AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96758

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96758.t1 MTR_1g082480 94.100 339 12 4 1 333 1 337 0.0 616
MS.gene96758.t1 MTR_1g082480 94.175 309 10 4 1 303 1 307 0.0 588
MS.gene96758.t1 MTR_7g113830 57.184 348 99 11 1 333 1 313 2.25e-123 357
MS.gene96758.t1 MTR_3g099620 50.606 330 134 7 14 329 1 315 2.51e-101 301
MS.gene96758.t1 MTR_5g064950 44.237 321 150 7 14 330 1 296 2.24e-81 249
MS.gene96758.t1 MTR_8g066770 54.245 212 86 2 126 332 104 309 6.12e-75 233
MS.gene96758.t1 MTR_5g064950 43.878 294 136 7 14 303 1 269 3.03e-71 224
MS.gene96758.t1 MTR_0194s0050 48.198 222 96 5 118 326 166 381 1.46e-58 193
MS.gene96758.t1 MTR_8g024210 51.244 201 88 2 126 326 171 361 4.63e-58 191
MS.gene96758.t1 MTR_1g028470 33.564 289 143 8 54 321 30 290 1.26e-36 134
MS.gene96758.t1 MTR_2g022280 40.860 186 107 2 136 321 1 183 8.78e-35 126
MS.gene96758.t1 MTR_3g090850 33.730 252 119 6 117 321 76 326 2.35e-34 128
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96758.t1 AT1G72210 46.491 342 133 9 14 330 1 317 2.22e-82 253
MS.gene96758.t1 AT1G22490 44.248 339 132 11 14 330 1 304 2.66e-79 244
MS.gene96758.t1 AT1G72210 46.984 315 117 10 14 303 1 290 7.86e-73 228
MS.gene96758.t1 AT1G22490 43.910 312 118 11 14 303 1 277 7.62e-68 216
MS.gene96758.t1 AT3G24140 44.000 225 111 3 115 327 176 397 1.46e-54 183
MS.gene96758.t1 AT3G24140 44.000 225 111 3 115 327 176 397 1.83e-54 184
MS.gene96758.t1 AT4G01460 44.076 211 106 2 126 331 105 308 1.73e-53 178
MS.gene96758.t1 AT4G01460 44.076 211 106 2 126 331 105 308 1.73e-53 178
MS.gene96758.t1 AT5G46690 45.022 231 94 4 126 329 78 302 6.35e-52 174
MS.gene96758.t1 AT5G65320 44.550 211 107 4 124 329 90 295 1.69e-49 167
MS.gene96758.t1 AT3G61950 45.960 198 93 3 126 322 117 301 4.85e-48 164
MS.gene96758.t1 AT3G61950 45.500 200 95 3 126 324 168 354 1.13e-47 164
MS.gene96758.t1 AT2G46810 46.535 202 89 5 127 324 112 298 1.81e-47 162
MS.gene96758.t1 AT2G46810 46.535 202 89 5 127 324 172 358 6.29e-47 162
MS.gene96758.t1 AT2G46810 46.535 202 89 5 127 324 184 370 6.43e-47 162
MS.gene96758.t1 AT5G65320 45.652 184 91 3 124 303 90 268 1.63e-42 149
MS.gene96758.t1 AT3G61950 47.273 165 74 2 126 290 117 268 7.81e-42 147
MS.gene96758.t1 AT2G46810 41.304 230 88 6 127 324 112 326 7.89e-42 148
MS.gene96758.t1 AT3G61950 47.273 165 74 2 126 290 168 319 2.49e-41 147
MS.gene96758.t1 AT5G46690 43.902 205 82 4 126 303 78 276 1.99e-40 143
MS.gene96758.t1 AT3G06120 37.766 188 94 2 136 309 1 179 7.18e-33 121
MS.gene96758.t1 AT5G53210 58.462 65 27 0 134 198 100 164 2.08e-20 91.3
MS.gene96758.t1 AT5G53210 58.462 65 27 0 134 198 100 164 2.11e-20 90.9
