AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52391

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52391.t1 MTR_2g436400 96.429 280 10 0 1 280 102 381 0.0 553
MS.gene52391.t1 MTR_2g437060 79.570 279 57 0 2 280 111 389 2.77e-159 449
MS.gene52391.t1 MTR_2g437080 69.643 280 85 0 1 280 95 374 1.16e-136 391
MS.gene52391.t1 MTR_2g437030 68.929 280 87 0 1 280 181 460 9.16e-132 382
MS.gene52391.t1 MTR_2g436440 65.714 280 96 0 1 280 101 380 1.87e-127 368
MS.gene52391.t1 MTR_2g437020 65.480 281 94 2 2 280 95 374 4.41e-126 364
MS.gene52391.t1 MTR_2g437040 62.857 280 104 0 1 280 95 374 4.66e-123 356
MS.gene52391.t1 MTR_4g119550 51.957 281 134 1 1 280 104 384 2.16e-103 306
MS.gene52391.t1 MTR_2g437960 51.590 283 134 2 1 280 108 390 2.98e-97 291
MS.gene52391.t1 MTR_2g437170 52.632 285 130 3 1 280 110 394 4.21e-97 291
MS.gene52391.t1 MTR_2g437960 51.590 283 134 2 1 280 108 390 5.84e-97 291
MS.gene52391.t1 MTR_2g438010 51.228 285 132 2 1 280 125 407 1.05e-96 291
MS.gene52391.t1 MTR_2g437180 52.330 279 128 3 1 276 104 380 5.13e-95 285
MS.gene52391.t1 MTR_2g437150 52.500 280 128 3 1 275 110 389 5.41e-95 286
MS.gene52391.t1 MTR_2g437160 51.064 282 136 1 1 280 118 399 7.63e-94 283
MS.gene52391.t1 MTR_2g437120 53.047 279 127 2 1 276 106 383 1.04e-93 283
MS.gene52391.t1 MTR_2g437990 49.645 282 140 1 1 280 105 386 5.09e-93 281
MS.gene52391.t1 MTR_2g437100 53.381 281 126 3 1 276 115 395 9.18e-93 280
MS.gene52391.t1 MTR_2g076320 49.826 287 131 2 2 280 106 387 4.86e-92 278
MS.gene52391.t1 MTR_2g437200 46.815 314 129 2 1 276 85 398 1.28e-91 277
MS.gene52391.t1 MTR_2g437130 47.766 291 130 3 1 280 96 375 6.40e-90 272
MS.gene52391.t1 MTR_2g437240 44.969 318 137 2 1 280 85 402 5.97e-89 271
MS.gene52391.t1 MTR_2g438020 46.178 314 131 3 1 276 124 437 1.44e-85 265
MS.gene52391.t1 MTR_2g436460 46.209 277 148 1 1 276 100 376 2.54e-83 255
MS.gene52391.t1 MTR_2g437260 44.765 277 151 1 1 275 89 365 3.14e-83 255
MS.gene52391.t1 MTR_2g019840 47.518 282 144 3 1 280 96 375 2.95e-81 250
MS.gene52391.t1 MTR_2g437940 48.214 280 120 2 1 280 104 358 4.06e-81 249
MS.gene52391.t1 MTR_2g437090 69.136 162 50 0 119 280 1 162 4.95e-78 234
MS.gene52391.t1 MTR_4g120380 44.526 274 152 0 1 274 97 370 6.56e-77 238
MS.gene52391.t1 MTR_2g019810 44.643 280 151 3 1 278 84 361 1.42e-75 234
MS.gene52391.t1 MTR_4g119580 43.066 274 156 0 1 274 97 370 1.07e-74 233
