AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054092

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054092.t1 MTR_1g027950 74.528 318 51 6 1 294 1 312 5.27e-160 451
MS.gene054092.t1 MTR_1g027710 72.258 310 77 6 1 304 1 307 2.95e-150 424
MS.gene054092.t1 MTR_1g027880 69.355 310 72 6 1 294 1 303 8.77e-145 410
MS.gene054092.t1 MTR_6g044970 66.026 312 82 8 1 307 1 293 8.62e-134 382
MS.gene054092.t1 MTR_1g027830 55.674 282 102 7 9 284 7 271 5.29e-92 287
MS.gene054092.t1 MTR_1g028250 52.027 296 116 9 15 303 3 279 5.42e-89 267
MS.gene054092.t1 MTR_3g028640 53.788 264 98 8 36 294 14 258 4.66e-84 254
MS.gene054092.t1 MTR_1g027050 45.253 316 110 11 26 290 1 304 1.42e-76 249
MS.gene054092.t1 MTR_1g027070 49.306 288 116 11 15 290 6 275 4.80e-73 238
MS.gene054092.t1 MTR_1g027140 48.110 291 107 10 36 290 25 307 7.46e-73 239
MS.gene054092.t1 MTR_1g027030 47.950 317 111 11 15 290 6 309 1.30e-72 237
MS.gene054092.t1 MTR_1g027030 47.950 317 111 11 15 290 6 309 2.60e-72 237
MS.gene054092.t1 MTR_1g026950 46.739 276 109 10 25 284 6 259 1.37e-66 210
MS.gene054092.t1 MTR_1g027450 41.935 279 125 8 24 284 4 263 5.87e-63 201
MS.gene054092.t1 MTR_1g027260 42.282 298 127 11 34 308 14 289 6.03e-61 196
MS.gene054092.t1 MTR_1g027380 42.205 263 115 7 36 284 19 258 9.17e-60 193
MS.gene054092.t1 MTR_1g026970 43.426 251 107 7 50 284 31 262 7.11e-58 188
MS.gene054092.t1 MTR_1g027180 42.647 272 117 9 34 286 19 270 9.67e-58 189
MS.gene054092.t1 MTR_1g027360 43.478 276 110 10 50 301 31 284 6.65e-57 186
MS.gene054092.t1 MTR_1g027520 41.825 263 109 8 17 260 1 238 1.10e-55 181
MS.gene054092.t1 MTR_1g027990 35.889 287 155 11 18 294 12 279 1.66e-44 161
MS.gene054092.t1 MTR_1g027680 37.063 286 151 12 18 294 11 276 1.14e-43 159
MS.gene054092.t1 MTR_1g028090 38.372 258 118 9 47 284 29 265 2.43e-43 152
MS.gene054092.t1 MTR_1g028280 35.507 276 141 8 22 295 7 247 1.05e-42 155
MS.gene054092.t1 MTR_1g028280 35.507 276 141 8 22 295 7 247 1.17e-42 156
MS.gene054092.t1 MTR_1g028150 37.450 251 123 9 47 284 29 258 4.33e-41 144
MS.gene054092.t1 MTR_1g031560 31.839 223 119 8 55 264 33 235 3.02e-23 100
MS.gene054092.t1 MTR_1g031450 30.588 255 142 9 16 265 1 225 1.72e-21 94.7
MS.gene054092.t1 MTR_1g031535 29.317 249 144 8 22 265 4 225 9.47e-21 90.1
MS.gene054092.t1 MTR_1g031510 32.000 225 119 8 53 264 35 238 3.64e-20 91.3
