AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029746

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029746.t1 MTR_1g062780 96.970 297 7 2 1 295 1 297 0.0 595
MS.gene029746.t1 MTR_1g090703 36.944 360 145 15 5 295 9 355 6.65e-50 169
MS.gene029746.t1 MTR_4g057230 38.629 321 137 11 3 295 5 293 3.28e-49 165
MS.gene029746.t1 MTR_2g084315 38.486 317 136 15 9 295 6 293 2.90e-47 160
MS.gene029746.t1 MTR_7g023560 42.553 141 38 3 80 220 12 109 2.20e-25 100
MS.gene029746.t1 MTR_1g115345 42.553 141 44 4 80 220 16 119 4.72e-25 99.8
MS.gene029746.t1 MTR_1g067650 35.468 203 80 5 68 269 4 156 2.76e-24 97.1
MS.gene029746.t1 MTR_1g067640 34.975 203 81 5 68 269 3 155 1.17e-23 95.1
MS.gene029746.t1 MTR_1g067660 38.125 160 52 5 72 230 3 116 1.58e-21 89.4
MS.gene029746.t1 MTR_4g028610 33.906 233 100 8 76 264 158 380 2.11e-21 94.0
MS.gene029746.t1 MTR_1g106730 32.804 189 79 5 76 264 56 196 1.08e-19 86.7
MS.gene029746.t1 MTR_1g018420 37.436 195 88 6 76 269 39 200 1.10e-19 86.3
MS.gene029746.t1 MTR_1g077730 35.152 165 87 4 111 263 37 193 2.73e-19 84.0
MS.gene029746.t1 MTR_3g102980 32.308 195 97 5 76 269 48 208 5.51e-17 79.0
MS.gene029746.t1 MTR_4g109340 35.057 174 83 7 104 264 331 487 1.64e-16 79.7
MS.gene029746.t1 MTR_1g077700 34.568 162 86 3 102 263 44 185 9.56e-16 74.3
MS.gene029746.t1 MTR_4g027440 34.014 147 76 2 118 264 220 345 1.21e-14 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029746.t1 AT5G03510 39.871 311 147 15 3 295 4 292 8.83e-55 179
MS.gene029746.t1 AT5G04390 35.112 356 145 13 19 295 14 362 1.87e-49 168
MS.gene029746.t1 AT2G28200 38.014 292 161 7 11 295 8 286 4.24e-49 165
MS.gene029746.t1 AT3G10470 31.043 393 144 14 19 295 17 398 4.07e-37 136
MS.gene029746.t1 AT2G37430 32.870 216 94 7 68 279 3 171 1.39e-21 89.7
MS.gene029746.t1 AT2G28710 32.701 211 83 8 68 276 3 156 5.76e-21 87.8
MS.gene029746.t1 AT2G45120 32.367 207 90 7 77 276 148 311 6.68e-20 88.2
MS.gene029746.t1 AT3G19580 34.872 195 95 8 76 266 67 233 1.72e-19 86.3
MS.gene029746.t1 AT3G19580 34.872 195 95 8 76 266 67 233 1.72e-19 86.3
MS.gene029746.t1 AT1G02040 35.079 191 112 5 76 265 107 286 8.27e-19 85.5
MS.gene029746.t1 AT3G53600 32.512 203 85 7 68 267 3 156 1.88e-18 81.3
MS.gene029746.t1 AT5G67450 32.039 206 100 7 76 266 60 240 4.08e-18 82.0
MS.gene029746.t1 AT3G60580 30.144 209 94 7 77 277 124 288 2.02e-17 80.9
