AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene036498

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036498.t1 MTR_4g119550 88.542 192 21 1 11 202 202 392 2.63e-123 354
MS.gene036498.t1 MTR_2g437020 58.427 178 68 2 23 200 209 380 4.08e-67 210
MS.gene036498.t1 MTR_2g437240 58.621 174 72 0 27 200 235 408 9.06e-67 211
MS.gene036498.t1 MTR_2g437060 55.114 176 79 0 25 200 220 395 1.26e-66 209
MS.gene036498.t1 MTR_2g436400 57.059 170 73 0 25 194 212 381 3.88e-65 205
MS.gene036498.t1 MTR_2g437080 54.286 175 80 0 26 200 206 380 6.48e-65 205
MS.gene036498.t1 MTR_2g437090 52.381 168 80 0 33 200 1 168 1.30e-63 194
MS.gene036498.t1 MTR_2g437130 55.814 172 76 0 27 198 208 379 1.01e-61 197
MS.gene036498.t1 MTR_2g437200 56.098 164 72 0 27 190 235 398 3.50e-61 196
MS.gene036498.t1 MTR_2g437960 53.448 174 81 0 27 200 223 396 6.36e-61 195
MS.gene036498.t1 MTR_2g437990 51.724 174 84 0 27 200 219 392 6.77e-61 196
MS.gene036498.t1 MTR_2g436440 49.714 175 88 0 25 199 211 385 6.83e-61 194
MS.gene036498.t1 MTR_2g437040 48.571 175 90 0 26 200 206 380 6.97e-61 194
MS.gene036498.t1 MTR_2g437960 53.448 174 81 0 27 200 223 396 9.11e-61 195
MS.gene036498.t1 MTR_2g438020 55.882 170 75 0 27 196 274 443 1.88e-60 196
MS.gene036498.t1 MTR_2g437160 51.724 174 84 0 27 200 141 314 7.14e-60 190
MS.gene036498.t1 MTR_2g076320 51.124 178 87 0 23 200 216 393 1.37e-59 192
MS.gene036498.t1 MTR_2g437940 53.488 172 80 0 27 198 191 362 1.60e-59 191
MS.gene036498.t1 MTR_2g437160 51.724 174 84 0 27 200 232 405 7.48e-59 190
MS.gene036498.t1 MTR_2g437120 52.841 176 82 1 23 198 217 391 1.05e-58 190
MS.gene036498.t1 MTR_2g437180 53.448 174 79 1 27 200 219 390 1.72e-58 189
MS.gene036498.t1 MTR_2g437150 50.265 189 93 1 12 200 213 400 2.48e-58 188
MS.gene036498.t1 MTR_2g437170 50.794 189 92 1 12 200 213 400 3.05e-58 188
MS.gene036498.t1 MTR_2g437030 51.462 171 83 0 30 200 296 466 8.23e-58 189
MS.gene036498.t1 MTR_2g437100 53.073 179 83 1 12 190 218 395 9.27e-58 187
MS.gene036498.t1 MTR_2g438010 50.000 174 87 0 27 200 240 413 1.93e-57 187
MS.gene036498.t1 MTR_2g436460 50.968 155 75 1 40 193 225 379 4.16e-53 174
MS.gene036498.t1 MTR_2g437260 46.584 161 86 0 35 195 211 371 1.47e-51 171
MS.gene036498.t1 MTR_2g019840 45.556 180 90 3 20 199 209 380 7.41e-46 155
MS.gene036498.t1 MTR_2g019810 50.000 154 75 2 37 190 208 359 2.23e-45 154
MS.gene036498.t1 MTR_4g119580 44.149 188 101 2 4 188 184 370 3.91e-44 151
MS.gene036498.t1 MTR_4g120380 37.234 188 114 2 4 188 184 370 1.17e-40 142
MS.gene036498.t1 MTR_4g120380 38.095 168 100 2 4 168 184 350 1.44e-36 132
MS.gene036498.t1 MTR_4g119570 36.257 171 76 1 18 188 92 229 9.27e-33 117
MS.gene036498.t1 MTR_3g450500 35.443 158 102 0 31 188 213 370 4.16e-32 119
