AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene033812

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene033812.t1 MTR_2g049780 99.000 300 3 0 1 300 14 313 0.0 603
MS.gene033812.t1 MTR_5g041630 42.491 273 151 1 30 296 25 297 3.68e-68 214
MS.gene033812.t1 MTR_2g067230 39.076 238 140 2 56 293 69 301 4.93e-57 187
MS.gene033812.t1 MTR_7g081270 40.654 214 123 4 81 291 67 279 2.27e-42 147
MS.gene033812.t1 MTR_2g034600 30.165 242 154 6 57 297 322 549 2.18e-25 106
MS.gene033812.t1 MTR_2g034600 30.165 242 154 6 57 297 261 488 2.20e-25 105
MS.gene033812.t1 MTR_2g034600 30.165 242 154 6 57 297 326 553 2.27e-25 105
MS.gene033812.t1 MTR_4g070060 28.112 249 170 6 55 296 344 590 1.80e-21 94.7
MS.gene033812.t1 MTR_5g068860 26.136 264 154 7 69 293 223 484 1.75e-19 89.0
MS.gene033812.t1 MTR_6g003960 25.000 228 159 3 70 291 366 587 5.80e-18 84.3
MS.gene033812.t1 MTR_5g094610 24.215 223 154 4 57 268 227 445 1.66e-17 82.8
MS.gene033812.t1 MTR_4g084630 23.600 250 181 4 52 291 69 318 3.86e-17 80.9
MS.gene033812.t1 MTR_1g115415 25.556 270 160 5 63 293 185 452 4.93e-17 81.6
MS.gene033812.t1 MTR_0320s0040 35.556 90 57 1 56 145 48 136 2.92e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene033812.t1 AT2G34620 66.212 293 92 3 9 295 3 294 1.84e-129 370
MS.gene033812.t1 AT2G03050 48.101 237 122 1 56 291 32 268 7.64e-70 218
MS.gene033812.t1 AT2G03050 48.101 237 122 1 56 291 33 269 9.57e-70 218
MS.gene033812.t1 AT2G36000 37.037 243 144 4 58 296 75 312 4.31e-51 171
MS.gene033812.t1 AT2G36000 37.037 243 144 4 58 296 75 312 5.56e-51 171
MS.gene033812.t1 AT3G18870 37.705 244 143 4 51 291 31 268 5.91e-46 156
MS.gene033812.t1 AT2G21710 28.340 247 168 6 57 296 353 597 3.38e-24 102
MS.gene033812.t1 AT4G14605 29.787 235 160 5 58 291 237 467 1.07e-21 95.1
MS.gene033812.t1 AT4G14605 29.787 235 160 5 58 291 237 467 1.07e-21 95.1
MS.gene033812.t1 AT1G78930 25.328 229 167 2 65 291 348 574 1.59e-19 89.0
MS.gene033812.t1 AT5G55580 24.771 218 160 4 60 273 226 443 7.02e-17 81.3
MS.gene033812.t1 AT5G55580 24.771 218 160 4 60 273 120 337 7.55e-17 80.5
MS.gene033812.t1 AT4G02990 26.667 270 157 8 63 293 225 492 4.46e-16 79.0
MS.gene033812.t1 AT4G02990 26.667 270 157 8 63 293 225 492 4.46e-16 79.0
MS.gene033812.t1 AT4G38160 24.506 253 180 4 52 293 70 322 1.17e-15 76.6
MS.gene033812.t1 AT4G38160 24.506 253 180 4 52 293 70 322 1.17e-15 76.6