MS.gene054092.t1 MTR_1g031490 30.204 245 138 8 55 287 36 259 4.95e-20 88.2
MS.gene054092.t1 MTR_1g027440 36.424 151 75 6 155 305 44 173 2.63e-19 88.6
MS.gene054092.t1 MTR_1g031280 31.839 223 128 9 55 266 37 246 1.73e-18 86.3
MS.gene054092.t1 MTR_1g031520 31.278 227 114 10 55 264 33 234 2.02e-18 85.9
MS.gene054092.t1 MTR_1g031200 43.434 99 52 2 37 134 9 104 1.37e-12 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 60 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCCATTCGTCGCTTATTC+AGG 0.303980 1.3:+14141159 MS.gene054092:CDS
GCAATTACCCTCTTGAATTC+CGG 0.306653 1.3:-14140626 None:intergenic
TTCTGATCACCACAGATTCT+TGG 0.311431 1.3:-14140496 None:intergenic
ACATTATCATTGATTTCATA+TGG 0.317079 1.3:-14140721 None:intergenic
TGATATTGATTCCGCATAAT+AGG 0.340150 1.3:-14140308 None:intergenic
CAATAACCACCATCCCAATT+TGG 0.341915 1.3:-14140345 None:intergenic
AAAAGCATAAAGATAGCTTT+TGG 0.362256 1.3:-14140830 None:intergenic
CAATTACCCTCTTGAATTCC+GGG 0.362332 1.3:-14140625 None:intergenic
CTTTCATACGAGGAAATTCA+TGG 0.382308 1.3:+14141006 MS.gene054092:CDS
TCTGATCACCACAGATTCTT+GGG 0.422006 1.3:-14140495 None:intergenic
GAATAAGCGACGAATGGATA+AGG 0.426793 1.3:-14141156 None:intergenic
AAGAAGGTGGACAATATGTT+TGG 0.429047 1.3:-14140423 None:intergenic
ACTACGTAAACTACACAATT+CGG 0.446333 1.3:+14140593 MS.gene054092:CDS
TACTCAGGATCGTCCTTCAC+TGG 0.474542 1.3:-14140775 None:intergenic
ATTCATGGAATCCTGCTGTA+TGG 0.480917 1.3:+14141021 MS.gene054092:CDS
AATAAGCGACGAATGGATAA+GGG 0.497987 1.3:-14141155 None:intergenic
CCACCGTTGATATCAATGTA+AGG 0.513057 1.3:-14140694 None:intergenic
ACATCCGTTTCGATTGATGA+AGG 0.522302 1.3:+14140471 MS.gene054092:CDS
AGCTACCACTCCTTCTCCGT+CGG 0.533767 1.3:+14140871 MS.gene054092:CDS
GGTCGATGTTGATGTCGATC+TGG 0.547084 1.3:-14140982 None:intergenic
TTCGGGTAAATACTACGTGC+AGG 0.547549 1.3:+14140564 MS.gene054092:CDS
TGAATTTCCTCGTATGAAAG+TGG 0.547707 1.3:-14141003 None:intergenic
CTGACCTTGACACTGTCACT+AGG 0.553304 1.3:-14140949 None:intergenic
GCTACCACTCCTTCTCCGTC+GGG 0.557485 1.3:+14140872 MS.gene054092:CDS
GATCCTTACATTGATATCAA+CGG 0.558389 1.3:+14140691 MS.gene054092:CDS
TTTGGAGTCGGAGTTGACGC+AGG 0.558522 1.3:-14140812 None:intergenic
GAAGGACGATCCTGAGTATG+TGG 0.559493 1.3:+14140780 MS.gene054092:CDS
GACAGTGTCAAGGTCAGAGA+AGG 0.562750 1.3:+14140955 MS.gene054092:CDS