MS.gene029746.t1 AT3G46080 35.057 174 58 5 70 235 4 130 5.68e-17 77.0
MS.gene029746.t1 AT3G49930 34.694 147 62 4 76 219 56 171 5.72e-16 75.5
MS.gene029746.t1 AT2G17180 29.508 183 80 5 75 241 120 269 2.62e-14 72.0
MS.gene029746.t1 AT1G27730 34.759 187 79 6 76 262 51 194 4.26e-14 70.5
MS.gene029746.t1 AT4G35280 36.054 147 53 4 75 219 137 244 1.56e-13 69.7
MS.gene029746.t1 AT5G56200 37.069 116 63 3 120 235 344 449 9.66e-12 65.5

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTTCTCTAATTCTTCTT+TGG 0.193682 1.2:-47771087 MS.gene029746:CDS
GTAGTAGTAATAGTAGTAAT+AGG 0.197989 1.2:+47771386 None:intergenic
TTCTTTGCTTCATGAGATTT+AGG 0.214536 1.2:+47771209 None:intergenic
TAGTAGTAATAGTAGTAATA+GGG 0.291671 1.2:+47771387 None:intergenic
CATACACAACAAATCATAAA+AGG 0.299770 1.2:-47771893 MS.gene029746:CDS
AATAATAGCAACAACAATTC+TGG 0.306288 1.2:-47771785 MS.gene029746:CDS
ACATTACAATTTGCCTTGTT+AGG 0.331743 1.2:+47771509 None:intergenic
TTCTCATCGGGGCAAGCGTT+AGG 0.342012 1.2:-47771320 MS.gene029746:CDS
CAAAGAGAGTATGGTATTCA+TGG 0.363698 1.2:+47771427 None:intergenic
CGCTTGCCCCGATGAGAATT+CGG 0.366069 1.2:+47771325 None:intergenic
TTCCCTTCATTTCAAGCACT+TGG 0.369504 1.2:-47771557 MS.gene029746:CDS
ACAATTTGCCTTGTTAGGTT+TGG 0.388660 1.2:+47771514 None:intergenic
GTTTCAAATTCTTGCAATGA+AGG 0.402330 1.2:-47771818 MS.gene029746:CDS
TCTCATCGGGGCAAGCGTTA+GGG 0.409631 1.2:-47771319 MS.gene029746:CDS
GAAGGCTTGCAAAGAGAGTA+TGG 0.416171 1.2:+47771418 None:intergenic
TCTAGGCTGAAACGAAAACT+TGG 0.422075 1.2:+47771121 None:intergenic
TTTCTCTAATTCTTCTTTGG+TGG 0.430350 1.2:-47771084 MS.gene029746:CDS
CCTTCATTTCAAGCACTTGG+TGG 0.431156 1.2:-47771554 MS.gene029746:CDS
CCACCAAGTGCTTGAAATGA+AGG 0.452956 1.2:+47771554 None:intergenic
TCCACTTAGGTTAACTATGC+CGG 0.455854 1.2:-47771840 MS.gene029746:CDS
GATTTGTTGTGTATGATCCT+TGG 0.463931 1.2:+47771901 None:intergenic
TGTGGTGCCGAATTCTCATC+GGG 0.470426 1.2:-47771332 MS.gene029746:CDS
ACTCTCTTTGCAAGCCTTCG+CGG 0.480099 1.2:-47771414 MS.gene029746:CDS
TCATTGCAAGAATTTGAAAC+CGG 0.487346 1.2:+47771821 None:intergenic
TCCAACTTAAAACCATTCCT+AGG 0.495975 1.2:+47771185 None:intergenic
GGGGACATATGCGGAGACAT+AGG 0.522526 1.2:-47771298 MS.gene029746:CDS
CTCATCGGGGCAAGCGTTAG+GGG 0.525637 1.2:-47771318 MS.gene029746:CDS
ATGTGGTGCCGAATTCTCAT+CGG 0.538737 1.2:-47771333 MS.gene029746:CDS
AGTAATAGGGGTTGCCGCGA+AGG 0.540108 1.2:+47771400 None:intergenic