MS.gene033812.t1 AT4G38160 24.506 253 180 4 52 293 70 322 1.60e-15 76.6
MS.gene033812.t1 AT4G38160 24.506 253 180 4 52 293 70 322 1.79e-15 76.3
MS.gene033812.t1 AT2G44020 25.481 208 119 2 86 293 286 457 3.95e-15 75.9
MS.gene033812.t1 AT2G21710 25.243 206 145 6 57 255 353 556 3.29e-13 70.1
MS.gene033812.t1 AT2G21710 24.878 205 145 6 57 254 353 555 2.52e-12 67.4

Find 56 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTAAGCATTTGGAGAGTA+TGG 0.202455 2.3:+41576386 MS.gene033812:CDS
AAAGTACTGATGATGAATTT+AGG 0.234140 2.3:+41576646 MS.gene033812:CDS
TTATCAAGATTGTGTTCTTT+TGG 0.240932 2.3:+41576332 MS.gene033812:CDS
TTTGGGTTTGGGAGTTAAAT+TGG 0.262027 2.3:-41575878 None:intergenic
GAAGTAATGGGCATTGATTC+AGG 0.276282 2.3:+41575982 MS.gene033812:CDS
ATGCTTGATGTGAGAATCTT+AGG 0.276341 2.3:-41576129 None:intergenic
TGTGGAAATGAAGGGGAAAT+TGG 0.285794 2.3:+41576509 MS.gene033812:CDS
AAGTACTGATGATGAATTTA+GGG 0.305836 2.3:+41576647 MS.gene033812:CDS
GGACACATGCCAAAGATTCT+TGG 0.310114 2.3:-41576108 None:intergenic
AAAGACCTTCCAAGAATCTT+TGG 0.314251 2.3:+41576099 MS.gene033812:CDS
AAGGTAGCTGTATGAAGGTT+AGG 0.324878 2.3:-41576024 None:intergenic
GTCTTTATGTTGGATACCTT+TGG 0.333066 2.3:-41576082 None:intergenic
AATGGAATGAATGGATTCTA+AGG 0.339360 2.3:-41576043 None:intergenic
TATTCCTAAACTTAAGCATT+TGG 0.349186 2.3:+41576377 MS.gene033812:CDS
CTCTCCAAATGCTTAAGTTT+AGG 0.351147 2.3:-41576381 None:intergenic
TAGTTTGGAGAATAGGATAA+AGG 0.362241 2.3:+41576566 MS.gene033812:CDS
ATCCTTTGTCTTGAAGTAAT+GGG 0.365238 2.3:+41575970 MS.gene033812:CDS
AATCCTTTGTCTTGAAGTAA+TGG 0.396956 2.3:+41575969 MS.gene033812:CDS
GGAGACAAGAAAAGTGATAA+TGG 0.414952 2.3:-41576061 None:intergenic
ACACTAGAAGTAAGCAATCT+TGG 0.430968 2.3:-41576240 None:intergenic
AAAAGTGATAATGGAATGAA+TGG 0.434056 2.3:-41576052 None:intergenic
ATTAAGAGATTTAGAAGCAT+TGG 0.444652 2.3:+41576308 MS.gene033812:CDS
TTTAGGGAGTTGATAAAGAA+GGG 0.454349 2.3:+41576663 MS.gene033812:CDS
AGAGCTATGGTTCTAGCAGC+TGG 0.458017 2.3:-41575799 None:intergenic
GGTTAGACACATGGAGGTTG+TGG 0.463307 2.3:+41576587 MS.gene033812:CDS
TTCTTGGAAGGTCTTTATGT+TGG 0.468294 2.3:-41576092 None:intergenic
CACATGGAGGTTGTGGAAAG+TGG 0.473398 2.3:+41576594 MS.gene033812:CDS
TTGGTTGAAGGAGGTGATGA+TGG 0.480821 2.3:-41575859 None:intergenic
AGGTAGCTGTATGAAGGTTA+GGG 0.481780 2.3:-41576023 None:intergenic