MS.gene96758.t1 AT3G61950 73.810 42 11 0 126 167 168 209 2.16e-13 68.9
MS.gene96758.t1 AT3G61950 73.810 42 11 0 126 167 168 209 2.16e-13 68.9
MS.gene96758.t1 AT1G32640 26.531 196 110 7 116 303 435 604 3.15e-11 64.7

Find 44 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTTGATTCCATAACTAAA+AGG 0.292800 1.1:+61035416 None:intergenic
GGTGATCAAGCTTCTATAAT+TGG 0.293785 1.1:-61034708 MS.gene96758:CDS
ACTCTATCTCTTTCCTCTTC+AGG 0.299868 1.1:+61035485 None:intergenic
CAGCTCTTGAAAATGGTATC+TGG 0.309667 1.1:-61034408 MS.gene96758:CDS
AATGAAAAGAATTCAGAAAA+TGG 0.318161 1.1:+61034579 None:intergenic
GCCAAAACAGCTCTTGAAAA+TGG 0.324313 1.1:-61034415 MS.gene96758:CDS
TCTAATTCTGCAGCTACTAT+TGG 0.326308 1.1:-61034531 MS.gene96758:CDS
ATTGTCCTCCTTATGTAGAT+TGG 0.357399 1.1:-61035304 MS.gene96758:CDS
TTTCTTGAACTTCATTCAAA+TGG 0.360903 1.1:+61035252 None:intergenic
CTAAAAGGATCTTGTGTTTG+TGG 0.365756 1.1:+61035431 None:intergenic
TTCTTGAACTTCATTCAAAT+GGG 0.379399 1.1:+61035253 None:intergenic
GTTGAAGATGATTGCAAGTT+GGG 0.381610 1.1:-61034194 MS.gene96758:CDS
TCTTTACTCTCTCAGTGTTA+AGG 0.389543 1.1:-61034325 MS.gene96758:intron
GTTGAATCCTATTGACCATC+TGG 0.393376 1.1:+61034141 None:intergenic
CTGTATACCAGATGGTCAAT+AGG 0.406963 1.1:-61034148 MS.gene96758:CDS
CATTTGAATGTTACTACTAC+TGG 0.419836 1.1:-61034357 MS.gene96758:CDS
ACCCTTTGGATGTAAGAATC+TGG 0.440881 1.1:+61035014 None:intergenic
TTGTTATTCCAATCTACATA+AGG 0.465642 1.1:+61035296 None:intergenic
TTAAAATAAGATCAAGAAAG+AGG 0.490885 1.1:-61034437 MS.gene96758:CDS
TGCCAGATTCTTACATCCAA+AGG 0.505226 1.1:-61035016 MS.gene96758:CDS
GGTTGAAGATGATTGCAAGT+TGG 0.515979 1.1:-61034195 MS.gene96758:CDS
GCCAGATTCTTACATCCAAA+GGG 0.516817 1.1:-61035015 MS.gene96758:intron
TTAGTAATAGTATTACTACT+TGG 0.517777 1.1:+61035218 None:intergenic
TGTTATGTGTTTACCTGAAG+AGG 0.521964 1.1:-61035498 None:intergenic
ACACAGTTATTCGACCGAAA+AGG 0.549875 1.1:-61035160 MS.gene96758:CDS
GATCAAGCTTCTATAATTGG+AGG 0.557225 1.1:-61034705 MS.gene96758:CDS
TGAACTTCATTCAAATGGGG+TGG 0.566537 1.1:+61035257 None:intergenic
ATTACTACTTGGATCAGTAG+TGG 0.576946 1.1:+61035229 None:intergenic
TGATTGCAAGTTGGGATCAG+TGG 0.579380 1.1:-61034186 MS.gene96758:CDS
TTATCACTTGTTGAATACTG+TGG 0.584055 1.1:+61034555 None:intergenic
GGTCAATAGGATTCAACAAG+AGG 0.595940 1.1:-61034135 MS.gene96758:CDS
AGCTTCAGCTGTATACCAGA+TGG 0.597796 1.1:-61034156 MS.gene96758:CDS
CATTCAAATGCAAGATTGTG+AGG 0.599658 1.1:+61034370 None:intergenic
TCGAATAACTGTGTTCACAG+AGG 0.602322 1.1:+61035169 None:intergenic
CGAATAACTGTGTTCACAGA+GGG 0.602536 1.1:+61035170 None:intergenic
TATGTAGATTGGAATAACAA+TGG 0.602597 1.1:-61035293 MS.gene96758:CDS
TTATTCCAATCTACATAAGG+AGG 0.614549 1.1:+61035299 None:intergenic
