AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03246

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03246.t1 MTR_0558s0020 86.799 303 17 3 1 287 1 296 0.0 531
MS.gene03246.t1 MTR_1g083640 85.315 286 18 3 1 262 1 286 1.45e-176 488
MS.gene03246.t1 MTR_8g446020 73.927 303 16 4 1 287 1 256 1.54e-151 424
MS.gene03246.t1 MTR_2g014100 85.714 245 18 3 1 228 1 245 5.54e-147 412
MS.gene03246.t1 MTR_6g090505 86.522 230 15 2 73 286 1 230 8.34e-142 404
MS.gene03246.t1 MTR_0337s0040 69.403 268 20 4 1 252 1 222 4.54e-120 343
MS.gene03246.t1 MTR_3g008240 80.476 210 18 3 1 194 1 203 1.73e-114 328
MS.gene03246.t1 MTR_4g040430 79.524 210 15 4 1 194 1 198 2.92e-111 320
MS.gene03246.t1 MTR_5g071590 73.333 180 27 3 1 159 1 180 1.58e-88 262
MS.gene03246.t1 MTR_0019s0290 78.947 152 16 2 90 225 9 160 9.29e-79 236
MS.gene03246.t1 MTR_1g055240 82.517 143 9 2 98 224 2 144 2.91e-78 234
MS.gene03246.t1 MTR_1281s0010 85.294 102 7 1 27 120 1 102 8.69e-56 176
MS.gene03246.t1 MTR_8g046060 88.636 88 9 1 1 87 91 178 1.02e-42 146
MS.gene03246.t1 MTR_4g008820 82.759 87 8 1 1 87 125 204 1.50e-38 143
MS.gene03246.t1 MTR_6g051425 30.417 240 154 4 48 280 22 255 8.27e-25 102
MS.gene03246.t1 MTR_1g070355 27.984 243 156 7 49 283 80 311 1.26e-16 80.1
MS.gene03246.t1 MTR_0337s0050 83.333 36 6 0 251 286 14 49 1.09e-14 68.2
MS.gene03246.t1 MTR_1g013060 28.241 216 120 9 48 245 29 227 3.75e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03246.t1 AT4G38180 26.984 252 171 5 42 287 72 316 5.29e-21 93.2
MS.gene03246.t1 AT5G28530 25.101 247 165 5 48 279 60 301 1.51e-14 73.9
MS.gene03246.t1 AT5G28530 25.101 247 165 5 48 279 60 301 1.51e-14 73.9
MS.gene03246.t1 AT5G28530 25.101 247 165 5 48 279 60 301 1.76e-14 73.9
MS.gene03246.t1 AT1G10240 23.529 238 170 5 57 287 62 294 1.09e-11 65.5
MS.gene03246.t1 AT1G10240 23.529 238 170 5 57 287 62 294 1.09e-11 65.5

Find 37 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTAGATTATTCTCTATT+TGG 0.147857 6.2:+28599462 MS.gene03246:CDS
ATAACACTGGATTCTCTATT+AGG 0.309117 6.2:+28598872 MS.gene03246:CDS
ACAAACTCAATAAAGTTGTT+AGG 0.316138 6.2:-28599003 None:intergenic
GGCGATATTGATTGTTTGTT+CGG 0.357702 6.2:-28599512 None:intergenic
AGTACAAAATACTAACCTAA+TGG 0.379112 6.2:-28599534 None:intergenic
GAGAACGTCTTATGAAGTTA+TGG 0.394356 6.2:+28599221 MS.gene03246:CDS