TAAAGAAGAGGCTAGGTGTA+TGG 0.485234 2.3:+41576416 MS.gene033812:CDS
CTTAAGCATTTGGAGAGTAT+GGG 0.487893 2.3:+41576387 MS.gene033812:CDS
AATAAGTGTCCTTTCAACAT+TGG 0.489396 2.3:-41576358 None:intergenic
ATTTAGGGAGTTGATAAAGA+AGG 0.499226 2.3:+41576662 MS.gene033812:CDS
TTGGGAGTTAAATTGGTTGA+AGG 0.501320 2.3:-41575871 None:intergenic
GGAGTTAAATTGGTTGAAGG+AGG 0.504389 2.3:-41575868 None:intergenic
TCATGAGTTGGTGTGTAAAG+TGG 0.520744 2.3:-41575919 None:intergenic
AGAAGATGAGTGTAGAGCTA+TGG 0.532807 2.3:-41575812 None:intergenic
AGGCTAGGTGTATGGTGTTG+AGG 0.553273 2.3:+41576424 MS.gene033812:CDS
ATTGCTTACTTCTAGTGTGG+TGG 0.553869 2.3:+41576245 MS.gene033812:CDS
CTGTTAAGATAAAACAAAGC+AGG 0.557661 2.3:-41576279 None:intergenic
ATACTAAAAGTCAACAATGC+AGG 0.557976 2.3:-41576450 None:intergenic
AAGATTGCTTACTTCTAGTG+TGG 0.564951 2.3:+41576242 MS.gene033812:CDS
ATTCTAAGGTAGCTGTATGA+AGG 0.573875 2.3:-41576029 None:intergenic
TAGGGAGTTGATAAAGAAGG+GGG 0.580226 2.3:+41576665 MS.gene033812:CDS
GGAAATGAAGGGGAAATTGG+AGG 0.580999 2.3:+41576512 MS.gene033812:CDS
ACATGGAGGTTGTGGAAAGT+GGG 0.587398 2.3:+41576595 MS.gene033812:CDS
GAGCTATGGTTCTAGCAGCT+GGG 0.599605 2.3:-41575798 None:intergenic
TATGGGATTTACTAAAGAAG+AGG 0.599972 2.3:+41576404 MS.gene033812:CDS
TGCCCATTACTTCAAGACAA+AGG 0.602484 2.3:-41575972 None:intergenic
TTAGGGAGTTGATAAAGAAG+GGG 0.610325 2.3:+41576664 MS.gene033812:CDS
GAGTTGGTGTGTAAAGTGGA+TGG 0.622825 2.3:-41575915 None:intergenic
GATTTACTAAAGAAGAGGCT+AGG 0.635507 2.3:+41576409 MS.gene033812:CDS
TAGGATAAAGGTTAGACACA+TGG 0.648833 2.3:+41576578 MS.gene033812:CDS
ACATGCCAAAGATTCTTGGA+AGG 0.652767 2.3:-41576104 None:intergenic
AAACTAAAAGAGAAATACTG+AGG 0.668925 2.3:-41576549 None:intergenic
GATAAAGGTTAGACACATGG+AGG 0.698797 2.3:+41576581 MS.gene033812:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATTTGAGTATTTTTCTG+TGG + chr2.3:41576491-41576510 MS.gene033812:CDS 20.0%
!!! ACAGAAAAATACTCAAATTT+TGG - chr2.3:41576492-41576511 None:intergenic 20.0%
!!! TTGTTTTATCTTAACAGATT+AGG + chr2.3:41576285-41576304 MS.gene033812:CDS 20.0%
! AAACTAAAAGAGAAATACTG+AGG - chr2.3:41576552-41576571 None:intergenic 25.0%
! TATTCCTAAACTTAAGCATT+TGG + chr2.3:41576377-41576396 MS.gene033812:CDS 25.0%
! TGTATGAGAAAATCAAAAAC+TGG - chr2.3:41576171-41576190 None:intergenic 25.0%