GGGTCCTTCATCAATCGAAA+CGG 0.566190 1.3:-14140475 None:intergenic
GGAGCTGTGTCCACATACTC+AGG 0.566585 1.3:-14140790 None:intergenic
AAGCTTCCTCCAAATTGGGA+TGG 0.567417 1.3:+14140336 MS.gene054092:CDS
TGCTACTTCAATGAAACTAT+CGG 0.574601 1.3:+14141102 MS.gene054092:CDS
TGATTCCGCATAATAGGTGA+AGG 0.577211 1.3:-14140302 None:intergenic
ACAATTCGGCTAGTTGATCC+CGG 0.577912 1.3:+14140607 MS.gene054092:CDS
AGATGCATTTCTTACTGCAG+TGG 0.582343 1.3:-14141182 None:intergenic
ATAGCTGAAATCCATACAGC+AGG 0.584086 1.3:-14141032 None:intergenic
TAAGAAATAGCGAGGAATGG+AGG 0.590856 1.3:-14140650 None:intergenic
CTTCCTCCAAATTGGGATGG+TGG 0.592975 1.3:+14140339 MS.gene054092:CDS
ACATAGCAACAAGCTTCACT+TGG 0.593630 1.3:-14140912 None:intergenic
ATCTCCCGACGGAGAAGGAG+TGG 0.594346 1.3:-14140876 None:intergenic
CTTACATTGATATCAACGGT+GGG 0.606079 1.3:+14140695 MS.gene054092:CDS
TGGCCTGAATAAGCGACGAA+TGG 0.606730 1.3:-14141162 None:intergenic
GAACTGTAGCAAACCAGTGA+AGG 0.608808 1.3:+14140762 MS.gene054092:CDS
GGATAAGGGCAATAATTCGA+TGG 0.612580 1.3:-14141141 None:intergenic
TTGGAGTCGGAGTTGACGCA+GGG 0.612603 1.3:-14140811 None:intergenic
AGTTGATCCCGGAATTCAAG+AGG 0.622904 1.3:+14140618 MS.gene054092:CDS
TTTCAGCTATCGTGGATCAG+TGG 0.632783 1.3:+14141045 MS.gene054092:CDS
TAACCACCATCCCAATTTGG+AGG 0.641833 1.3:-14140342 None:intergenic
AGTTAAGAAATAGCGAGGAA+TGG 0.644010 1.3:-14140653 None:intergenic
CCTTACATTGATATCAACGG+TGG 0.649004 1.3:+14140694 MS.gene054092:CDS
TATTGTCCACCTTCTTCATG+CGG 0.651102 1.3:+14140430 MS.gene054092:CDS
GAAATCCTTCACCTATTATG+CGG 0.657547 1.3:+14140297 MS.gene054092:CDS
AGGAGTGGTAGCTCTCGTCA+AGG 0.659030 1.3:-14140861 None:intergenic
TGTATGGATTTCAGCTATCG+TGG 0.661377 1.3:+14141037 MS.gene054092:CDS
AATGCAGTTAAGAAATAGCG+AGG 0.661931 1.3:-14140658 None:intergenic
GTTGATCCCGGAATTCAAGA+GGG 0.665740 1.3:+14140619 MS.gene054092:CDS
GGTGCTTGTAAAGACTCTTG+TGG 0.666075 1.3:+14141066 MS.gene054092:CDS
TTACATTGATATCAACGGTG+GGG 0.677909 1.3:+14140696 MS.gene054092:CDS
ATGAAGGACCCAAGAATCTG+TGG 0.688942 1.3:+14140487 MS.gene054092:CDS
ACATCGACCACTTTCATACG+AGG 0.720190 1.3:+14140996 MS.gene054092:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATTATCATTGATTTCATA+TGG - chr1.3:14140724-14140743 None:intergenic 20.0%
!!! AAAAGCATAAAGATAGCTTT+TGG - chr1.3:14140833-14140852 None:intergenic 25.0%