MS.gene52391.t1 MTR_4g120380 44.882 254 140 0 1 254 97 350 5.33e-71 224
MS.gene52391.t1 MTR_2g437160 54.082 196 87 1 88 280 113 308 1.15e-66 210
MS.gene52391.t1 MTR_4g119570 39.271 247 117 2 26 272 14 227 8.36e-53 172
MS.gene52391.t1 MTR_3g450500 32.155 283 182 4 2 276 92 372 1.23e-43 152
MS.gene52391.t1 MTR_2g436370 75.789 95 23 0 1 95 101 195 1.00e-40 140
MS.gene52391.t1 MTR_4g007490 30.634 284 190 4 1 278 90 372 5.67e-37 135
MS.gene52391.t1 MTR_2g436380 54.867 113 44 3 119 231 1 106 1.88e-30 115
MS.gene52391.t1 MTR_8g080990 28.889 270 188 3 4 270 100 368 2.13e-30 117
MS.gene52391.t1 MTR_8g081000 25.993 277 202 2 1 274 109 385 1.10e-26 107
MS.gene52391.t1 MTR_8g081000 25.993 277 202 2 1 274 109 385 1.42e-26 107
MS.gene52391.t1 MTR_8g081000 25.993 277 202 2 1 274 109 385 1.81e-26 107
MS.gene52391.t1 MTR_3g085240 62.264 53 20 0 178 230 176 228 7.20e-16 75.9
MS.gene52391.t1 MTR_4g119615 60.000 50 20 0 218 267 26 75 3.45e-14 67.4
MS.gene52391.t1 MTR_2g019830 52.857 70 32 1 207 276 131 199 1.50e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52391.t1 AT5G07900 35.125 279 175 3 1 273 121 399 9.19e-52 174
MS.gene52391.t1 AT1G21150 29.474 285 191 5 1 277 72 354 1.47e-35 130
MS.gene52391.t1 AT1G21150 29.474 285 191 5 1 277 108 390 2.80e-35 130
MS.gene52391.t1 AT1G21150 29.474 285 191 5 1 277 172 454 8.86e-35 130
MS.gene52391.t1 AT1G61980 26.557 305 181 6 1 265 104 405 3.50e-26 106
MS.gene52391.t1 AT1G61980 26.557 305 181 6 1 265 104 405 3.50e-26 106
MS.gene52391.t1 AT1G61980 26.557 305 181 6 1 265 104 405 3.50e-26 106
MS.gene52391.t1 AT5G64950 30.175 285 179 6 6 274 96 376 2.79e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G61970 26.756 299 176 6 1 259 104 399 2.85e-24 101
MS.gene52391.t1 AT1G62010 25.704 284 170 6 20 265 109 389 1.82e-23 99.0
MS.gene52391.t1 AT1G62120 25.733 307 183 7 1 265 108 411 1.23e-21 94.4
MS.gene52391.t1 AT1G61990 26.349 315 180 7 1 273 104 408 9.22e-20 88.6
MS.gene52391.t1 AT1G61990 26.349 315 180 7 1 273 104 408 9.22e-20 88.6
MS.gene52391.t1 AT3G46950 30.303 198 121 3 1 191 104 291 3.19e-17 81.6
MS.gene52391.t1 AT1G62110 27.273 198 129 3 1 189 104 295 3.44e-15 75.5
MS.gene52391.t1 AT1G61960 29.843 191 132 2 1 189 104 294 8.36e-15 74.3
MS.gene52391.t1 AT1G62085 25.146 342 176 10 1 265 107 445 3.61e-14 72.4
MS.gene52391.t1 AT1G62085 25.146 342 176 10 1 265 107 445 3.61e-14 72.4