!! ATTAAGAGATTTAGAAGCAT+TGG + chr2.3:41576308-41576327 MS.gene033812:CDS 25.0%
!! TATTTTTCTGTGGAAATGAA+GGG + chr2.3:41576501-41576520 MS.gene033812:CDS 25.0%
!! TTATCAAGATTGTGTTCTTT+TGG + chr2.3:41576332-41576351 MS.gene033812:CDS 25.0%
!!! AAAAGTGATAATGGAATGAA+TGG - chr2.3:41576055-41576074 None:intergenic 25.0%
!!! AAAGTACTGATGATGAATTT+AGG + chr2.3:41576646-41576665 MS.gene033812:CDS 25.0%
!!! AAGTACTGATGATGAATTTA+GGG + chr2.3:41576647-41576666 MS.gene033812:CDS 25.0%
!!! TCAGTATTTCTCTTTTAGTT+TGG + chr2.3:41576551-41576570 MS.gene033812:CDS 25.0%
AATAAGTGTCCTTTCAACAT+TGG - chr2.3:41576361-41576380 None:intergenic 30.0%
AATCCTTTGTCTTGAAGTAA+TGG + chr2.3:41575969-41575988 MS.gene033812:CDS 30.0%
ATACTAAAAGTCAACAATGC+AGG - chr2.3:41576453-41576472 None:intergenic 30.0%
ATCCTTTGTCTTGAAGTAAT+GGG + chr2.3:41575970-41575989 MS.gene033812:CDS 30.0%
CTGTTAAGATAAAACAAAGC+AGG - chr2.3:41576282-41576301 None:intergenic 30.0%
TAGTTTGGAGAATAGGATAA+AGG + chr2.3:41576566-41576585 MS.gene033812:CDS 30.0%
TATGGGATTTACTAAAGAAG+AGG + chr2.3:41576404-41576423 MS.gene033812:CDS 30.0%
! AATGGAATGAATGGATTCTA+AGG - chr2.3:41576046-41576065 None:intergenic 30.0%
! ATTTTTCTGTGGAAATGAAG+GGG + chr2.3:41576502-41576521 MS.gene033812:CDS 30.0%
! CTTTTAAGCATCAATGACAA+AGG - chr2.3:41576630-41576649 None:intergenic 30.0%
! GTATTTTTCTGTGGAAATGA+AGG + chr2.3:41576500-41576519 MS.gene033812:CDS 30.0%
!! ATTTAGGGAGTTGATAAAGA+AGG + chr2.3:41576662-41576681 MS.gene033812:CDS 30.0%
!! TTTAGGGAGTTGATAAAGAA+GGG + chr2.3:41576663-41576682 MS.gene033812:CDS 30.0%
!!! ACTTTTCTAAAGCTATGATC+AGG - chr2.3:41576207-41576226 None:intergenic 30.0%
!!! TCTCTTTTAGTTTGGAGAAT+AGG + chr2.3:41576559-41576578 MS.gene033812:CDS 30.0%
!!! TTTTGGTTTCCAATGTTGAA+AGG + chr2.3:41576349-41576368 MS.gene033812:CDS 30.0%
AAAGACCTTCCAAGAATCTT+TGG + chr2.3:41576099-41576118 MS.gene033812:CDS 35.0%
AAGATTGCTTACTTCTAGTG+TGG + chr2.3:41576242-41576261 MS.gene033812:CDS 35.0%
ACACTAGAAGTAAGCAATCT+TGG - chr2.3:41576243-41576262 None:intergenic 35.0%
ACTTAAGCATTTGGAGAGTA+TGG + chr2.3:41576386-41576405 MS.gene033812:CDS 35.0%
ATGCTTGATGTGAGAATCTT+AGG - chr2.3:41576132-41576151 None:intergenic 35.0%
CTCTCCAAATGCTTAAGTTT+AGG - chr2.3:41576384-41576403 None:intergenic 35.0%
GATTTACTAAAGAAGAGGCT+AGG + chr2.3:41576409-41576428 MS.gene033812:CDS 35.0%