ACTACGTAAACTACACAATT+CGG + chr1.3:14140593-14140612 MS.gene054092:CDS 30.0%
GATCCTTACATTGATATCAA+CGG + chr1.3:14140691-14140710 MS.gene054092:CDS 30.0%
! AAGCTATCTTTATGCTTTTG+CGG + chr1.3:14140834-14140853 MS.gene054092:CDS 30.0%
! TGCTACTTCAATGAAACTAT+CGG + chr1.3:14141102-14141121 MS.gene054092:CDS 30.0%
! TTTTAAGCTTCCTCCAAATT+GGG + chr1.3:14140332-14140351 MS.gene054092:CDS 30.0%
!! TGATATTGATTCCGCATAAT+AGG - chr1.3:14140311-14140330 None:intergenic 30.0%
!!! ATAAAGATAGCTTTTGGAGT+CGG - chr1.3:14140827-14140846 None:intergenic 30.0%
AAGAAGGTGGACAATATGTT+TGG - chr1.3:14140426-14140445 None:intergenic 35.0%
AATAAGCGACGAATGGATAA+GGG - chr1.3:14141158-14141177 None:intergenic 35.0%
AATGCAGTTAAGAAATAGCG+AGG - chr1.3:14140661-14140680 None:intergenic 35.0%
AGTTAAGAAATAGCGAGGAA+TGG - chr1.3:14140656-14140675 None:intergenic 35.0%
CTTACATTGATATCAACGGT+GGG + chr1.3:14140695-14140714 MS.gene054092:CDS 35.0%
CTTTCATACGAGGAAATTCA+TGG + chr1.3:14141006-14141025 MS.gene054092:CDS 35.0%
GAAATCCTTCACCTATTATG+CGG + chr1.3:14140297-14140316 MS.gene054092:CDS 35.0%
TGAATTTCCTCGTATGAAAG+TGG - chr1.3:14141006-14141025 None:intergenic 35.0%
TTACATTGATATCAACGGTG+GGG + chr1.3:14140696-14140715 MS.gene054092:CDS 35.0%
! ACAGTGTTAACTCTGTTTTC+GGG + chr1.3:14140547-14140566 MS.gene054092:CDS 35.0%
! ATAGTCTTTTAATCTCCCGA+CGG - chr1.3:14140890-14140909 None:intergenic 35.0%
! CACAGTGTTAACTCTGTTTT+CGG + chr1.3:14140546-14140565 MS.gene054092:CDS 35.0%
! CTTTTAAGCTTCCTCCAAAT+TGG + chr1.3:14140331-14140350 MS.gene054092:CDS 35.0%
ACATAGCAACAAGCTTCACT+TGG - chr1.3:14140915-14140934 None:intergenic 40.0%
ACATCCGTTTCGATTGATGA+AGG + chr1.3:14140471-14140490 MS.gene054092:CDS 40.0%
AGATGCATTTCTTACTGCAG+TGG - chr1.3:14141185-14141204 None:intergenic 40.0%
ATAGCTGAAATCCATACAGC+AGG - chr1.3:14141035-14141054 None:intergenic 40.0%
ATTCATGGAATCCTGCTGTA+TGG + chr1.3:14141021-14141040 MS.gene054092:CDS 40.0%
CAATAACCACCATCCCAATT+TGG - chr1.3:14140348-14140367 None:intergenic 40.0%
CAATTACCCTCTTGAATTCC+GGG - chr1.3:14140628-14140647 None:intergenic 40.0%
CCACCGTTGATATCAATGTA+AGG - chr1.3:14140697-14140716 None:intergenic 40.0%
CCTTACATTGATATCAACGG+TGG + chr1.3:14140694-14140713 MS.gene054092:CDS 40.0%
GAATAAGCGACGAATGGATA+AGG - chr1.3:14141159-14141178 None:intergenic 40.0%
GCAATTACCCTCTTGAATTC+CGG - chr1.3:14140629-14140648 None:intergenic 40.0%