AGTAGTAATAGTAGTAATAG+GGG 0.550970 1.2:+47771388 None:intergenic
TGTCTCATTCTATTAGCTCA+AGG 0.553385 1.2:-47771689 MS.gene029746:CDS
GAAAACGAACAAAGCGTCAA+AGG 0.554393 1.2:-47771871 MS.gene029746:CDS
GAGAGTATGGTATTCATGGT+TGG 0.560913 1.2:+47771431 None:intergenic
AAAGGCTACCATCTCCACTT+AGG 0.563673 1.2:-47771853 MS.gene029746:CDS
CTTGGAAGATCAACTCGTGA+TGG 0.581786 1.2:-47771927 MS.gene029746:CDS
AACTTGAGGAACTTTAGTAA+TGG 0.582855 1.2:+47771057 None:intergenic
ATAGTTAACCTAAGTGGAGA+TGG 0.586474 1.2:+47771845 None:intergenic
TCAACTCGTGATGGTTTCCA+AGG 0.587185 1.2:-47771918 MS.gene029746:CDS
ACCGGCATAGTTAACCTAAG+TGG 0.587977 1.2:+47771839 None:intergenic
AAGTCATACCAAACCTAACA+AGG 0.591535 1.2:-47771522 MS.gene029746:CDS
CACCAAGTGCTTGAAATGAA+GGG 0.594958 1.2:+47771555 None:intergenic
TCATCGGGGCAAGCGTTAGG+GGG 0.598586 1.2:-47771317 MS.gene029746:CDS
CTCATGAAGCAAAGAAACCT+AGG 0.601432 1.2:-47771202 MS.gene029746:CDS
GTTCATGAGTGTTCGATATG+TGG 0.609307 1.2:-47771350 MS.gene029746:CDS
GAAGCAAAGAAACCTAGGAA+TGG 0.624910 1.2:-47771197 MS.gene029746:CDS
ACTTCTATGAGTTTGAGTAT+CGG 0.635000 1.2:-47771236 MS.gene029746:CDS
AATAGCAACAACAATTCTGG+AGG 0.652305 1.2:-47771782 MS.gene029746:CDS
GTGGTGCCGAATTCTCATCG+GGG 0.789843 1.2:-47771331 MS.gene029746:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGTAGTAATAGTAGTAATA+GGG + chr1.2:47771621-47771640 None:intergenic 20.0%
! AATAATAGCAACAACAATTC+TGG - chr1.2:47771220-47771239 MS.gene029746:CDS 25.0%
! AGAAAAAGAAGAAGAAGATT+TGG - chr1.2:47771288-47771307 MS.gene029746:CDS 25.0%
! AGTAGTAATAGTAGTAATAG+GGG + chr1.2:47771620-47771639 None:intergenic 25.0%
! CATACACAACAAATCATAAA+AGG - chr1.2:47771112-47771131 MS.gene029746:CDS 25.0%
! GTAGTAGTAATAGTAGTAAT+AGG + chr1.2:47771622-47771641 None:intergenic 25.0%
!! AAAGCAATAACATTTTCTCT+AGG + chr1.2:47771904-47771923 None:intergenic 25.0%
ACTTCTATGAGTTTGAGTAT+CGG - chr1.2:47771769-47771788 MS.gene029746:CDS 30.0%
GTTTCAAATTCTTGCAATGA+AGG - chr1.2:47771187-47771206 MS.gene029746:CDS 30.0%
TGCTTTCTCTAATTCTTCTT+TGG - chr1.2:47771918-47771937 MS.gene029746:CDS 30.0%
TTCTTTGCTTCATGAGATTT+AGG + chr1.2:47771799-47771818 None:intergenic 30.0%
TTTCTCTAATTCTTCTTTGG+TGG - chr1.2:47771921-47771940 MS.gene029746:CDS 30.0%
! ACATTACAATTTGCCTTGTT+AGG + chr1.2:47771499-47771518 None:intergenic 30.0%