TCTTGAACTTCATTCAAATG+GGG 0.614700 1.1:+61035254 None:intergenic
AGACATGGCACTAGAAGCAG+TGG 0.632855 1.1:-61035459 MS.gene96758:CDS
AAGAGATAGAGTGAAAGACA+TGG 0.656321 1.1:-61035474 MS.gene96758:CDS
GTGAAATCTGATGAAGCTGG+TGG 0.684533 1.1:-61034615 MS.gene96758:CDS
TGCTGACATAGAAGTGACAA+TGG 0.687267 1.1:-61034478 MS.gene96758:CDS
GAAGTGAAATCTGATGAAGC+TGG 0.693568 1.1:-61034618 MS.gene96758:CDS
TGACATAGAAGTGACAATGG+TGG 0.780182 1.1:-61034475 MS.gene96758:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAAAGAATTCAGAAAA+TGG + chr1.1:61035039-61035058 None:intergenic 20.0%
!! TTAAAATAAGATCAAGAAAG+AGG - chr1.1:61035178-61035197 MS.gene96758:CDS 20.0%
!! TTAGTAATAGTATTACTACT+TGG + chr1.1:61034400-61034419 None:intergenic 20.0%
!!! AGATTTCTTTGAACAATTTT+TGG - chr1.1:61035353-61035372 MS.gene96758:CDS 20.0%
!!! ATCTTATTTTAAGATTTGCA+TGG + chr1.1:61035170-61035189 None:intergenic 20.0%
!!! GCATTGAATTTTTTTTAATC+AGG - chr1.1:61035399-61035418 MS.gene96758:CDS 20.0%
! TATGTAGATTGGAATAACAA+TGG - chr1.1:61034322-61034341 MS.gene96758:intron 25.0%
! TCTTTGATTCCATAACTAAA+AGG + chr1.1:61034202-61034221 None:intergenic 25.0%
! TTCTTGAACTTCATTCAAAT+GGG + chr1.1:61034365-61034384 None:intergenic 25.0%
! TTTCTTGAACTTCATTCAAA+TGG + chr1.1:61034366-61034385 None:intergenic 25.0%
!! TTGTTATTCCAATCTACATA+AGG + chr1.1:61034322-61034341 None:intergenic 25.0%
!!! TGTGTTTGTTTTTTTGTTGT+TGG - chr1.1:61034875-61034894 MS.gene96758:intron 25.0%
CATTTGAATGTTACTACTAC+TGG - chr1.1:61035258-61035277 MS.gene96758:CDS 30.0%
TCTTGAACTTCATTCAAATG+GGG + chr1.1:61034364-61034383 None:intergenic 30.0%
TTATTCCAATCTACATAAGG+AGG + chr1.1:61034319-61034338 None:intergenic 30.0%
! GAGGACAATTATTTTCTGTT+TGG + chr1.1:61034300-61034319 None:intergenic 30.0%
! TTATCACTTGTTGAATACTG+TGG + chr1.1:61035063-61035082 None:intergenic 30.0%
!! ACACAAGATCCTTTTAGTTA+TGG - chr1.1:61034190-61034209 MS.gene96758:CDS 30.0%
AACATGCAGTTACATGTTCT+TGG - chr1.1:61034774-61034793 MS.gene96758:intron 35.0%
AAGAGATAGAGTGAAAGACA+TGG - chr1.1:61034141-61034160 MS.gene96758:CDS 35.0%
ATTACTACTTGGATCAGTAG+TGG + chr1.1:61034389-61034408 None:intergenic 35.0%
ATTGTCCTCCTTATGTAGAT+TGG - chr1.1:61034311-61034330 MS.gene96758:intron 35.0%
CAGTGAGTTTAGTAGAATCA+CGG - chr1.1:61034669-61034688 MS.gene96758:CDS 35.0%
CATTCAAATGCAAGATTGTG+AGG + chr1.1:61035248-61035267 None:intergenic 35.0%
CTAAAAGGATCTTGTGTTTG+TGG + chr1.1:61034187-61034206 None:intergenic 35.0%
GATCAAGCTTCTATAATTGG+AGG - chr1.1:61034910-61034929 MS.gene96758:intron 35.0%
GCTACTATTGGTGAAAAAGT+TGG - chr1.1:61035096-61035115 MS.gene96758:CDS 35.0%
GGTGATCAAGCTTCTATAAT+TGG - chr1.1:61034907-61034926 MS.gene96758:intron 35.0%