GTACAAAATACTAACCTAAT+GGG 0.422907 6.2:-28599533 None:intergenic
ATGTCTATAAGATATATAGA+TGG 0.423693 6.2:+28599076 MS.gene03246:CDS
GAAGTTATGGGTCAAGGAGT+TGG 0.428685 6.2:+28599234 MS.gene03246:CDS
CGAGAAGTAAATGAAGTTCA+AGG 0.430014 6.2:+28599159 MS.gene03246:CDS
AACAATCAATATCGCCCATT+AGG 0.430510 6.2:+28599519 MS.gene03246:CDS
TCCATGATTCTTTATTGCTA+GGG 0.444266 6.2:-28598792 None:intergenic
TTCCATGATTCTTTATTGCT+AGG 0.445442 6.2:-28598793 None:intergenic
TCTAATGACAATTCGTCAAA+AGG 0.456711 6.2:+28599302 MS.gene03246:CDS
GCTTTAATAAATTCTAAAGC+TGG 0.465202 6.2:+28599189 MS.gene03246:CDS
AGAACGTCTTATGAAGTTAT+GGG 0.466325 6.2:+28599222 MS.gene03246:CDS
CGTTATGTTTGTAACAAACA+AGG 0.494754 6.2:+28598955 MS.gene03246:CDS
CCCCTAGCAATAAAGAATCA+TGG 0.497001 6.2:+28598791 MS.gene03246:CDS
TGTCTTGTGCAGCATCAACT+TGG 0.502977 6.2:-28599407 None:intergenic
TAACAAACAAGGTTTCAAGA+AGG 0.511682 6.2:+28598966 MS.gene03246:CDS
GGTAATTATGCATATAACAC+TGG 0.523547 6.2:+28598859 MS.gene03246:CDS
TGTCTATAAGATATATAGAT+GGG 0.523615 6.2:+28599077 MS.gene03246:CDS
TTTAAGTCCGAAAACCGAAA+AGG 0.524077 6.2:-28599273 None:intergenic
AAATGCCCTGGTTTATGTAA+TGG 0.529222 6.2:-28599117 None:intergenic
ACAAAATAAGAAATCAGATA+AGG 0.530342 6.2:+28598921 MS.gene03246:CDS
CCATGATTCTTTATTGCTAG+GGG 0.537011 6.2:-28598791 None:intergenic
AACAAACAAGGTTTCAAGAA+GGG 0.554561 6.2:+28598967 MS.gene03246:CDS
CGTCAAAAGGAGATGGTGGT+TGG 0.556443 6.2:+28599315 MS.gene03246:CDS
CTCAAGTAACACAAATGCCC+TGG 0.558368 6.2:-28599129 None:intergenic
GACAATTCGTCAAAAGGAGA+TGG 0.566160 6.2:+28599308 MS.gene03246:CDS
TAAGATATATAGATGGGATG+TGG 0.567659 6.2:+28599083 MS.gene03246:CDS
GTTATGGGTCAAGGAGTTGG+AGG 0.578191 6.2:+28599237 MS.gene03246:CDS
TCTTATGAAGTTATGGGTCA+AGG 0.580120 6.2:+28599228 MS.gene03246:CDS
TGTCATCCATTACATAAACC+AGG 0.618164 6.2:+28599111 MS.gene03246:CDS
AATTCGTCAAAAGGAGATGG+TGG 0.636402 6.2:+28599311 MS.gene03246:CDS
GGGTCAAGGAGTTGGAGGCA+CGG 0.637387 6.2:+28599242 MS.gene03246:CDS
GTCATCCATTACATAAACCA+GGG 0.682651 6.2:+28599112 MS.gene03246:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAATAAGAAATCAGATA+AGG + chr6.2:28598921-28598940 MS.gene03246:CDS 20.0%
!! ATGTCTATAAGATATATAGA+TGG + chr6.2:28599076-28599095 MS.gene03246:CDS 20.0%
!! TGTCTATAAGATATATAGAT+GGG + chr6.2:28599077-28599096 MS.gene03246:CDS 20.0%
!!! AAAGAGATTGAAGATTTTTA+TGG + chr6.2:28598838-28598857 MS.gene03246:CDS 20.0%