MS.gene52391.t1 AT5G23930 20.544 331 195 8 1 264 107 436 2.88e-12 67.0
MS.gene52391.t1 AT1G62150 27.320 194 132 4 1 188 110 300 5.98e-12 65.9

Find 45 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATCTGACAAGGAAATTT+TGG 0.116874 2.3:-54855739 MS.gene52391:CDS
TAAATTTAGTGATGAACTTT+TGG 0.199642 2.3:-54855368 MS.gene52391:CDS
GTAAAGGAATTAAAGGATTT+GGG 0.236314 2.3:-54855564 MS.gene52391:CDS
GGTATTGTTTACTGTTGTTT+TGG 0.253046 2.3:+54855500 None:intergenic
GGTAAAGGAATTAAAGGATT+TGG 0.272443 2.3:-54855565 MS.gene52391:CDS
AAACTTAATGACAAAATATA+AGG 0.279924 2.3:+54855303 None:intergenic
ATAGATGTTAACATAGAATA+AGG 0.294532 2.3:+54855399 None:intergenic
AAACTTTGGCAACACAGTTT+TGG 0.307791 2.3:+54855890 None:intergenic
TGACAAAATATAAGGTTGTT+TGG 0.318444 2.3:+54855311 None:intergenic
AGTTGATGTCTTTAAGAAAT+GGG 0.334222 2.3:-54855463 MS.gene52391:CDS
CAAGTCGGTAAAGGAATTAA+AGG 0.349745 2.3:-54855571 MS.gene52391:CDS
AAGTTGATGTCTTTAAGAAA+TGG 0.356329 2.3:-54855464 MS.gene52391:CDS
TTGGGTCAATCAGTTGGGTT+GGG 0.365374 2.3:-54855349 MS.gene52391:CDS
AACTTATCAGTCACTACAAA+TGG 0.416436 2.3:+54855195 None:intergenic
GTCAGAGGTAGAAGCACCTT+TGG 0.417863 2.3:+54855854 None:intergenic
GGTTTGCAGGAAAGCAGCTC+TGG 0.441213 2.3:+54855915 None:intergenic
AATAGTCCCAGCCTATGAAT+TGG 0.452259 2.3:-54855775 MS.gene52391:CDS
ATCACAATGCTGATTGAGAA+TGG 0.457142 2.3:-54855663 MS.gene52391:CDS
CATCAACTTTCTCTTTCCAT+AGG 0.457918 2.3:+54855478 None:intergenic
GGAAAGCAGCTCTGGCATCT+TGG 0.471973 2.3:+54855923 None:intergenic
GAATCTGTACACCAATTCAT+AGG 0.473956 2.3:+54855764 None:intergenic
TTTGGGTCAATCAGTTGGGT+TGG 0.480856 2.3:-54855350 MS.gene52391:CDS
CTGTACACCAATTCATAGGC+TGG 0.485721 2.3:+54855768 None:intergenic
CTGGGACTATTTGTTTGTTG+AGG 0.489503 2.3:+54855787 None:intergenic
TCAGTTGGGTTGGGATGCTA+TGG 0.506950 2.3:-54855340 MS.gene52391:CDS
TCACAATGCTGATTGAGAAT+GGG 0.508211 2.3:-54855662 MS.gene52391:CDS
AATATAAGGTTGTTTGGCAA+TGG 0.508469 2.3:+54855317 None:intergenic
GTTGATGTCTTTAAGAAATG+GGG 0.513781 2.3:-54855462 MS.gene52391:CDS
ATCAACTTTCTCTTTCCATA+GGG 0.518323 2.3:+54855479 None:intergenic
CAACAGTAAACAATACCCTA+TGG 0.530932 2.3:-54855494 MS.gene52391:CDS
TGACATGCTCAAGTCGGTAA+AGG 0.531848 2.3:-54855580 MS.gene52391:CDS
GTGCAATTTCTTCTCAACAA+AGG 0.536369 2.3:-54855249 MS.gene52391:CDS
AATTGCACAACAGCGGCCCT+CGG 0.562081 2.3:+54855264 None:intergenic
