AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene81844


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81844.t1 MTR_0558s0020 89.389 311 18 1 1 311 1 296 0.0 581
MS.gene81844.t1 MTR_1g083640 93.706 286 18 0 1 286 1 286 0.0 565
MS.gene81844.t1 MTR_8g446020 77.492 311 15 2 1 311 1 256 1.97e-171 476
MS.gene81844.t1 MTR_2g014100 88.142 253 21 2 1 252 1 245 1.20e-163 456
MS.gene81844.t1 MTR_6g090505 90.435 230 22 0 81 310 1 230 7.03e-156 441
MS.gene81844.t1 MTR_0337s0040 73.188 276 20 2 1 276 1 222 3.42e-138 390
MS.gene81844.t1 MTR_3g008240 83.945 218 20 1 1 218 1 203 4.70e-132 374
MS.gene81844.t1 MTR_4g040430 84.404 218 14 2 1 218 1 198 2.37e-131 372
MS.gene81844.t1 MTR_5g071590 86.885 183 21 1 1 183 1 180 5.76e-117 335
MS.gene81844.t1 MTR_1g055240 94.366 142 8 0 107 248 3 144 6.77e-98 285
MS.gene81844.t1 MTR_0019s0290 88.889 153 14 1 100 249 8 160 7.07e-97 283
MS.gene81844.t1 MTR_1281s0010 95.413 109 5 0 35 143 1 109 1.86e-72 219
MS.gene81844.t1 MTR_8g046060 79.167 96 11 2 1 95 91 178 5.55e-40 140
MS.gene81844.t1 MTR_4g008820 76.842 95 7 1 1 95 125 204 1.13e-37 142
MS.gene81844.t1 MTR_6g051425 30.522 249 158 4 56 304 22 255 3.47e-32 122
MS.gene81844.t1 MTR_1g070355 24.919 309 207 7 3 307 24 311 1.65e-22 98.2
MS.gene81844.t1 MTR_0337s0050 70.213 47 11 1 275 318 14 60 7.83e-16 71.6
MS.gene81844.t1 MTR_0402s0040 25.946 185 118 4 65 249 40 205 2.58e-14 73.6
MS.gene81844.t1 MTR_1g013060 30.093 216 132 8 56 269 29 227 3.89e-14 70.9
MS.gene81844.t1 MTR_4g035820 23.194 263 177 5 56 313 80 322 2.78e-12 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81844.t1 AT4G38180 28.413 271 169 6 50 316 72 321 3.59e-26 109
MS.gene81844.t1 AT5G28530 25.185 270 168 7 56 313 60 307 7.51e-16 78.6
MS.gene81844.t1 AT5G28530 25.185 270 168 7 56 313 60 307 7.51e-16 78.6
MS.gene81844.t1 AT5G28530 25.185 270 168 7 56 313 60 307 7.67e-16 78.6
MS.gene81844.t1 AT1G10240 23.320 253 170 7 65 312 62 295 7.62e-14 72.8
MS.gene81844.t1 AT1G10240 23.320 253 170 7 65 312 62 295 7.62e-14 72.8
MS.gene81844.t1 AT4G15090 24.498 249 167 6 66 313 66 294 1.65e-11 65.5
MS.gene81844.t1 AT4G15090 24.498 249 167 6 66 313 66 294 1.65e-11 65.5
MS.gene81844.t1 AT4G15090 24.498 249 167 6 66 313 66 294 1.65e-11 65.5
MS.gene81844.t1 AT4G15090 24.498 249 167 6 66 313 66 294 1.65e-11 65.5
MS.gene81844.t1 AT4G15090 24.498 249 167 6 66 313 66 294 1.65e-11 65.5
MS.gene81844.t1 AT1G76320 23.485 264 166 8 57 316 3 234 7.52e-11 63.5
MS.gene81844.t1 AT1G76320 23.485 264 166 8 57 316 3 234 7.92e-11 63.5
MS.gene81844.t1 AT1G76320 23.485 264 166 8 57 316 3 234 7.92e-11 63.5