GGAGACAAGAAAAGTGATAA+TGG - chr2.3:41576064-41576083 None:intergenic 35.0%
GTCTTTATGTTGGATACCTT+TGG - chr2.3:41576085-41576104 None:intergenic 35.0%
TAGGATAAAGGTTAGACACA+TGG + chr2.3:41576578-41576597 MS.gene033812:CDS 35.0%
TTCTTGGAAGGTCTTTATGT+TGG - chr2.3:41576095-41576114 None:intergenic 35.0%
TTGGGAGTTAAATTGGTTGA+AGG - chr2.3:41575874-41575893 None:intergenic 35.0%
! AGTGAGAGTTTTTCATGAGT+TGG - chr2.3:41575934-41575953 None:intergenic 35.0%
! CTTAAGCATTTGGAGAGTAT+GGG + chr2.3:41576387-41576406 MS.gene033812:CDS 35.0%
! TTTGGGTTTGGGAGTTAAAT+TGG - chr2.3:41575881-41575900 None:intergenic 35.0%
!! ATCACTTTTCTTGTCTCCAA+AGG + chr2.3:41576066-41576085 MS.gene033812:CDS 35.0%
!! ATTCTAAGGTAGCTGTATGA+AGG - chr2.3:41576032-41576051 None:intergenic 35.0%
!! TTAGGGAGTTGATAAAGAAG+GGG + chr2.3:41576664-41576683 MS.gene033812:CDS 35.0%
!!! ATGGTTTTGAAGGAGACTTT+TGG - chr2.3:41575899-41575918 None:intergenic 35.0%
!!! TGGTTTTGAAGGAGACTTTT+GGG - chr2.3:41575898-41575917 None:intergenic 35.0%
!!! TGTAAAGTGGATGGTTTTGA+AGG - chr2.3:41575909-41575928 None:intergenic 35.0%
AAGGTAGCTGTATGAAGGTT+AGG - chr2.3:41576027-41576046 None:intergenic 40.0%
ACATGCCAAAGATTCTTGGA+AGG - chr2.3:41576107-41576126 None:intergenic 40.0%
AGAAGATGAGTGTAGAGCTA+TGG - chr2.3:41575815-41575834 None:intergenic 40.0%
AGGTAGCTGTATGAAGGTTA+GGG - chr2.3:41576026-41576045 None:intergenic 40.0%
ATTGCTTACTTCTAGTGTGG+TGG + chr2.3:41576245-41576264 MS.gene033812:CDS 40.0%
GATAAAGGTTAGACACATGG+AGG + chr2.3:41576581-41576600 MS.gene033812:CDS 40.0%
GGAGTTAAATTGGTTGAAGG+AGG - chr2.3:41575871-41575890 None:intergenic 40.0%
TAAAGAAGAGGCTAGGTGTA+TGG + chr2.3:41576416-41576435 MS.gene033812:CDS 40.0%
TGCCCATTACTTCAAGACAA+AGG - chr2.3:41575975-41575994 None:intergenic 40.0%
TGTGGAAATGAAGGGGAAAT+TGG + chr2.3:41576509-41576528 MS.gene033812:CDS 40.0%
!! GAAGTAATGGGCATTGATTC+AGG + chr2.3:41575982-41576001 MS.gene033812:CDS 40.0%
!! TAGGGAGTTGATAAAGAAGG+GGG + chr2.3:41576665-41576684 MS.gene033812:CDS 40.0%
!! TCATGAGTTGGTGTGTAAAG+TGG - chr2.3:41575922-41575941 None:intergenic 40.0%
!!! TGAAGGAGACTTTTGGGTTT+GGG - chr2.3:41575892-41575911 None:intergenic 40.0%
!!! TTGAAGGAGACTTTTGGGTT+TGG - chr2.3:41575893-41575912 None:intergenic 40.0%
ACATGGAGGTTGTGGAAAGT+GGG + chr2.3:41576595-41576614 MS.gene033812:CDS 45.0%
GGAAATGAAGGGGAAATTGG+AGG + chr2.3:41576512-41576531 MS.gene033812:CDS 45.0%