AGGCTTACATACAAGACTCT+AGG 0.563542 2.3:+54855807 None:intergenic
TAAAGGAATTAAAGGATTTG+GGG 0.564846 2.3:-54855563 MS.gene52391:CDS
CATTGCTGAGGGAACAGACT+CGG 0.569500 2.3:-54855617 MS.gene52391:CDS
CAGATTCTTGCAATCTGACA+AGG 0.575407 2.3:-54855748 MS.gene52391:CDS
AAACATTAAATCATTGCTGA+GGG 0.598387 2.3:-54855628 MS.gene52391:CDS
TGTACACCAATTCATAGGCT+GGG 0.603503 2.3:+54855769 None:intergenic
ATGTCTTTAAGAAATGGGGT+TGG 0.604281 2.3:-54855458 MS.gene52391:CDS
CAAACATTAAATCATTGCTG+AGG 0.611140 2.3:-54855629 MS.gene52391:CDS
GACAATGTTAACAATGTCAG+AGG 0.615619 2.3:+54855839 None:intergenic
CACAATGCTGATTGAGAATG+GGG 0.632348 2.3:-54855661 MS.gene52391:CDS
GAGAAGAAATTGCACAACAG+CGG 0.635644 2.3:+54855257 None:intergenic
GAGACGTGACATGCTCAAGT+CGG 0.669830 2.3:-54855586 MS.gene52391:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTTAATGACAAAATATA+AGG + chr2.3:54855740-54855759 None:intergenic 15.0%
!!! TTATATTTTGTCATTAAGTT+TGG - chr2.3:54855739-54855758 MS.gene52391:CDS 15.0%
!! ATAGATGTTAACATAGAATA+AGG + chr2.3:54855644-54855663 None:intergenic 20.0%
!!! AAATTTAGTGATGAACTTTT+GGG - chr2.3:54855673-54855692 MS.gene52391:CDS 20.0%
!!! TAAATTTAGTGATGAACTTT+TGG - chr2.3:54855672-54855691 MS.gene52391:CDS 20.0%
!!! TTATCTTTTAAAGTTGTATG+AGG - chr2.3:54855910-54855929 MS.gene52391:CDS 20.0%
! AAACATTAAATCATTGCTGA+GGG - chr2.3:54855412-54855431 MS.gene52391:CDS 25.0%
! GAGAGAAAAAATTGAAACTT+TGG + chr2.3:54855167-54855186 None:intergenic 25.0%
! GTAAAGGAATTAAAGGATTT+GGG - chr2.3:54855476-54855495 MS.gene52391:CDS 25.0%
! TAAAGGAATTAAAGGATTTG+GGG - chr2.3:54855477-54855496 MS.gene52391:CDS 25.0%
! TGACAAAATATAAGGTTGTT+TGG + chr2.3:54855732-54855751 None:intergenic 25.0%
! TGTCATTAAGTTTGGAAAAA+AGG - chr2.3:54855747-54855766 MS.gene52391:CDS 25.0%
!! AATCCTTCAAAAACAACTTT+TGG - chr2.3:54855503-54855522 MS.gene52391:CDS 25.0%
!! AGTTGATGTCTTTAAGAAAT+GGG - chr2.3:54855577-54855596 MS.gene52391:CDS 25.0%
!!! AAGTTGATGTCTTTAAGAAA+TGG - chr2.3:54855576-54855595 MS.gene52391:CDS 25.0%
!!! TATAAAACGTTTTGAGAATG+AGG - chr2.3:54855883-54855902 MS.gene52391:CDS 25.0%
!!! TTTCAATTTTTTCTCTCCAA+AGG - chr2.3:54855170-54855189 MS.gene52391:CDS 25.0%
AACTTATCAGTCACTACAAA+TGG + chr2.3:54855848-54855867 None:intergenic 30.0%
AATATAAGGTTGTTTGGCAA+TGG + chr2.3:54855726-54855745 None:intergenic 30.0%
ATCAACTTTCTCTTTCCATA+GGG + chr2.3:54855564-54855583 None:intergenic 30.0%