MS.gene81844.t1 AT1G80010 25.940 266 156 10 57 310 101 337 8.26e-11 63.5
MS.gene81844.t1 AT1G76320 23.485 264 166 8 57 316 3 234 8.66e-11 63.2

Find 41 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGTTGTTGGCCTGTTGTT+AGG 0.292589 6.4:-53874680 None:intergenic
TTACTTCTCGAAATGATCTA+AGG 0.311482 6.4:-53874871 None:intergenic
CAACTAGATTATTCTCTATT+CGG 0.323831 6.4:+53875187 MS.gene81844:CDS
GCCGATATTTATTGTTTGTT+CGG 0.341758 6.4:-53875237 None:intergenic
AACAATAAATATCGGCCATT+AGG 0.388497 6.4:+53875244 MS.gene81844:CDS
ACCGAACAAACAATAAATAT+CGG 0.389395 6.4:+53875236 MS.gene81844:CDS
GAGAACGTCTTATGAAGTTA+TGG 0.394356 6.4:+53874946 MS.gene81844:CDS
GTCTTATGAAGTTATGGGTC+AGG 0.415385 6.4:+53874952 MS.gene81844:CDS
GAAGTTATGGGTCAGGGAGT+TGG 0.426260 6.4:+53874959 MS.gene81844:CDS
CGTTATGTTTGTAACAAAGA+AGG 0.427485 6.4:+53874632 MS.gene81844:CDS
CGAGAAGTAAATGAAGTTCA+AGG 0.430014 6.4:+53874884 MS.gene81844:CDS
TCCATGATTCTTTATTGCTA+GGG 0.444266 6.4:-53874469 None:intergenic
TTCCATGATTCTTTATTGCT+AGG 0.445442 6.4:-53874470 None:intergenic
GAAAGGGTTGGTTGTAAAGC+TGG 0.447509 6.4:+53874749 MS.gene81844:CDS
ATGTGTATAAGATATATAGA+TGG 0.452819 6.4:+53874801 MS.gene81844:CDS
ACATCAACTTCATCTGATAG+TGG 0.459514 6.4:+53874344 MS.gene81844:CDS
GCTCTTATAAATTCTAAAGC+TGG 0.462891 6.4:+53874914 MS.gene81844:CDS
ACCTGTGGACTGTCTGTTGT+TGG 0.465317 6.4:-53874692 None:intergenic
AGAACGTCTTATGAAGTTAT+GGG 0.466325 6.4:+53874947 MS.gene81844:CDS
GTTTACTTAATCCTAACAAC+AGG 0.470860 6.4:+53874669 MS.gene81844:CDS
TTTAAGTCTGAAAACCGAAA+AGG 0.483010 6.4:-53874998 None:intergenic
CCCCTAGCAATAAAGAATCA+TGG 0.497001 6.4:+53874468 MS.gene81844:CDS
TTACAACCAACCCTTTCCTC+AGG 0.505082 6.4:-53874743 None:intergenic
AGCTGGAATATATTTGAAGC+TGG 0.507410 6.4:+53874766 MS.gene81844:CDS
ACAAAACAAGAAATCTGATA+AGG 0.511435 6.4:+53874598 MS.gene81844:CDS
CTAAGGTAACACGAATGCTC+TGG 0.517941 6.4:-53874854 None:intergenic
GTCAGCATGAATCATTGCTA+GGG 0.522802 6.4:-53874429 None:intergenic
GGTAATTATGCATATAACAC+TGG 0.523547 6.4:+53874536 MS.gene81844:CDS
TAACAAAGAAGGTTTCAAGA+AGG 0.525236 6.4:+53874643 MS.gene81844:CDS
TAAGATATATAGATGGGATG+TGG 0.528498 6.4:+53874808 MS.gene81844:CDS
GAATGCTCTGGTTTATGTAA+TGG 0.534744 6.4:-53874842 None:intergenic
CCATGATTCTTTATTGCTAG+GGG 0.537011 6.4:-53874468 None:intergenic
TGTCAGCATGAATCATTGCT+AGG 0.540740 6.4:-53874430 None:intergenic
AACAAAGAAGGTTTCAAGAA+GGG 0.545537 6.4:+53874644 MS.gene81844:CDS
GTTATGGGTCAGGGAGTTGG+AGG 0.547221 6.4:+53874962 MS.gene81844:CDS
TGTGTATAAGATATATAGAT+GGG 0.601002 6.4:+53874802 MS.gene81844:CDS
TCACTGATTCATGCTGAGAG+TGG 0.606950 6.4:+53874389 MS.gene81844:CDS