GGATAAGGGCAATAATTCGA+TGG - chr1.3:14141144-14141163 None:intergenic 40.0%
TAAGAAATAGCGAGGAATGG+AGG - chr1.3:14140653-14140672 None:intergenic 40.0%
TATCCATTCGTCGCTTATTC+AGG + chr1.3:14141159-14141178 MS.gene054092:CDS 40.0%
TATTGTCCACCTTCTTCATG+CGG + chr1.3:14140430-14140449 MS.gene054092:CDS 40.0%
TCTGATCACCACAGATTCTT+GGG - chr1.3:14140498-14140517 None:intergenic 40.0%
TGATTCCGCATAATAGGTGA+AGG - chr1.3:14140305-14140324 None:intergenic 40.0%
TGTATGGATTTCAGCTATCG+TGG + chr1.3:14141037-14141056 MS.gene054092:CDS 40.0%
TTCTGATCACCACAGATTCT+TGG - chr1.3:14140499-14140518 None:intergenic 40.0%
! TTTTCCTAGTGACAGTGTCA+AGG + chr1.3:14140945-14140964 MS.gene054092:CDS 40.0%
!!! CACTGTGATGTTGTTTTCAC+AGG - chr1.3:14140533-14140552 None:intergenic 40.0%
AAGCTTCCTCCAAATTGGGA+TGG + chr1.3:14140336-14140355 MS.gene054092:CDS 45.0%
ACATCGACCACTTTCATACG+AGG + chr1.3:14140996-14141015 MS.gene054092:CDS 45.0%
AGTTGATCCCGGAATTCAAG+AGG + chr1.3:14140618-14140637 MS.gene054092:CDS 45.0%
ATGAAGGACCCAAGAATCTG+TGG + chr1.3:14140487-14140506 MS.gene054092:CDS 45.0%
GAACTGTAGCAAACCAGTGA+AGG + chr1.3:14140762-14140781 MS.gene054092:CDS 45.0%
GGGTCCTTCATCAATCGAAA+CGG - chr1.3:14140478-14140497 None:intergenic 45.0%
GGTGCTTGTAAAGACTCTTG+TGG + chr1.3:14141066-14141085 MS.gene054092:CDS 45.0%
GTTGATCCCGGAATTCAAGA+GGG + chr1.3:14140619-14140638 MS.gene054092:CDS 45.0%
TAACCACCATCCCAATTTGG+AGG - chr1.3:14140345-14140364 None:intergenic 45.0%
TTCGGGTAAATACTACGTGC+AGG + chr1.3:14140564-14140583 MS.gene054092:CDS 45.0%
TTTCAGCTATCGTGGATCAG+TGG + chr1.3:14141045-14141064 MS.gene054092:CDS 45.0%
! ACAATTCGGCTAGTTGATCC+CGG + chr1.3:14140607-14140626 MS.gene054092:CDS 45.0%
! ATTTTGCCGCATGAAGAAGG+TGG - chr1.3:14140439-14140458 None:intergenic 45.0%
! GTGATTTTGCCGCATGAAGA+AGG - chr1.3:14140442-14140461 None:intergenic 45.0%
! TTTTAATCTCCCGACGGAGA+AGG - chr1.3:14140884-14140903 None:intergenic 45.0%
CTGACCTTGACACTGTCACT+AGG - chr1.3:14140952-14140971 None:intergenic 50.0%
CTTCCTCCAAATTGGGATGG+TGG + chr1.3:14140339-14140358 MS.gene054092:CDS 50.0%
GAAGGACGATCCTGAGTATG+TGG + chr1.3:14140780-14140799 MS.gene054092:CDS 50.0%
GACAGTGTCAAGGTCAGAGA+AGG + chr1.3:14140955-14140974 MS.gene054092:CDS 50.0%
GGTCGATGTTGATGTCGATC+TGG - chr1.3:14140985-14141004 None:intergenic 50.0%