MS.gene036498.t1 MTR_4g007490 32.911 158 106 0 31 188 211 368 2.54e-24 98.6
MS.gene036498.t1 MTR_2g436380 37.931 116 63 4 33 147 1 108 3.65e-18 80.5
MS.gene036498.t1 MTR_2g019830 51.852 81 38 1 115 195 125 204 2.40e-17 77.0
MS.gene036498.t1 MTR_3g085240 44.944 89 32 1 92 180 176 247 2.07e-15 72.8
MS.gene036498.t1 MTR_8g080990 27.215 158 115 0 27 184 211 368 1.49e-14 71.6
MS.gene036498.t1 MTR_8g081000 25.949 158 117 0 31 188 228 385 2.63e-13 67.8
MS.gene036498.t1 MTR_8g081000 25.949 158 117 0 31 188 228 385 2.92e-13 67.8
MS.gene036498.t1 MTR_8g081000 25.949 158 117 0 31 188 228 385 2.95e-13 67.8
MS.gene036498.t1 MTR_4g119615 53.061 49 23 0 132 180 26 74 4.53e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036498.t1 AT5G07900 34.437 151 98 1 38 187 249 399 6.93e-31 117
MS.gene036498.t1 AT1G21150 30.519 154 106 1 35 187 197 350 3.19e-20 87.4
MS.gene036498.t1 AT1G21150 30.921 152 104 1 35 185 233 384 4.24e-20 87.4
MS.gene036498.t1 AT1G21150 30.921 152 104 1 35 185 297 448 5.95e-20 87.0
MS.gene036498.t1 AT1G61990 25.128 195 106 3 32 187 215 408 7.08e-13 66.6
MS.gene036498.t1 AT1G61990 25.128 195 106 3 32 187 215 408 7.08e-13 66.6
MS.gene036498.t1 AT5G64950 28.873 142 97 1 42 179 225 366 8.29e-12 63.5
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4
MS.gene036498.t1 AT1G61970 26.286 175 93 3 35 173 225 399 2.09e-11 62.4

Find 41 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGTTAGGTTTGAATTCTT+TGG 0.234752 8.4:-12202817 MS.gene036498:CDS
TATGACAGAGAAGTTGTTTC+TGG 0.244337 8.4:-12202664 MS.gene036498:CDS
TCATTTGTTGAAGCTGTATC+AGG 0.289926 8.4:-12202607 MS.gene036498:CDS
AACACATTCTTCAAGCATTT+AGG 0.305458 8.4:-12202905 MS.gene036498:CDS
TTTGGTAAAAGTACCTTGTT+GGG 0.357862 8.4:+12203371 None:intergenic
CAACCTGTTGGAGACTGTTC+AGG 0.388932 8.4:-12203057 MS.gene036498:CDS
CTTTGGTAAAAGTACCTTGT+TGG 0.403823 8.4:+12203370 None:intergenic
ACCTTACTGTATGTTGTCTT+CGG 0.415933 8.4:-12202877 MS.gene036498:CDS
TTGCAGTTCCTTGTATCTAA+AGG 0.428240 8.4:-12202726 MS.gene036498:CDS
AAATTCGTAATATCATCAAA+AGG 0.437298 8.4:-12203421 MS.gene036498:CDS
AGCGCTTGGGTTGATCAGTT+AGG 0.440546 8.4:-12202831 MS.gene036498:CDS
AACTGCAAAACTGCAGCCCT+TGG 0.446416 8.4:+12202741 None:intergenic
TTTGGATCTTGTTAATGCTC+CGG 0.453825 8.4:-12202799 MS.gene036498:CDS
TTTATTGAGACTCGAGAAAC+GGG 0.454508 8.4:-12202769 MS.gene036498:CDS
ATTCCTGAACAGTCTCCAAC+AGG 0.475079 8.4:+12203054 None:intergenic
TTGGATCTTGTTAATGCTCC+GGG 0.475407 8.4:-12202798 MS.gene036498:CDS
TTCTCAAACCTTTAGATACA+AGG 0.476085 8.4:+12202718 None:intergenic
AACTTCTCTGTCATAGCAAA+CGG 0.496374 8.4:+12202672 None:intergenic
AAAGTACCTTGTTGGGGTCG+AGG 0.506736 8.4:+12203378 None:intergenic
AATTCGTAATATCATCAAAA+GGG 0.515448 8.4:-12203420 MS.gene036498:CDS
ATATTGTTCATCCAACCTGT+TGG 0.532063 8.4:-12203069 MS.gene036498:CDS