TCTTATGAAGTTATGGGTCA+GGG 0.609153 6.4:+53874953 MS.gene81844:CDS
GCCAACAACAGACAGTCCAC+AGG 0.619933 6.4:+53874691 MS.gene81844:CDS
TTCACAAACTCAATAACCTG+TGG 0.626760 6.4:-53874707 None:intergenic
TCAGCATGAATCATTGCTAG+GGG 0.681156 6.4:-53874428 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTGTATAAGATATATAGA+TGG + chr6.4:53874801-53874820 MS.gene81844:CDS 20.0%
!! TGAATATCATAGTAAAAAGA+TGG - chr6.4:53875115-53875134 None:intergenic 20.0%
!! TGTGTATAAGATATATAGAT+GGG + chr6.4:53874802-53874821 MS.gene81844:CDS 20.0%
!!! AAAGAGATTGAAGATTTTTA+TGG + chr6.4:53874515-53874534 MS.gene81844:CDS 20.0%
!!! TTAATTTCATTAAGTTGTTC+TGG + chr6.4:53875305-53875324 MS.gene81844:intron 20.0%
! ACAAAACAAGAAATCTGATA+AGG + chr6.4:53874598-53874617 MS.gene81844:CDS 25.0%
! ACCGAACAAACAATAAATAT+CGG + chr6.4:53875236-53875255 MS.gene81844:CDS 25.0%
! AGTAAAAAACACTAACCTAA+TGG - chr6.4:53875262-53875281 None:intergenic 25.0%
! CAACTAGATTATTCTCTATT+CGG + chr6.4:53875187-53875206 MS.gene81844:CDS 25.0%
! TCTTACTTATTTGAACTACA+CGG + chr6.4:53875381-53875400 MS.gene81844:intron 25.0%
!! ATAACACTGGATTTTCTATT+AGG + chr6.4:53874549-53874568 MS.gene81844:CDS 25.0%
!! TTAACCATGTTGTTTGTTTA+GGG + chr6.4:53875406-53875425 MS.gene81844:intron 25.0%
!! TTTAACCATGTTGTTTGTTT+AGG + chr6.4:53875405-53875424 MS.gene81844:intron 25.0%
!!! AAGACATAGCTAGTATTTTT+TGG + chr6.4:53875149-53875168 MS.gene81844:CDS 25.0%
!!! ATTTATATTTTGAACTGCCT+AGG + chr6.4:53875483-53875502 MS.gene81844:intron 25.0%
AAATCCCTAAACAAACAACA+TGG - chr6.4:53875413-53875432 None:intergenic 30.0%
AACAAAGAAGGTTTCAAGAA+GGG + chr6.4:53874644-53874663 MS.gene81844:CDS 30.0%
AACAATAAATATCGGCCATT+AGG + chr6.4:53875244-53875263 MS.gene81844:CDS 30.0%
AGAACGTCTTATGAAGTTAT+GGG + chr6.4:53874947-53874966 MS.gene81844:CDS 30.0%
CGTTATGTTTGTAACAAAGA+AGG + chr6.4:53874632-53874651 MS.gene81844:CDS 30.0%
CTTACTTATTTGAACTACAC+GGG + chr6.4:53875382-53875401 MS.gene81844:intron 30.0%
GCCGATATTTATTGTTTGTT+CGG - chr6.4:53875240-53875259 None:intergenic 30.0%
GGTAATTATGCATATAACAC+TGG + chr6.4:53874536-53874555 MS.gene81844:CDS 30.0%
GTTTACTTAATCCTAACAAC+AGG + chr6.4:53874669-53874688 MS.gene81844:CDS 30.0%
TAACAAAGAAGGTTTCAAGA+AGG + chr6.4:53874643-53874662 MS.gene81844:CDS 30.0%
TAAGATATATAGATGGGATG+TGG + chr6.4:53874808-53874827 MS.gene81844:CDS 30.0%
TAAGTTTGTCTCAAACCAAA+TGG - chr6.4:53875447-53875466 None:intergenic 30.0%
TCCATGATTCTTTATTGCTA+GGG - chr6.4:53874472-53874491 None:intergenic 30.0%
TTACTTCTCGAAATGATCTA+AGG - chr6.4:53874874-53874893 None:intergenic 30.0%
TTCCATGATTCTTTATTGCT+AGG - chr6.4:53874473-53874492 None:intergenic 30.0%