! ACAAACTCAATAAAGTTGTT+AGG - chr6.2:28599006-28599025 None:intergenic 25.0%
! CAACTAGATTATTCTCTATT+TGG + chr6.2:28599462-28599481 MS.gene03246:CDS 25.0%
! TGGATATCATAGTAAAAAGA+TGG - chr6.2:28599390-28599409 None:intergenic 25.0%
!!! ACTTGGAATAATTTTGAAGT+TGG + chr6.2:28599041-28599060 MS.gene03246:CDS 25.0%
!!! GCTTTAATAAATTCTAAAGC+TGG + chr6.2:28599189-28599208 MS.gene03246:CDS 25.0%
AACAAACAAGGTTTCAAGAA+GGG + chr6.2:28598967-28598986 MS.gene03246:CDS 30.0%
AGAACGTCTTATGAAGTTAT+GGG + chr6.2:28599222-28599241 MS.gene03246:CDS 30.0%
ATAACACTGGATTCTCTATT+AGG + chr6.2:28598872-28598891 MS.gene03246:CDS 30.0%
CGTTATGTTTGTAACAAACA+AGG + chr6.2:28598955-28598974 MS.gene03246:CDS 30.0%
GGTAATTATGCATATAACAC+TGG + chr6.2:28598859-28598878 MS.gene03246:CDS 30.0%
GTGAAAGTGAAAGAAAAACT+TGG + chr6.2:28599024-28599043 MS.gene03246:CDS 30.0%
TAACAAACAAGGTTTCAAGA+AGG + chr6.2:28598966-28598985 MS.gene03246:CDS 30.0%
TAAGATATATAGATGGGATG+TGG + chr6.2:28599083-28599102 MS.gene03246:CDS 30.0%
TCCATGATTCTTTATTGCTA+GGG - chr6.2:28598795-28598814 None:intergenic 30.0%
TCTAATGACAATTCGTCAAA+AGG + chr6.2:28599302-28599321 MS.gene03246:CDS 30.0%
TTCCATGATTCTTTATTGCT+AGG - chr6.2:28598796-28598815 None:intergenic 30.0%
!!! AAGACATAGCTAGCATTTTT+TGG + chr6.2:28599424-28599443 MS.gene03246:CDS 30.0%
!!! AGACATAGCTAGCATTTTTT+GGG + chr6.2:28599425-28599444 MS.gene03246:CDS 30.0%
AAATGCCCTGGTTTATGTAA+TGG - chr6.2:28599120-28599139 None:intergenic 35.0%
AACAATCAATATCGCCCATT+AGG + chr6.2:28599519-28599538 MS.gene03246:CDS 35.0%
CCATGATTCTTTATTGCTAG+GGG - chr6.2:28598794-28598813 None:intergenic 35.0%
CGAGAAGTAAATGAAGTTCA+AGG + chr6.2:28599159-28599178 MS.gene03246:CDS 35.0%
GAGAACGTCTTATGAAGTTA+TGG + chr6.2:28599221-28599240 MS.gene03246:CDS 35.0%
GTCATCCATTACATAAACCA+GGG + chr6.2:28599112-28599131 MS.gene03246:CDS 35.0%
TCTTATGAAGTTATGGGTCA+AGG + chr6.2:28599228-28599247 MS.gene03246:CDS 35.0%
TGTCATCCATTACATAAACC+AGG + chr6.2:28599111-28599130 MS.gene03246:CDS 35.0%
TTTAAGTCCGAAAACCGAAA+AGG - chr6.2:28599276-28599295 None:intergenic 35.0%
! GAATCTTCCTTTTCGGTTTT+CGG + chr6.2:28599266-28599285 MS.gene03246:CDS 35.0%
! GGCGATATTGATTGTTTGTT+CGG - chr6.2:28599515-28599534 None:intergenic 35.0%
AATTCGTCAAAAGGAGATGG+TGG + chr6.2:28599311-28599330 MS.gene03246:CDS 40.0%