GTTGAAGATGATTGCAAGTT+GGG - chr1.1:61035421-61035440 MS.gene96758:CDS 35.0%
TCTAATTCTGCAGCTACTAT+TGG - chr1.1:61035084-61035103 MS.gene96758:CDS 35.0%
TCTTTACTCTCTCAGTGTTA+AGG - chr1.1:61035290-61035309 MS.gene96758:CDS 35.0%
TGTAAGTAGTAAGTACCCTT+TGG + chr1.1:61034618-61034637 None:intergenic 35.0%
! AGCTCTGGTAATCTAAAGTT+CGG + chr1.1:61034810-61034829 None:intergenic 35.0%
! GAGCACAAGTTTCATTTTCT+TGG - chr1.1:61034958-61034977 MS.gene96758:intron 35.0%
!! ACCATTTTCAAGAGCTGTTT+TGG + chr1.1:61035204-61035223 None:intergenic 35.0%
!!! TTTTGTTGTTGGTGAATGCA+GGG - chr1.1:61034886-61034905 MS.gene96758:intron 35.0%
!!! TTTTTGTTGTTGGTGAATGC+AGG - chr1.1:61034885-61034904 MS.gene96758:intron 35.0%
ACACAGTTATTCGACCGAAA+AGG - chr1.1:61034455-61034474 MS.gene96758:CDS 40.0%
ACCCTTTGGATGTAAGAATC+TGG + chr1.1:61034604-61034623 None:intergenic 40.0%
ACTCTATCTCTTTCCTCTTC+AGG + chr1.1:61034133-61034152 None:intergenic 40.0%
CAGCTCTTGAAAATGGTATC+TGG - chr1.1:61035207-61035226 MS.gene96758:CDS 40.0%
CGAATAACTGTGTTCACAGA+GGG + chr1.1:61034448-61034467 None:intergenic 40.0%
CTGTATACCAGATGGTCAAT+AGG - chr1.1:61035467-61035486 MS.gene96758:CDS 40.0%
GAAGTGAAATCTGATGAAGC+TGG - chr1.1:61034997-61035016 MS.gene96758:intron 40.0%
GCCAAAACAGCTCTTGAAAA+TGG - chr1.1:61035200-61035219 MS.gene96758:CDS 40.0%
GCCAGATTCTTACATCCAAA+GGG - chr1.1:61034600-61034619 MS.gene96758:CDS 40.0%
GGTCAATAGGATTCAACAAG+AGG - chr1.1:61035480-61035499 MS.gene96758:CDS 40.0%
GGTTGAAGATGATTGCAAGT+TGG - chr1.1:61035420-61035439 MS.gene96758:CDS 40.0%
GTTGAATCCTATTGACCATC+TGG + chr1.1:61035477-61035496 None:intergenic 40.0%
TCGAATAACTGTGTTCACAG+AGG + chr1.1:61034449-61034468 None:intergenic 40.0%
TGAACTTCATTCAAATGGGG+TGG + chr1.1:61034361-61034380 None:intergenic 40.0%
TGACATAGAAGTGACAATGG+TGG - chr1.1:61035140-61035159 MS.gene96758:CDS 40.0%
TGCCAGATTCTTACATCCAA+AGG - chr1.1:61034599-61034618 MS.gene96758:CDS 40.0%
TGCTGACATAGAAGTGACAA+TGG - chr1.1:61035137-61035156 MS.gene96758:CDS 40.0%
! CCCTCTAGTTTCTAGAAGAA+GGG + chr1.1:61034833-61034852 None:intergenic 40.0%
! CCCTTCTTCTAGAAACTAGA+GGG - chr1.1:61034830-61034849 MS.gene96758:intron 40.0%
! TCCCTTCTTCTAGAAACTAG+AGG - chr1.1:61034829-61034848 MS.gene96758:intron 40.0%
AGCTTCAGCTGTATACCAGA+TGG - chr1.1:61035459-61035478 MS.gene96758:CDS 45.0%
CAAATGGGGTGGTGAAAAAG+TGG + chr1.1:61034350-61034369 None:intergenic 45.0%
GTGAAATCTGATGAAGCTGG+TGG - chr1.1:61035000-61035019 MS.gene96758:intron 45.0%
! GCCCTCTAGTTTCTAGAAGA+AGG + chr1.1:61034834-61034853 None:intergenic 45.0%
! TGATTGCAAGTTGGGATCAG+TGG - chr1.1:61035429-61035448 MS.gene96758:CDS 45.0%
! TTTCTAGAAGAAGGGAGCTC+TGG + chr1.1:61034825-61034844 None:intergenic 45.0%