CAAACATTAAATCATTGCTG+AGG - chr2.3:54855411-54855430 MS.gene52391:CDS 30.0%
GGTAAAGGAATTAAAGGATT+TGG - chr2.3:54855475-54855494 MS.gene52391:CDS 30.0%
! GTTGATGTCTTTAAGAAATG+GGG - chr2.3:54855578-54855597 MS.gene52391:CDS 30.0%
!! GGTATTGTTTACTGTTGTTT+TGG + chr2.3:54855543-54855562 None:intergenic 30.0%
!!! ACACCAAAAGTTGTTTTTGA+AGG + chr2.3:54855509-54855528 None:intergenic 30.0%
CAACAGTAAACAATACCCTA+TGG - chr2.3:54855546-54855565 MS.gene52391:CDS 35.0%
CAAGTCGGTAAAGGAATTAA+AGG - chr2.3:54855469-54855488 MS.gene52391:CDS 35.0%
CATCAACTTTCTCTTTCCAT+AGG + chr2.3:54855565-54855584 None:intergenic 35.0%
GAATCTGTACACCAATTCAT+AGG + chr2.3:54855279-54855298 None:intergenic 35.0%
GACAATGTTAACAATGTCAG+AGG + chr2.3:54855204-54855223 None:intergenic 35.0%
GTGCAATTTCTTCTCAACAA+AGG - chr2.3:54855791-54855810 MS.gene52391:CDS 35.0%
TATGAGGAAAAACGCAATCT+AGG - chr2.3:54855926-54855945 MS.gene52391:CDS 35.0%
! AAACTTTGGCAACACAGTTT+TGG + chr2.3:54855153-54855172 None:intergenic 35.0%
! ATCACAATGCTGATTGAGAA+TGG - chr2.3:54855377-54855396 MS.gene52391:CDS 35.0%
! ATGTCTTTAAGAAATGGGGT+TGG - chr2.3:54855582-54855601 MS.gene52391:CDS 35.0%
! GCAATCTGACAAGGAAATTT+TGG - chr2.3:54855301-54855320 MS.gene52391:CDS 35.0%
! TCACAATGCTGATTGAGAAT+GGG - chr2.3:54855378-54855397 MS.gene52391:CDS 35.0%
!! AACTTTTGGGTCAATCAGTT+GGG - chr2.3:54855686-54855705 MS.gene52391:CDS 35.0%
AATAGTCCCAGCCTATGAAT+TGG - chr2.3:54855265-54855284 MS.gene52391:CDS 40.0%
AGGCTTACATACAAGACTCT+AGG + chr2.3:54855236-54855255 None:intergenic 40.0%
CAGATTCTTGCAATCTGACA+AGG - chr2.3:54855292-54855311 MS.gene52391:CDS 40.0%
GAGAAGAAATTGCACAACAG+CGG + chr2.3:54855786-54855805 None:intergenic 40.0%
GGAAAAAAGGATCATTCCGA+GGG - chr2.3:54855760-54855779 MS.gene52391:CDS 40.0%
TGGAAAAAAGGATCATTCCG+AGG - chr2.3:54855759-54855778 MS.gene52391:CDS 40.0%
TGTACACCAATTCATAGGCT+GGG + chr2.3:54855274-54855293 None:intergenic 40.0%
! CACAATGCTGATTGAGAATG+GGG - chr2.3:54855379-54855398 MS.gene52391:CDS 40.0%
! CTGGGACTATTTGTTTGTTG+AGG + chr2.3:54855256-54855275 None:intergenic 40.0%
!! GAACTTTTGGGTCAATCAGT+TGG - chr2.3:54855685-54855704 MS.gene52391:CDS 40.0%
!!! TTTGGCAACACAGTTTTGGA+GGG + chr2.3:54855149-54855168 None:intergenic 40.0%
CTGTACACCAATTCATAGGC+TGG + chr2.3:54855275-54855294 None:intergenic 45.0%
TGACATGCTCAAGTCGGTAA+AGG - chr2.3:54855460-54855479 MS.gene52391:CDS 45.0%