TTTAAGTCTGAAAACCGAAA+AGG - chr6.4:53875001-53875020 None:intergenic 30.0%
!! GCTCTTATAAATTCTAAAGC+TGG + chr6.4:53874914-53874933 MS.gene81844:CDS 30.0%
!!! TAGTGTTTTTTACTTCTCTC+AGG + chr6.4:53875268-53875287 MS.gene81844:intron 30.0%
AATTCGTCAAAAAGAGATGG+TGG + chr6.4:53875036-53875055 MS.gene81844:CDS 35.0%
ACATCAACTTCATCTGATAG+TGG + chr6.4:53874344-53874363 MS.gene81844:CDS 35.0%
AGTAAAAAGATGGTTTCGAG+AGG - chr6.4:53875105-53875124 None:intergenic 35.0%
CCATGATTCTTTATTGCTAG+GGG - chr6.4:53874471-53874490 None:intergenic 35.0%
CGAGAAGTAAATGAAGTTCA+AGG + chr6.4:53874884-53874903 MS.gene81844:CDS 35.0%
GAAAGAAAAACCTGAGGAAA+GGG + chr6.4:53874733-53874752 MS.gene81844:CDS 35.0%
GAAAGTGAAAGAAAAACCTG+AGG + chr6.4:53874727-53874746 MS.gene81844:CDS 35.0%
GACAATTCGTCAAAAAGAGA+TGG + chr6.4:53875033-53875052 MS.gene81844:CDS 35.0%
GAGAACGTCTTATGAAGTTA+TGG + chr6.4:53874946-53874965 MS.gene81844:CDS 35.0%
GTAAAAAGATGGTTTCGAGA+GGG - chr6.4:53875104-53875123 None:intergenic 35.0%
TAAGACCTATAGTCAATCCT+AGG - chr6.4:53875366-53875385 None:intergenic 35.0%
TCTTATGAAGTTATGGGTCA+GGG + chr6.4:53874953-53874972 MS.gene81844:CDS 35.0%
TGAAAGAAAAACCTGAGGAA+AGG + chr6.4:53874732-53874751 MS.gene81844:CDS 35.0%
TTCACAAACTCAATAACCTG+TGG - chr6.4:53874710-53874729 None:intergenic 35.0%
! AGCTGGAATATATTTGAAGC+TGG + chr6.4:53874766-53874785 MS.gene81844:CDS 35.0%
! GAATGCTCTGGTTTATGTAA+TGG - chr6.4:53874845-53874864 None:intergenic 35.0%
!!! GCTAGTATTTTTTGGTCAGA+TGG + chr6.4:53875157-53875176 MS.gene81844:CDS 35.0%
AACTGCCTAGGATTGACTAT+AGG + chr6.4:53875358-53875377 MS.gene81844:intron 40.0%
CCCCTAGCAATAAAGAATCA+TGG + chr6.4:53874468-53874487 MS.gene81844:CDS 40.0%
GTCAGCATGAATCATTGCTA+GGG - chr6.4:53874432-53874451 None:intergenic 40.0%
GTCTTATGAAGTTATGGGTC+AGG + chr6.4:53874952-53874971 MS.gene81844:CDS 40.0%
TCACACAAGACAAAATGCCT+AGG - chr6.4:53875503-53875522 None:intergenic 40.0%
TCAGCATGAATCATTGCTAG+GGG - chr6.4:53874431-53874450 None:intergenic 40.0%
TGTCAGCATGAATCATTGCT+AGG - chr6.4:53874433-53874452 None:intergenic 40.0%
! ATTTTCTCGCTTCTGCCATT+TGG + chr6.4:53875429-53875448 MS.gene81844:intron 40.0%
! CAGTACATTTTGAACTGCCT+AGG + chr6.4:53875346-53875365 MS.gene81844:intron 40.0%
! GCACAGAGAATCTTCCTTTT+CGG + chr6.4:53874984-53875003 MS.gene81844:CDS 40.0%
CTAAGGTAACACGAATGCTC+TGG - chr6.4:53874857-53874876 None:intergenic 45.0%
GAAAAACCTGAGGAAAGGGT+TGG + chr6.4:53874737-53874756 MS.gene81844:CDS 45.0%
TTACAACCAACCCTTTCCTC+AGG - chr6.4:53874746-53874765 None:intergenic 45.0%
! CGTCAAAAAGAGATGGTGGT+TGG + chr6.4:53875040-53875059 MS.gene81844:CDS 45.0%