GGACACATGCCAAAGATTCT+TGG - chr2.3:41576111-41576130 None:intergenic 45.0%
TTGGTTGAAGGAGGTGATGA+TGG - chr2.3:41575862-41575881 None:intergenic 45.0%
!! GAGTTGGTGTGTAAAGTGGA+TGG - chr2.3:41575918-41575937 None:intergenic 45.0%
CACATGGAGGTTGTGGAAAG+TGG + chr2.3:41576594-41576613 MS.gene033812:CDS 50.0%
GGTTAGACACATGGAGGTTG+TGG + chr2.3:41576587-41576606 MS.gene033812:CDS 50.0%
! AGGCTAGGTGTATGGTGTTG+AGG + chr2.3:41576424-41576443 MS.gene033812:CDS 50.0%
!! AGAGCTATGGTTCTAGCAGC+TGG - chr2.3:41575802-41575821 None:intergenic 50.0%
!! GAGCTATGGTTCTAGCAGCT+GGG - chr2.3:41575801-41575820 None:intergenic 50.0%
!! GAGTTGATAAAGAAGGGGGC+TGG + chr2.3:41576669-41576688 MS.gene033812:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 41575793 41576695 41575793 ID=MS.gene033812
chr2.3 mRNA 41575793 41576695 41575793 ID=MS.gene033812.t1;Parent=MS.gene033812
chr2.3 exon 41575793 41576695 41575793 ID=MS.gene033812.t1.exon1;Parent=MS.gene033812.t1
chr2.3 CDS 41575793 41576695 41575793 ID=cds.MS.gene033812.t1;Parent=MS.gene033812.t1
Gene Sequence

>MS.gene033812

ATGTTCCCAGCTGCTAGAACCATAGCTCTACACTCATCTTCTCTATGCTCAGTCTCTTCTGATAAACCATCATCACCTCCTTCAACCAATTTAACTCCCAAACCCAAAAGTCTCCTTCAAAACCATCCACTTTACACACCAACTCATGAAAAACTCTCACTTCAATTCAAAGAAAAAATCCTTTGTCTTGAAGTAATGGGCATTGATTCAGGTAAAGCACTCTCTCAAAACCCTAACCTTCATACAGCTACCTTAGAATCCATTCATTCCATTATCACTTTTCTTGTCTCCAAAGGTATCCAACATAAAGACCTTCCAAGAATCTTTGGCATGTGTCCTAAGATTCTCACATCAAGCATCAAAACTGATCTTAATCCAGTTTTTGATTTTCTCATACATGATCTTAAAGTGCCTGATCATAGCTTTAGAAAAGTTATCAAAAAGTGTCCAAGATTGCTTACTTCTAGTGTGGTGGATCAGCTTAAACCTGCTTTGTTTTATCTTAACAGATTAGGATTAAGAGATTTAGAAGCATTGGCTTATCAAGATTGTGTTCTTTTGGTTTCCAATGTTGAAAGGACACTTATTCCTAAACTTAAGCATTTGGAGAGTATGGGATTTACTAAAGAAGAGGCTAGGTGTATGGTGTTGAGGTGTCCTGCATTGTTGACTTTTAGTATTGAGAATAATTTTCAGCCAAAATTTGAGTATTTTTCTGTGGAAATGAAGGGGAAATTGGAGGAGTTGAAAGAGTTTCCTCAGTATTTCTCTTTTAGTTTGGAGAATAGGATAAAGGTTAGACACATGGAGGTTGTGGAAAGTGGGATCAATTTGCCTTTGTCATTGATGCTTAAAAGTACTGATGATGAATTTAGGGAGTTGATAAAGAAGGGGGCTGGATGA
Protein sequence

>MS.gene033812.t1

MFPAARTIALHSSSLCSVSSDKPSSPPSTNLTPKPKSLLQNHPLYTPTHEKLSLQFKEKILCLEVMGIDSGKALSQNPNLHTATLESIHSIITFLVSKGIQHKDLPRIFGMCPKILTSSIKTDLNPVFDFLIHDLKVPDHSFRKVIKKCPRLLTSSVVDQLKPALFYLNRLGLRDLEALAYQDCVLLVSNVERTLIPKLKHLESMGFTKEEARCMVLRCPALLTFSIENNFQPKFEYFSVEMKGKLEELKEFPQYFSFSLENRIKVRHMEVVESGINLPLSLMLKSTDDEFRELIKKGAG