! CTTCTTTTTCTTCTTCTGAT+CGG + chr1.2:47771279-47771298 None:intergenic 30.0%
! TCATTGCAAGAATTTGAAAC+CGG + chr1.2:47771187-47771206 None:intergenic 30.0%
! TGATCTTTTTGATCAACTTC+TGG + chr1.2:47771862-47771881 None:intergenic 30.0%
AAGTCATACCAAACCTAACA+AGG - chr1.2:47771483-47771502 MS.gene029746:CDS 35.0%
AATAGCAACAACAATTCTGG+AGG - chr1.2:47771223-47771242 MS.gene029746:CDS 35.0%
ATAGTTAACCTAAGTGGAGA+TGG + chr1.2:47771163-47771182 None:intergenic 35.0%
TCCAACTTAAAACCATTCCT+AGG + chr1.2:47771823-47771842 None:intergenic 35.0%
TGTCTCATTCTATTAGCTCA+AGG - chr1.2:47771316-47771335 MS.gene029746:CDS 35.0%
! ACAATTTGCCTTGTTAGGTT+TGG + chr1.2:47771494-47771513 None:intergenic 35.0%
! CAAAGAGAGTATGGTATTCA+TGG + chr1.2:47771581-47771600 None:intergenic 35.0%
!! GATTTGTTGTGTATGATCCT+TGG + chr1.2:47771107-47771126 None:intergenic 35.0%
!!! ACCTAGGAATGGTTTTAAGT+TGG - chr1.2:47771819-47771838 MS.gene029746:CDS 35.0%
CACCAAGTGCTTGAAATGAA+GGG + chr1.2:47771453-47771472 None:intergenic 40.0%
CTCATGAAGCAAAGAAACCT+AGG - chr1.2:47771803-47771822 MS.gene029746:CDS 40.0%
GAAGCAAAGAAACCTAGGAA+TGG - chr1.2:47771808-47771827 MS.gene029746:CDS 40.0%
GTTCATGAGTGTTCGATATG+TGG - chr1.2:47771655-47771674 MS.gene029746:CDS 40.0%
TCCACTTAGGTTAACTATGC+CGG - chr1.2:47771165-47771184 MS.gene029746:CDS 40.0%
TCTAGGCTGAAACGAAAACT+TGG + chr1.2:47771887-47771906 None:intergenic 40.0%
TTCCCTTCATTTCAAGCACT+TGG - chr1.2:47771448-47771467 MS.gene029746:CDS 40.0%
! GAAAACGAACAAAGCGTCAA+AGG - chr1.2:47771134-47771153 MS.gene029746:CDS 40.0%
! GAGAGTATGGTATTCATGGT+TGG + chr1.2:47771577-47771596 None:intergenic 40.0%
!!! TTTTGATCAACTTCTGGAGC+TGG + chr1.2:47771856-47771875 None:intergenic 40.0%
AAAGGCTACCATCTCCACTT+AGG - chr1.2:47771152-47771171 MS.gene029746:CDS 45.0%
ACCGGCATAGTTAACCTAAG+TGG + chr1.2:47771169-47771188 None:intergenic 45.0%
CCACCAAGTGCTTGAAATGA+AGG + chr1.2:47771454-47771473 None:intergenic 45.0%
CCTTCATTTCAAGCACTTGG+TGG - chr1.2:47771451-47771470 MS.gene029746:CDS 45.0%
CTTGGAAGATCAACTCGTGA+TGG - chr1.2:47771078-47771097 MS.gene029746:CDS 45.0%
GAAGGCTTGCAAAGAGAGTA+TGG + chr1.2:47771590-47771609 None:intergenic 45.0%
TCAACTCGTGATGGTTTCCA+AGG - chr1.2:47771087-47771106 MS.gene029746:CDS 45.0%
! ATGTGGTGCCGAATTCTCAT+CGG - chr1.2:47771672-47771691 MS.gene029746:CDS 45.0%
AAGCGTTAGGGGGACATATG+CGG - chr1.2:47771698-47771717 MS.gene029746:CDS 50.0%
