGT+TGG - chr6.3:49402510-49402529 None:intergenic 30.0%
!!! GTTAAACGGTTCTTTTTTGT+TGG - chr6.3:49403043-49403062 None:intergenic 30.0%
!!! TAAACGGTTCTTTTTTGTTG+GGG - chr6.3:49403041-49403060 None:intergenic 30.0%
!!! TTTTGCATTGACTCTTTTGA+GGG + chr6.3:49402414-49402433 MS.gene84795:CDS 30.0%
ATTCATGTGATGAATGTTCC+TGG + chr6.3:49403236-49403255 MS.gene84795:CDS 35.0%
CGTTGAAAAGTCAATTGGAT+GGG + chr6.3:49402234-49402253 MS.gene84795:CDS 35.0%
GGCAAAGAATCTTACTATCA+AGG - chr6.3:49403117-49403136 None:intergenic 35.0%
TCAATTGGATGGGATTACAA+AGG + chr6.3:49402244-49402263 MS.gene84795:CDS 35.0%
TCATGTTGATGTGGTTGAAA+AGG + chr6.3:49403003-49403022 MS.gene84795:CDS 35.0%
TCGTTGAAAAGTCAATTGGA+TGG + chr6.3:49402233-49402252 MS.gene84795:CDS 35.0%
TTGATTAGGTCATCACTCAA+AGG - chr6.3:49402899-49402918 None:intergenic 35.0%
TTGCTTGAGACCATGTTAAA+CGG - chr6.3:49403057-49403076 None:intergenic 35.0%
! AAACCCTCTAAGAATTGTTG+GGG - chr6.3:49402169-49402188 None:intergenic 35.0%
! TGCATCTGAAATATAAGGGA+GGG - chr6.3:49403201-49403220 None:intergenic 35.0%
! TTGCATCTGAAATATAAGGG+AGG - chr6.3:49403202-49403221 None:intergenic 35.0%
!! AAAAGAAGCATTAGAGCATG+TGG - chr6.3:49402398-49402417 None:intergenic 35.0%
!! TCCAATTGACTTTTCAACGA+TGG - chr6.3:49402233-49402252 None:intergenic 35.0%
!!! AAACGGTTCTTTTTTGTTGG+GGG - chr6.3:49403040-49403059 None:intergenic 35.0%
!!! CTTTTGCATTGACTCTTTTG+AGG + chr6.3:49402413-49402432 MS.gene84795:CDS 35.0%
ACTTCCCCAACAATTCTTAG+AGG + chr6.3:49402162-49402181 MS.gene84795:CDS 40.0%
ATATGCTCTCTTGTCAAACC+AGG - chr6.3:49403257-49403276 None:intergenic 40.0%
ATATGTGTCATGTGCAGTGA+TGG + chr6.3:49402802-49402821 MS.gene84795:intron 40.0%
ATCAACAAGTGCATCCATGA+AGG + chr6.3:49402835-49402854 MS.gene84795:CDS 40.0%
CTAAGGGCTGTGAATCAATT+TGG + chr6.3:49403091-49403110 MS.gene84795:CDS 40.0%
CTTCCCCAACAATTCTTAGA+GGG + chr6.3:49402163-49402182 MS.gene84795:CDS 40.0%
GCATATTGCTAGCCATTTAC+AGG + chr6.3:49403271-49403290 MS.gene84795:CDS 40.0%
GCCATCGTTGAAAAGTCAAT+TGG + chr6.3:49402229-49402248 MS.gene84795:CDS 40.0%
TATGTGTCATGTGCAGTGAT+GGG + chr6.3:49402803-49402822 MS.gene84795:intron 40.0%
TCCATGAAGGCTATTGCAAA+CGG + chr6.3:49402848-49402867 MS.gene84795:CDS 40.0%
! ACTTTTCAACGATGGCATTG+TGG - chr6.3:49402225-49402244 None:intergenic 40.0%
! GCATCTGAAATATAAGGGAG+GGG - chr6.3:49403200-49403219 None:intergenic 40.0%
! GTCAAAAGCGAACGTGATTT+TGG - chr6.3:49402624-49402643 None:intergenic 40.0%
!! ACTCTTTTGAGGGAAGCAAA+GGG + chr6.3:49402424-49402443 MS.gene84795:CDS 40.0%
AACGATGGCATTGTGGATAG+TGG - chr6.3:49402218-49402237 None:intergenic 45.0%
ACATGTGCAAACACGTTCCA+AGG + chr6.3:49402921-49402940 MS.gene84795:CDS 45.0%
CAATCAGTCACTCAAGCACA+AGG - chr6.3:49402732-49402751 None:intergenic 45.0%
CACACACACTTATGTGCAAC+AGG + chr6.3:49402590-49402609 MS.gene84795:intron 45.0%
CATGAAGGCTATTGCAAACG+GGG + chr6.3:49402850-49402869 MS.gene84795:CDS 45.0%
CCATGAAGGCTATTGCAAAC+GGG + chr6.3:49402849-49402868 MS.gene84795:CDS 45.0%
GCATTAGAGCATGTGGTAAC+TGG - chr6.3:49402391-49402410 None:intergenic 45.0%
!! GACTCTTTTGAGGGAAGCAA+AGG + chr6.3:49402423-49402442 MS.gene84795:CDS 45.0%
CCCGTTTGCAATAGCCTTCA+TGG - chr6.3:49402852-49402871 None:intergenic 50.0%
!! TGTGCAGTGATGGGTGTTGA+TGG + chr6.3:49402812-49402831 MS.gene84795:intron 50.0%
CAAGCACAAGGCGTGCTGAA+GGG - chr6.3:49402720-49402739 None:intergenic 55.0%
TCAAGCACAAGGCGTGCTGA+AGG - chr6.3:49402721-49402740 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 49402136 49403386 49402136 ID=MS.gene84795
chr6.3 mRNA 49402136 49403386 49402136 ID=MS.gene84795.t1;Parent=MS.gene84795
chr6.3 exon 49402136 49402265 49402136 ID=MS.gene84795.t1.exon1;Parent=MS.gene84795.t1
chr6.3 CDS 49402136 49402265 49402136 ID=cds.MS.gene84795.t1;Parent=MS.gene84795.t1
chr6.3 exon 49402392 49402544 49402392 ID=MS.gene84795.t1.exon2;Parent=MS.gene84795.t1
chr6.3 CDS 49402392 49402544 49402392 ID=cds.MS.gene84795.t1;Parent=MS.gene84795.t1
chr6.3 exon 49402819 49403121 49402819 ID=MS.gene84795.t1.exon3;Parent=MS.gene84795.t1
chr6.3 CDS 49402819 49403121 49402819 ID=cds.MS.gene84795.t1;Parent=MS.gene84795.t1
chr6.3 exon 49403216 49403292 49403216 ID=MS.gene84795.t1.exon4;Parent=MS.gene84795.t1
chr6.3 CDS 49403216 49403292 49403216 ID=cds.MS.gene84795.t1;Parent=MS.gene84795.t1
chr6.3 exon 49403375 49403386 49403375 ID=MS.gene84795.t1.exon5;Parent=MS.gene84795.t1
chr6.3 CDS 49403375 49403386 49403375 ID=cds.MS.gene84795.t1;Parent=MS.gene84795.t1
Gene Sequence