GATATTACGAATTTGAGTGT+TGG 0.541490 8.4:+12203430 None:intergenic
ACATTCTTCAAGCATTTAGG+AGG 0.543592 8.4:-12202902 MS.gene036498:CDS
TCGAGAAACGGGTTATTCCA+AGG 0.551680 8.4:-12202758 MS.gene036498:CDS
AATGAATCTTGCAAATAGCA+TGG 0.553137 8.4:-12202580 MS.gene036498:CDS
GTTCAGGAATTGAAGCAACT+AGG 0.561440 8.4:-12203041 MS.gene036498:CDS
AGAAGTTACACACTTCATGA+AGG 0.561506 8.4:+12202549 None:intergenic
TGATACAGCTTCAACAAATG+AGG 0.568471 8.4:+12202609 None:intergenic
AGAAAACTGTGAATGAAACT+AGG 0.580330 8.4:-12202974 MS.gene036498:CDS
CTGAACAGTCTCCAACAGGT+TGG 0.584404 8.4:+12203058 None:intergenic
GCCGAAGACAACATACAGTA+AGG 0.592002 8.4:+12202876 None:intergenic
TTTGAGTGTTGGAGAAGCCA+TGG 0.596210 8.4:+12203441 None:intergenic
AGCAAACGGTGCACTTAGTG+AGG 0.600976 8.4:+12202686 None:intergenic
AACTGTGAATGAAACTAGGT+GGG 0.613433 8.4:-12202970 MS.gene036498:CDS
CGAGAAACGGGTTATTCCAA+GGG 0.615093 8.4:-12202757 MS.gene036498:CDS
TTGAGTGTTGGAGAAGCCAT+GGG 0.633074 8.4:+12203442 None:intergenic
CTTATGCCTCGACCCCAACA+AGG 0.635453 8.4:-12203384 MS.gene036498:intron
AAACTGTGAATGAAACTAGG+TGG 0.639268 8.4:-12202971 MS.gene036498:CDS
ATATCATCAAAAGGGAACCT+CGG 0.640196 8.4:-12203412 MS.gene036498:CDS
TTGGTAAAAGTACCTTGTTG+GGG 0.646951 8.4:+12203372 None:intergenic
TCGAGGCATAAGAGTAACCG+AGG 0.694428 8.4:+12203395 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAACGATTAATACATTTAA+TGG + chr8.4:12202806-12202825 None:intergenic 15.0%
!!! AAGTTGAAATTTTTAAGAAA+TGG - chr8.4:12203061-12203080 MS.gene036498:CDS 15.0%
!!! AGTTGAAATTTTTAAGAAAT+GGG - chr8.4:12203062-12203081 MS.gene036498:CDS 15.0%
!! AAATTCGTAATATCATCAAA+AGG - chr8.4:12202581-12202600 MS.gene036498:CDS 20.0%
!! AATTCGTAATATCATCAAAA+GGG - chr8.4:12202582-12202601 MS.gene036498:CDS 20.0%
!! GAAAGTAAAAATTGAAACTT+TGG + chr8.4:12202652-12202671 None:intergenic 20.0%
!!! CAAATTTGTGAAATGTTTTA+AGG - chr8.4:12203362-12203381 MS.gene036498:intron 20.0%
!!! GTTGAAATTTTTAAGAAATG+GGG - chr8.4:12203063-12203082 MS.gene036498:CDS 20.0%
!!! TTTCAATTTTTACTTTCCAA+AGG - chr8.4:12202655-12202674 MS.gene036498:CDS 20.0%
! CTCTCATAAAATGATAAGTA+GGG + chr8.4:12202759-12202778 None:intergenic 25.0%
! GTCAAATTATTGCTTGATAA+TGG - chr8.4:12202862-12202881 MS.gene036498:CDS 25.0%
!! CTACTTATCATTTTATGAGA+GGG - chr8.4:12202758-12202777 MS.gene036498:CDS 25.0%
!!! AAATTTTTAAGAAATGGGGT+TGG - chr8.4:12203067-12203086 MS.gene036498:CDS 25.0%
!!! ATTTGTGAAATGTTTTAAGG+AGG - chr8.4:12203365-12203384 MS.gene036498:intron 25.0%
AAACTTCTTAAGAGGAATCT+AGG + chr8.4:12202721-12202740 None:intergenic 30.0%
AACACATTCTTCAAGCATTT+AGG - chr8.4:12203097-12203116 MS.gene036498:intron 30.0%
AACTTCTTAAGAGGAATCTA+GGG + chr8.4:12202720-12202739 None:intergenic 30.0%
AATGAATCTTGCAAATAGCA+TGG - chr8.4:12203422-12203441 MS.gene036498:CDS 30.0%