! TCTGTTGTTGGCCTGTTGTT+AGG - chr6.4:53874683-53874702 None:intergenic 45.0%
!! GAAAGGGTTGGTTGTAAAGC+TGG + chr6.4:53874749-53874768 MS.gene81844:CDS 45.0%
!! TCACTGATTCATGCTGAGAG+TGG + chr6.4:53874389-53874408 MS.gene81844:CDS 45.0%
GAAGTTATGGGTCAGGGAGT+TGG + chr6.4:53874959-53874978 MS.gene81844:CDS 50.0%
! ACCTGTGGACTGTCTGTTGT+TGG - chr6.4:53874695-53874714 None:intergenic 50.0%
GCCAACAACAGACAGTCCAC+AGG + chr6.4:53874691-53874710 MS.gene81844:CDS 55.0%
GTTATGGGTCAGGGAGTTGG+AGG + chr6.4:53874962-53874981 MS.gene81844:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 53874335 53875533 53874335 ID=MS.gene81844
chr6.4 mRNA 53874335 53875533 53874335 ID=MS.gene81844.t1;Parent=MS.gene81844
chr6.4 exon 53874335 53875265 53874335 ID=MS.gene81844.t1.exon1;Parent=MS.gene81844.t1
chr6.4 CDS 53874335 53875265 53874335 ID=cds.MS.gene81844.t1;Parent=MS.gene81844.t1
chr6.4 exon 53875505 53875533 53875505 ID=MS.gene81844.t1.exon2;Parent=MS.gene81844.t1
chr6.4 CDS 53875505 53875533 53875505 ID=cds.MS.gene81844.t1;Parent=MS.gene81844.t1
Gene Sequence

>MS.gene81844

ATGGATTTGACATCAACTTCATCTGATAGTGGACAACTGAGTGTTGAAACTTCATCACTGATTCATGCTGAGAGTGGACAATTGAGTGTTACTCCCCTAGCAATGATTCATGCTGACAGTTCTCAATGTTACTCCCCTAGCAATAAAGAATCATGGAAGTCTTTAGTCTTTCAATCTATTAAAGAGATTGAAGATTTTTATGGTAATTATGCATATAACACTGGATTTTCTATTAGGACTATGTTGAAGTCGAAGAATAATTCACAAAACAAGAAATCTGATAAGGTACATTATTTGCGTTATGTTTGTAACAAAGAAGGTTTCAAGAAGGGAAGTTTACTTAATCCTAACAACAGGCCAACAACAGACAGTCCACAGGTTATTGAGTTTGTGAAAGTGAAAGAAAAACCTGAGGAAAGGGTTGGTTGTAAAGCTGGAATATATTTGAAGCTGGATGAAGTTTTGAATGTGTATAAGATATATAGATGGGATGTGGATCACTGTCATCCATTACATAAACCAGAGCATTCGTGTTACCTTAGATCATTTCGAGAAGTAAATGAAGTTCAAGGACAACTAGCTCTTATAAATTCTAAAGCTGGAATGTCGATGAGAACGTCTTATGAAGTTATGGGTCAGGGAGTTGGAGGCACAGAGAATCTTCCTTTTCGGTTTTCAGACTTAAAGAACTATCTAATGACAATTCGTCAAAAAGAGATGGTGGTTGGTGAAGCAACTGTAATTCAAGAATTCTTTAGAAATGAAGCCCTCTCGAAACCATCTTTTTACTATGATATTCAAGTTGATGCTGCAGAAGACATAGCTAGTATTTTTTGGTCAGATGGAATTATGCAACTAGATTATTCTCTATTCGGCGATGTCATCAGTTTTGATACAACTTACCGAACAAACAATAAATATCGGCCATTAGGTTAGTGTTTTTTACTTCTCTCAGGTTTTAAATTATTGTTTAATTTCATTAAGTTGTTCTGGCATGTGTATTATAAGTAGCAGTACATTTTGAACTGCCTAGGATTGACTATAGGTCTTACTTATTTGAACTACACGGGTTTAACCATGTTGTTTGTTTAGGGATTTTCTCGCTTCTGCCATTTGGTTTGAGACAAACTTAAATGATGTTGATTGAAATTTATATTTTGAACTGCCTAGGCATTTTGTCTTGTGTGATCGAACTTTAG

Protein sequence

>MS.gene81844.t1

MDLTSTSSDSGQLSVETSSLIHAESGQLSVTPLAMIHADSSQCYSPSNKESWKSLVFQSIKEIEDFYGNYAYNTGFSIRTMLKSKNNSQNKKSDKVHYLRYVCNKEGFKKGSLLNPNNRPTTDSPQVIEFVKVKEKPEERVGCKAGIYLKLDEVLNVYKIYRWDVDHCHPLHKPEHSCYLRSFREVNEVQGQLALINSKAGMSMRTSYEVMGQGVGGTENLPFRFSDLKNYLMTIRQKEMVVGEATVIQEFFRNEALSKPSFYYDIQVDAAEDIASIFWSDGIMQLDYSLFGDVISFDTTYRTNNKYRPLGILSCVIEL