>MS.gene84795

ATGGCTCTTTCAACTGAGATGGAAGCACTTCCCCAACAATTCTTAGAGGGTTTAAGAGTTCTTGTGATTGATCATGACACCACTATCCACAATGCCATCGTTGAAAAGTCAATTGGATGGGATTACAAAGGTTTGTTAATTAAATTTTGATATCATACTCAATTATAAATTAAATTTTGTTAACATGTGAAAGTCTTGAACATTTTGTAACAATTCTTAATTTTATGTAAAAAAAATTTATGCTTGTTTGTTCCAGTTACCACATGCTCTAATGCTTCTTTTGCATTGACTCTTTTGAGGGAAGCAAAGGGTTGTTTTGATGTGATACTAATTGAAGAACAAATCTCAGACATGAATTCCTATGATTTTCTCCAACAAATTACCCAACAAATCAATATTCCTGTCATTAGTAAGAATATATATACATAATTAATTATATTATTATATCACATGACACACACACTTATGTGCAACAGGAGAACTTTCCAAAATCACGTTCGCTTTTGACTGTCATGTAATGTCTGTTTTTGCTTTATTGGCTAGTTCTAGCTTTATTGTTTTGTAATTAACATTTTTCAGCTCCCTTCAGCACGCCTTGTGCTTGAGTGACTGATTGTTTCTTTAATATATTTCGCTTAGTTTCTTAAAAAAAAAAATTATATATATATATGTGTCATGTGCAGTGATGGGTGTTGATGGATCAACAAGTGCATCCATGAAGGCTATTGCAAACGGGGCTTGTTGTGAGTATTGTGTTAAGCCTTTGAGTGATGACCTAATCAAAAACATGTGCAAACACGTTCCAAGGAAAACTTTGAATGAAACTAAACATGATCAAATTCATGTTGATAATGGCACAAAAGAATCTCATGTTGATGTGGTTGAAAAGGATAATTATCAACCCCCAACAAAAAAGAACCGTTTAACATGGTCTCAAGCAATGCATCAAGAATTTCTAAGGGCTGTGAATCAATTTGGCCTTGATAGTAAGATTCTTTGCCACTTTTTTTTTTCTTTCTTTTATTGTATAATTCAAGAAACTCAACTTGTGTGCATTTTTTCCCCTCCCTTATATTTCAGATGCAAAACCAAAAAAAATTATTCATGTGATGAATGTTCCTGGTTTGACAAGAGAGCATATTGCTAGCCATTTACAGGTTTGTTTTTTAGATTAATTTGGTTGATTCTGTTATACTTTCTCATGATTGAAGATCTGATAAATTTTATTATAACATATAGTTTACTAATTGA
Protein sequence

>MS.gene84795.t1

MALSTEMEALPQQFLEGLRVLVIDHDTTIHNAIVEKSIGWDYKVTTCSNASFALTLLREAKGCFDVILIEEQISDMNSYDFLQQITQQINIPVIMMGVDGSTSASMKAIANGACCEYCVKPLSDDLIKNMCKHVPRKTLNETKHDQIHVDNGTKESHVDVVEKDNYQPPTKKNRLTWSQAMHQEFLRAVNQFGLDNAKPKKIIHVMNVPGLTREHIASHLQFTN