AGAAAACTGTGAATGAAACT+AGG - chr8.4:12203028-12203047 MS.gene036498:CDS 30.0%
AGTCTCAATAAAAAGATTCC+CGG + chr8.4:12203225-12203244 None:intergenic 30.0%
ATAAGTAGGGATGATATGAT+TGG + chr8.4:12202746-12202765 None:intergenic 30.0%
CCTCTCATAAAATGATAAGT+AGG + chr8.4:12202760-12202779 None:intergenic 30.0%
GATATTACGAATTTGAGTGT+TGG + chr8.4:12202575-12202594 None:intergenic 30.0%
TAAGTAGGGATGATATGATT+GGG + chr8.4:12202745-12202764 None:intergenic 30.0%
TCAGTTAGGTTTGAATTCTT+TGG - chr8.4:12203185-12203204 MS.gene036498:intron 30.0%
TTCTCAAACCTTTAGATACA+AGG + chr8.4:12203287-12203306 None:intergenic 30.0%
TTGGATGAACAATATATCCT+AGG + chr8.4:12202928-12202947 None:intergenic 30.0%
! CCTACTTATCATTTTATGAG+AGG - chr8.4:12202757-12202776 MS.gene036498:CDS 30.0%
! TTTTATTGAGACTCGAGAAA+CGG - chr8.4:12203232-12203251 MS.gene036498:intron 30.0%
!! TTTGGTAAAAGTACCTTGTT+GGG + chr8.4:12202634-12202653 None:intergenic 30.0%
AAACTGTGAATGAAACTAGG+TGG - chr8.4:12203031-12203050 MS.gene036498:CDS 35.0%
AACTGTGAATGAAACTAGGT+GGG - chr8.4:12203032-12203051 MS.gene036498:CDS 35.0%
AACTTCTCTGTCATAGCAAA+CGG + chr8.4:12203333-12203352 None:intergenic 35.0%
ACATTCTTCAAGCATTTAGG+AGG - chr8.4:12203100-12203119 MS.gene036498:intron 35.0%
ACCTTACTGTATGTTGTCTT+CGG - chr8.4:12203125-12203144 MS.gene036498:intron 35.0%
ATATCATCAAAAGGGAACCT+CGG - chr8.4:12202590-12202609 MS.gene036498:CDS 35.0%
ATATTGTTCATCCAACCTGT+TGG - chr8.4:12202933-12202952 MS.gene036498:CDS 35.0%
TGATACAGCTTCAACAAATG+AGG + chr8.4:12203396-12203415 None:intergenic 35.0%
TGTAGCAATATTTGAGTGTG+TGG + chr8.4:12202890-12202909 None:intergenic 35.0%
TTGCAGTTCCTTGTATCTAA+AGG - chr8.4:12203276-12203295 MS.gene036498:intron 35.0%
TTTATTGAGACTCGAGAAAC+GGG - chr8.4:12203233-12203252 MS.gene036498:intron 35.0%
TTTGGATCTTGTTAATGCTC+CGG - chr8.4:12203203-12203222 MS.gene036498:intron 35.0%
! TATGACAGAGAAGTTGTTTC+TGG - chr8.4:12203338-12203357 MS.gene036498:intron 35.0%
! TCATTTGTTGAAGCTGTATC+AGG - chr8.4:12203395-12203414 MS.gene036498:CDS 35.0%
!! CTTTGGTAAAAGTACCTTGT+TGG + chr8.4:12202635-12202654 None:intergenic 35.0%
!! TTGGTAAAAGTACCTTGTTG+GGG + chr8.4:12202633-12202652 None:intergenic 35.0%
!! TTTTAAGAAATGGGGTTGGT+CGG - chr8.4:12203071-12203090 MS.gene036498:CDS 35.0%
!!! TTCAACTTTTGCTGTTGCAT+TGG - chr8.4:12202999-12203018 MS.gene036498:CDS 35.0%
GATTGGGCAAACTTCTTAAG+AGG + chr8.4:12202729-12202748 None:intergenic 40.0%
GTTCAGGAATTGAAGCAACT+AGG - chr8.4:12202961-12202980 MS.gene036498:CDS 40.0%
TTGGATCTTGTTAATGCTCC+GGG - chr8.4:12203204-12203223 MS.gene036498:intron 40.0%
!! ATCAGAAGTAGAAGCACCTT+TGG + chr8.4:12202674-12202693 None:intergenic 40.0%
ATTCCTGAACAGTCTCCAAC+AGG + chr8.4:12202951-12202970 None:intergenic 45.0%