TTGGGTCAATCAGTTGGGTT+GGG - chr2.3:54855691-54855710 MS.gene52391:CDS 45.0%
TTTGGGTCAATCAGTTGGGT+TGG - chr2.3:54855690-54855709 MS.gene52391:CDS 45.0%
!! CTTTGGCAACACAGTTTTGG+AGG + chr2.3:54855150-54855169 None:intergenic 45.0%
CATTGCTGAGGGAACAGACT+CGG - chr2.3:54855423-54855442 MS.gene52391:CDS 50.0%
GAGACGTGACATGCTCAAGT+CGG - chr2.3:54855454-54855473 MS.gene52391:CDS 50.0%
!! GTCAGAGGTAGAAGCACCTT+TGG + chr2.3:54855189-54855208 None:intergenic 50.0%
!! TCAGTTGGGTTGGGATGCTA+TGG - chr2.3:54855700-54855719 MS.gene52391:CDS 50.0%
!!! CACAGTTTTGGAGGGTTTGC+AGG + chr2.3:54855141-54855160 None:intergenic 50.0%
AATTGCACAACAGCGGCCCT+CGG + chr2.3:54855779-54855798 None:intergenic 55.0%
GGTTTGCAGGAAAGCAGCTC+TGG + chr2.3:54855128-54855147 None:intergenic 55.0%
! GGAAAGCAGCTCTGGCATCT+TGG + chr2.3:54855120-54855139 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 54855110 54855952 54855110 ID=MS.gene52391
chr2.3 mRNA 54855110 54855952 54855110 ID=MS.gene52391.t1;Parent=MS.gene52391
chr2.3 exon 54855110 54855952 54855110 ID=MS.gene52391.t1.exon1;Parent=MS.gene52391.t1
chr2.3 CDS 54855110 54855952 54855110 ID=cds.MS.gene52391.t1;Parent=MS.gene52391.t1
Gene Sequence

>MS.gene52391

ATGATTGCCAAGATGCCAGAGCTGCTTTCCTGCAAACCCTCCAAAACTGTGTTGCCAAAGTTTCAATTTTTTCTCTCCAAAGGTGCTTCTACCTCTGACATTGTTAACATTGTCACTAAGACTCCTAGAGTCTTGTATGTAAGCCTCAACAAACAAATAGTCCCAGCCTATGAATTGGTGTACAGATTCTTGCAATCTGACAAGGAAATTTTGGAAAAGTTGAATTACAGTGCAAATTTACTTTGTGATTGTACTGTGCAAAATAACATCACAATGCTGATTGAGAATGGGGTGTCTGACTCAAACATTAAATCATTGCTGAGGGAACAGACTCGGATATTCAAGAGACGTGACATGCTCAAGTCGGTAAAGGAATTAAAGGATTTGGGGTTTAATCCTTCAAAAACAACTTTTGGTGTAGCATTGCATGCCAAAACAACAGTAAACAATACCCTATGGAAAGAGAAAGTTGATGTCTTTAAGAAATGGGGTTGGTCTGAAGAAGATTCTCTCGAAGCATTTAGAAAGAAACCTTATTCTATGTTAACATCTATTGATAAAATAAATTTAGTGATGAACTTTTGGGTCAATCAGTTGGGTTGGGATGCTATGGCCATTGCCAAACAACCTTATATTTTGTCATTAAGTTTGGAAAAAAGGATCATTCCGAGGGCCGCTGTTGTGCAATTTCTTCTCAACAAAGGTTTGACAGATAAGAACGCAAGCTTAACTTATCCATTTGTAGTGACTGATAAGTTGTTTCTTAATATGTTTATAAAACGTTTTGAGAATGAGGCTTCTTATCTTTTAAAGTTGTATGAGGAAAAACGCAATCTAGGATAG
Protein sequence

>MS.gene52391.t1

MIAKMPELLSCKPSKTVLPKFQFFLSKGASTSDIVNIVTKTPRVLYVSLNKQIVPAYELVYRFLQSDKEILEKLNYSANLLCDCTVQNNITMLIENGVSDSNIKSLLREQTRIFKRRDMLKSVKELKDLGFNPSKTTFGVALHAKTTVNNTLWKEKVDVFKKWGWSEEDSLEAFRKKPYSMLTSIDKINLVMNFWVNQLGWDAMAIAKQPYILSLSLEKRIIPRAAVVQFLLNKGLTDKNASLTYPFVVTDKLFLNMFIKRFENEASYLLKLYEEKRNLG