CCCCTAGCAATAAAGAATCA+TGG + chr6.2:28598791-28598810 MS.gene03246:CDS 40.0%
GACAATTCGTCAAAAGGAGA+TGG + chr6.2:28599308-28599327 MS.gene03246:CDS 40.0%
!!! GCTAGCATTTTTTGGGCATA+TGG + chr6.2:28599432-28599451 MS.gene03246:CDS 40.0%
CTCAAGTAACACAAATGCCC+TGG - chr6.2:28599132-28599151 None:intergenic 45.0%
GAAGTTATGGGTCAAGGAGT+TGG + chr6.2:28599234-28599253 MS.gene03246:CDS 45.0%
TGTCTTGTGCAGCATCAACT+TGG - chr6.2:28599410-28599429 None:intergenic 45.0%
! GCACGGAGAATCTTCCTTTT+CGG + chr6.2:28599259-28599278 MS.gene03246:CDS 45.0%
GTTATGGGTCAAGGAGTTGG+AGG + chr6.2:28599237-28599256 MS.gene03246:CDS 50.0%
! CGTCAAAAGGAGATGGTGGT+TGG + chr6.2:28599315-28599334 MS.gene03246:CDS 50.0%
GGGTCAAGGAGTTGGAGGCA+CGG + chr6.2:28599242-28599261 MS.gene03246:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 28598682 28599545 28598682 ID=MS.gene03246
chr6.2 mRNA 28598682 28599545 28598682 ID=MS.gene03246.t1;Parent=MS.gene03246
chr6.2 exon 28598682 28599545 28598682 ID=MS.gene03246.t1.exon1;Parent=MS.gene03246.t1
chr6.2 CDS 28598682 28599545 28598682 ID=cds.MS.gene03246.t1;Parent=MS.gene03246.t1
Gene Sequence

>MS.gene03246

ATGGATTTGATATCAACTTCATCTGAGAGTGAACAATTGACTGTTGAAACTTCATCACTGATTCTTGCTGATAGTTCACTGATTCATGCTGATAGTTCTCAATGTTACTCCCCTAGCAATAAAGAATCATGGAAGTCTTTAGTCTTTGAATCTATTAAAGAGATTGAAGATTTTTATGGTAATTATGCATATAACACTGGATTCTCTATTAGGAGTATGTTGAAGTCGAAGAACAATTCACAAAATAAGAAATCAGATAAGGTACATTATGTGCGTTATGTTTGTAACAAACAAGGTTTCAAGAAGGGAAGTCTGCTTAATCCTAACAACTTTATTGAGTTTGTGAAAGTGAAAGAAAAACTTGGAATAATTTTGAAGTTGGATGAAGTTTTGAATGTCTATAAGATATATAGATGGGATGTGGCTCACTGTCATCCATTACATAAACCAGGGCATTTGTGTTACTTGAGATCATTTCGAGAAGTAAATGAAGTTCAAGGACAACTCGCTTTAATAAATTCTAAAGCTGGAATGTCGATGAGAACGTCTTATGAAGTTATGGGTCAAGGAGTTGGAGGCACGGAGAATCTTCCTTTTCGGTTTTCGGACTTAAAGAACTATCTAATGACAATTCGTCAAAAGGAGATGGTGGTTGGTGAAGCAACTGTAATTCAAGAATTCTTTAGAAATGAAGCTCTCTCGAAACCATCTTTTTACTATGATATCCAAGTTGATGCTGCACAAGACATAGCTAGCATTTTTTGGGCATATGGAATTATGCAACTAGATTATTCTCTATTTGGCGATGTCATCAGTTTTGATACAACTTACCGAACAAACAATCAATATCGCCCATTAGGTTAG
Protein sequence

>MS.gene03246.t1

MDLISTSSESEQLTVETSSLILADSSLIHADSSQCYSPSNKESWKSLVFESIKEIEDFYGNYAYNTGFSIRSMLKSKNNSQNKKSDKVHYVRYVCNKQGFKKGSLLNPNNFIEFVKVKEKLGIILKLDEVLNVYKIYRWDVAHCHPLHKPGHLCYLRSFREVNEVQGQLALINSKAGMSMRTSYEVMGQGVGGTENLPFRFSDLKNYLMTIRQKEMVVGEATVIQEFFRNEALSKPSFYYDIQVDAAQDIASIFWAYGIMQLDYSLFGDVISFDTTYRTNNQYRPLG