CATTGTTGCGTAATTCGCCT+AGG - chr8.4:12202908-12202927 MS.gene036498:CDS 45.0%
GCCGAAGACAACATACAGTA+AGG + chr8.4:12203129-12203148 None:intergenic 45.0%
!! CGAGAAACGGGTTATTCCAA+GGG - chr8.4:12203245-12203264 MS.gene036498:intron 45.0%
!! TCGAGAAACGGGTTATTCCA+AGG - chr8.4:12203244-12203263 MS.gene036498:intron 45.0%
AACTGCAAAACTGCAGCCCT+TGG + chr8.4:12203264-12203283 None:intergenic 50.0%
AGCAAACGGTGCACTTAGTG+AGG + chr8.4:12203319-12203338 None:intergenic 50.0%
CAACCTGTTGGAGACTGTTC+AGG - chr8.4:12202945-12202964 MS.gene036498:CDS 50.0%
CTGAACAGTCTCCAACAGGT+TGG + chr8.4:12202947-12202966 None:intergenic 50.0%
TCGAGGCATAAGAGTAACCG+AGG + chr8.4:12202610-12202629 None:intergenic 50.0%
! AAAGTACCTTGTTGGGGTCG+AGG + chr8.4:12202627-12202646 None:intergenic 50.0%
!! AGCGCTTGGGTTGATCAGTT+AGG - chr8.4:12203171-12203190 MS.gene036498:intron 50.0%
!!! CGATGCAGTTTTGAGCGCTT+GGG - chr8.4:12203158-12203177 MS.gene036498:intron 50.0%
!!! TCGATGCAGTTTTGAGCGCT+TGG - chr8.4:12203157-12203176 MS.gene036498:intron 50.0%
CTTATGCCTCGACCCCAACA+AGG - chr8.4:12202618-12202637 MS.gene036498:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 12202563 12203461 12202563 ID=MS.gene036498
chr8.4 mRNA 12202563 12203461 12202563 ID=MS.gene036498.t1;Parent=MS.gene036498
chr8.4 exon 12203385 12203461 12203385 ID=MS.gene036498.t1.exon1;Parent=MS.gene036498.t1
chr8.4 CDS 12203385 12203461 12203385 ID=cds.MS.gene036498.t1;Parent=MS.gene036498.t1
chr8.4 exon 12202563 12203094 12202563 ID=MS.gene036498.t1.exon2;Parent=MS.gene036498.t1
chr8.4 CDS 12202563 12203094 12202563 ID=cds.MS.gene036498.t1;Parent=MS.gene036498.t1
Gene Sequence

>MS.gene036498

ATGGCTTCTCCAACACTCAAATTCGTAATATCATCAAAAGGGAACCTCGGTTACTCTTATGCCTCGACCCCAACAAGGTACTTTTACCAAAGTTTCAATTTTTACTTTCCAAAGGTGCTTCTACTTCTGATATTGTTCGCATTGTAAATGCTAACCCTAGATTCCTCTTAAGAAGTTTGCCCAATCATATCATCCCTACTTATCATTTTATGAGAGGGTTTCTTAAATCTGATAAACAAACCATTAAATGTATTAATCGTTATGCTTCTTTTATCTCTGATTCTCGTGTCGAAAGTAATGTCAAATTATTGCTTGATAATGGAGCCACACACTCAAATATTGCTACATTGTTGCGTAATTCGCCTAGGATATATTGTTCATCCAACCTGTTGGAGACTGTTCAGGAATTGAAGCAACTAGGTTTCAATTCTTCAACTTCAACTTTTGCTGTTGCATTGGTTGCTAAGAAAACTGTGAATGAAACTAGGTGGGCTGAGAAAGTTGAAATTTTTAAGAAATGGGGTTGGTCGGATGAACACATTCTTCAAGCATTTAGGAGGCAACCTTACTGTATGTTGTCTTCGGCTCAAAAAATCGATGCAGTTTTGAGCGCTTGGGTTGATCAGTTAGGTTTGAATTCTTTGGATCTTGTTAATGCTCCGGGAATCTTTTTATTGAGACTCGAGAAACGGGTTATTCCAAGGGCTGCAGTTTTGCAGTTCCTTGTATCTAAAGGTTTGAGAAGAAAGAACGCCTCACTAAGTGCACCGTTTGCTATGACAGAGAAGTTGTTTCTGGACAAATTTGTGAAATGTTTTAAGGAGGATTCTCCTCATTTGTTGAAGCTGTATCAGGAAAAAATGAATCTTGCAAATAGCATGGAGAAGAGTCCTTCATGA
Protein sequence

>MS.gene036498.t1

MASPTLKFVISSKGNLGYSYASTPTRIYCSSNLLETVQELKQLGFNSSTSTFAVALVAKKTVNETRWAEKVEIFKKWGWSDEHILQAFRRQPYCMLSSAQKIDAVLSAWVDQLGLNSLDLVNAPGIFLLRLEKRVIPRAAVLQFLVSKGLRRKNASLSAPFAMTEKLFLDKFVKCFKEDSPHLLKLYQEKMNLANSMEKSPS