TACTCAGGATCGTCCTTCAC+TGG - chr1.3:14140778-14140797 None:intergenic 50.0%
TGGCCTGAATAAGCGACGAA+TGG - chr1.3:14141165-14141184 None:intergenic 50.0%
AGCTACCACTCCTTCTCCGT+CGG + chr1.3:14140871-14140890 MS.gene054092:CDS 55.0%
AGGAGTGGTAGCTCTCGTCA+AGG - chr1.3:14140864-14140883 None:intergenic 55.0%
GGAGCTGTGTCCACATACTC+AGG - chr1.3:14140793-14140812 None:intergenic 55.0%
TTGGAGTCGGAGTTGACGCA+GGG - chr1.3:14140814-14140833 None:intergenic 55.0%
! TTTGGAGTCGGAGTTGACGC+AGG - chr1.3:14140815-14140834 None:intergenic 55.0%
ATCTCCCGACGGAGAAGGAG+TGG - chr1.3:14140879-14140898 None:intergenic 60.0%
GCTACCACTCCTTCTCCGTC+GGG + chr1.3:14140872-14140891 MS.gene054092:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 14140286 14141215 14140286 ID=MS.gene054092
chr1.3 mRNA 14140286 14141215 14140286 ID=MS.gene054092.t1;Parent=MS.gene054092
chr1.3 exon 14140286 14141215 14140286 ID=MS.gene054092.t1.exon1;Parent=MS.gene054092.t1
chr1.3 CDS 14140286 14141215 14140286 ID=cds.MS.gene054092.t1;Parent=MS.gene054092.t1
Gene Sequence

>MS.gene054092

ATGAGCAGAGGGAAATCCTTCACCTATTATGCGGAATCAATATCACTTTTAAGCTTCCTCCAAATTGGGATGGTGGTTATTGTCTTACTATTGCATCATCATCATCAAACATGTGATGCAATTACTAATACAAATAACCAAACATATTGTCCACCTTCTTCATGCGGCAAAATCACAAACATAAAACATCCGTTTCGATTGATGAAGGACCCAAGAATCTGTGGTGATCAGAAGTACGAGTTATCCTGTGAAAACAACATCACAGTGTTAACTCTGTTTTCGGGTAAATACTACGTGCAGGAAATCAACTACGTAAACTACACAATTCGGCTAGTTGATCCCGGAATTCAAGAGGGTAATTGCTCCTCCATTCCTCGCTATTTCTTAACTGCATTCAATTTCTTAGATCCTTACATTGATATCAACGGTGGGGATCCATATGAAATCAATGATAATGTTGCACACATTATATATTTGAACTGTAGCAAACCAGTGAAGGACGATCCTGAGTATGTGGACACAGCTCCCTGCGTCAACTCCGACTCCAAAAGCTATCTTTATGCTTTTGCGGCAGACCTTGACGAGAGCTACCACTCCTTCTCCGTCGGGAGATTAAAAGACTATTGCCAAGTGAAGCTTGTTGCTATGTCATCTTCAGATTTTCCTAGTGACAGTGTCAAGGTCAGAGAAGGTGTACCAGATCGACATCAACATCGACCACTTTCATACGAGGAAATTCATGGAATCCTGCTGTATGGATTTCAGCTATCGTGGATCAGTGGTGCTTGTAAAGACTCTTGTGGCGATAATCAAGAGTGCTACTTCAATGAAACTATCGGAGATCTTAAATGCACACCATCGAATTATTGCCCTTATCCATTCGTCGCTTATTCAGGCCACTGCAGTAAGAAATGCATCTTTTTATTTTAA
Protein sequence

>MS.gene054092.t1

MSRGKSFTYYAESISLLSFLQIGMVVIVLLLHHHHQTCDAITNTNNQTYCPPSSCGKITNIKHPFRLMKDPRICGDQKYELSCENNITVLTLFSGKYYVQEINYVNYTIRLVDPGIQEGNCSSIPRYFLTAFNFLDPYIDINGGDPYEINDNVAHIIYLNCSKPVKDDPEYVDTAPCVNSDSKSYLYAFAADLDESYHSFSVGRLKDYCQVKLVAMSSSDFPSDSVKVREGVPDRHQHRPLSYEEIHGILLYGFQLSWISGACKDSCGDNQECYFNETIGDLKCTPSNYCPYPFVAYSGHCSKKCIFLF