ACTCTCTTTGCAAGCCTTCG+CGG - chr1.2:47771591-47771610 MS.gene029746:CDS 50.0%
! TGTGGTGCCGAATTCTCATC+GGG - chr1.2:47771673-47771692 MS.gene029746:CDS 50.0%
AGTAATAGGGGTTGCCGCGA+AGG + chr1.2:47771608-47771627 None:intergenic 55.0%
CGCTTGCCCCGATGAGAATT+CGG + chr1.2:47771683-47771702 None:intergenic 55.0%
GGGGACATATGCGGAGACAT+AGG - chr1.2:47771707-47771726 MS.gene029746:CDS 55.0%
TCTCATCGGGGCAAGCGTTA+GGG - chr1.2:47771686-47771705 MS.gene029746:CDS 55.0%
TTCTCATCGGGGCAAGCGTT+AGG - chr1.2:47771685-47771704 MS.gene029746:CDS 55.0%
! GTGGTGCCGAATTCTCATCG+GGG - chr1.2:47771674-47771693 MS.gene029746:CDS 55.0%
CTCATCGGGGCAAGCGTTAG+GGG - chr1.2:47771687-47771706 MS.gene029746:CDS 60.0%
TCATCGGGGCAAGCGTTAGG+GGG - chr1.2:47771688-47771707 MS.gene029746:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 47771070 47771957 47771070 ID=MS.gene029746
chr1.2 mRNA 47771070 47771957 47771070 ID=MS.gene029746.t1;Parent=MS.gene029746
chr1.2 exon 47771070 47771957 47771070 ID=MS.gene029746.t1.exon1;Parent=MS.gene029746.t1
chr1.2 CDS 47771070 47771957 47771070 ID=cds.MS.gene029746.t1;Parent=MS.gene029746.t1
Gene Sequence

>MS.gene029746

ATGCAAGTCTTGGAAGATCAACTCGTGATGGTTTCCAAGGATCATACACAACAAATCATAAAAGGAAAACGAACAAAGCGTCAAAGGCTACCATCTCCACTTAGGTTAACTATGCCGGTTTCAAATTCTTGCAATGAAGGTACAAGTTATAATAATAGCAACAACAATTCTGGAGGAATTGAGTTTGTTAAAATTGATTCGCGCGACCGATCAGAAGAAGAAAAAGAAGAAGAAGATTTGGCGAATTGTCTCATTCTATTAGCTCAAGGTCATAATCATCGTCATGATCAAAACACACATGTATCAAATCATCGCGATCACAATAACAACAAATCTTCAAATTTTTATCTTTACGAATGCAAGACTTGCAATCGTTGCTTCCCTTCATTTCAAGCACTTGGTGGACATAGAGCAAGTCATACCAAACCTAACAAGGCAAATTGTAATGTTACACAACAAAAGCAAGCAGTTACAACATCGTCTTTTGTTGATGATCATTATGATCCAACCATGAATACCATACTCTCTTTGCAAGCCTTCGCGGCAACCCCTATTACTACTATTACTACTACAAAAAAATCAAAAGTTCATGAGTGTTCGATATGTGGTGCCGAATTCTCATCGGGGCAAGCGTTAGGGGGACATATGCGGAGACATAGGAATCTTGTGAACACGTCTACAACGACAACAACGACGACAACTTCTATGAGTTTGAGTATCGGTAGTCCTAAATCTCATGAAGCAAAGAAACCTAGGAATGGTTTTAAGTTGGATTTGAATCTTCCAGCTCCAGAAGTTGATCAAAAAGATCAATCCAAGTTTTCGTTTCAGCCTAGAGAAAATGTTATTGCTTTCTCTAATTCTTCTTTGGTGGATTGCCATTACTAA
Protein sequence

>MS.gene029746.t1

MQVLEDQLVMVSKDHTQQIIKGKRTKRQRLPSPLRLTMPVSNSCNEGTSYNNSNNNSGGIEFVKIDSRDRSEEEKEEEDLANCLILLAQGHNHRHDQNTHVSNHRDHNNNKSSNFYLYECKTCNRCFPSFQALGGHRASHTKPNKANCNVTQQKQAVTTSSFVDDHYDPTMNTILSLQAFAATPITTITTTKKSKVHECSICGAEFSSGQALGGHMRRHRNLVNTSTTTTTTTTSMSLSIGSPKSHEAKKPRNGFKLDLNLPAPEVDQKDQSKFSFQPRENVIAFSNSSLVDCHY