AGACATGGCACTAGAAGCAG+TGG - chr1.1:61034156-61034175 MS.gene96758:CDS 50.0%
!!! CTTCTAGCTCTGCGCCTTTT+CGG + chr1.1:61034472-61034491 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 61034121 61035516 61034121 ID=MS.gene96758
chr1.1 mRNA 61034121 61035516 61034121 ID=MS.gene96758.t1;Parent=MS.gene96758
chr1.1 exon 61035016 61035516 61035016 ID=MS.gene96758.t1.exon1;Parent=MS.gene96758.t1
chr1.1 CDS 61035016 61035516 61035016 ID=cds.MS.gene96758.t1;Parent=MS.gene96758.t1
chr1.1 exon 61034326 61034730 61034326 ID=MS.gene96758.t1.exon2;Parent=MS.gene96758.t1
chr1.1 CDS 61034326 61034730 61034326 ID=cds.MS.gene96758.t1;Parent=MS.gene96758.t1
chr1.1 exon 61034121 61034216 61034121 ID=MS.gene96758.t1.exon3;Parent=MS.gene96758.t1
chr1.1 CDS 61034121 61034216 61034121 ID=cds.MS.gene96758.t1;Parent=MS.gene96758.t1
Gene Sequence

>MS.gene96758

ATGTGTTTACCTGAAGAGGAAAGAGATAGAGTGAAAGACATGGCACTAGAAGCAGTGGTTTATCCACAAACACAAGATCCTTTTAGTTATGGAATCAAAGATTTTTACAACTTCAACTTCAACACTTTTGTTGCAAAAGAACAACAAGAACAGAGATCTTTCAGTTTTGTAGAAAACCAAACAGAAAATAATTGTCCTCCTTATGTAGATTGGAATAACAATGGTTCCACTTTTTCACCACCCCATTTGAATGAAGTTCAAGAAACCACTACTGATCCAAGTAGTAATACTATTACTAATAACACTCAAAACTTTCATGCTTCACCCTCTGTGAACACAGTTATTCGACCGAAAAGGCGCAGAGCTAGAAGCAGAAAAAACAAAGAAGAAATTGAGAATCAGAGAATGACTCACATTGCTGTTGAGCGTAATAGAAGAAAGCAGATGAATGAGTATCTTTCTATTCTTCGCTCTCTAATGCCAGATTCTTACATCCAAAGGGTACTTACTACTTACATAACATCACTTAGAATATATGTTTAGATTAACAGTGAGTTTAGTAGAATCACGGTGTGTCACTTTGATTTTAACATAAACTTCACTTTAGAGTTTTAAAAAAATCACTGTGATTTCGTCAAACTCATCGTGATTATAACATGCAGTTACATGTTCTTGGTACTCACATGCCGAACTTTAGATTACCAGAGCTCCCTTCTTCTAGAAACTAGAGGGCTAAGACAAACAAAAAACTGAGTGTGTTTGTTTTTTTGTTGTTGGTGAATGCAGGGTGATCAAGCTTCTATAATTGGAGGTGCTATTAACTTTGTTAAAGAGCTTGAGCACAAGTTTCATTTTCTTGGTACTAAGAAAGAAAGAGAAGTGAAATCTGATGAAGCTGGTGGATCAAACAACATGCCATTTTCTGAATTCTTTTCATTTCCACAGTATTCAACAAGTGATAATTCTAATTCTGCAGCTACTATTGGTGAAAAAGTTGGTGAGATTCAATCTTGCATTGCTGACATAGAAGTGACAATGGTGGAAAACCATGCAAATCTTAAAATAAGATCAAGAAAGAGGCCAAAACAGCTCTTGAAAATGGTATCTGGTTTGCAAAACATGCGCCTCACAATCTTGCATTTGAATGTTACTACTACTGGTGAAATTGTTCTTTACTCTCTCAGTGTTAAGGTTTGTGTTTGTTATTTCTTTTCACTTTTTCTTGTTGCTTTAGATTTCTTTGAACAATTTTTGGAAGTGCTTAATTAAAGTGAAAATGCATTGAATTTTTTTTAATCAGGTTGAAGATGATTGCAAGTTGGGATCAGTGGATGATATAGCTTCAGCTGTATACCAGATGGTCAATAGGATTCAACAAGAGGCAATGTTGAATTAA
Protein sequence

>MS.gene96758.t1

MCLPEEERDRVKDMALEAVVYPQTQDPFSYGIKDFYNFNFNTFVAKEQQEQRSFSFVENQTENNCPPYVDWNNNGSTFSPPHLNEVQETTTDPSSNTITNNTQNFHASPSVNTVIRPKRRRARSRKNKEEIENQRMTHIAVERNRRKQMNEYLSILRSLMPDSYIQRGDQASIIGGAINFVKELEHKFHFLGTKKEREVKSDEAGGSNNMPFSEFFSFPQYSTSDNSNSAATIGEKVGEIQSCIADIEVTMVENHANLKIRSRKRPKQLLKMVSGLQNMRLTILHLNVTTTGEIVLYSLSVKVEDDCKLGSVDDIASAVYQMVNRIQQEAMLN