AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84318

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84318.t1 MTR_2g086590 92.748 262 18 1 1 262 1 261 1.10e-169 469
MS.gene84318.t1 MTR_4g052880 38.224 259 131 9 1 246 1 243 3.93e-35 126
MS.gene84318.t1 MTR_7g113950 40.000 110 60 2 112 219 106 211 1.78e-15 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84318.t1 AT5G22390 33.190 232 94 7 1 221 1 182 8.08e-21 87.8
MS.gene84318.t1 AT1G54740 33.043 115 74 2 106 219 33 145 1.05e-11 64.3

Find 65 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAGCCTTGGGTTTATTTC+AGG 0.143738 2.2:-12061443 MS.gene84318:CDS
TTCAGGTCTATTAGGAATAA+TGG 0.250900 2.2:-12061426 MS.gene84318:CDS
GGGTTTATTTCAGGTCTATT+AGG 0.260287 2.2:-12061434 MS.gene84318:CDS
TCCTCCTTTACTGAGATATT+TGG 0.276616 2.2:-12061858 MS.gene84318:CDS
AAGAAGCTGAAGATGGAGTT+TGG 0.330013 2.2:+12061748 None:intergenic
GATGAAGGAGAGAATGATAT+AGG 0.344412 2.2:-12061282 MS.gene84318:CDS
AGTAAAGGAGGAGGACTCTA+TGG 0.362243 2.2:+12061869 None:intergenic
CATCTTTGCACCGAAGGTCT+TGG 0.374924 2.2:-12061645 MS.gene84318:CDS
AGTCCTCCCTATGCTTGAAA+TGG 0.379725 2.2:+12061467 None:intergenic
CTGTTGGTATGCCTTGCTAT+TGG 0.401166 2.2:+12061714 None:intergenic
TTGATAATGATTCCTTGAAA+TGG 0.405177 2.2:+12061829 None:intergenic
TAGGGAGGACTGGGAAGCCT+TGG 0.408356 2.2:-12061455 MS.gene84318:CDS
AGGGAGGACTGGGAAGCCTT+GGG 0.428523 2.2:-12061454 MS.gene84318:CDS
CGGACTCTTTGATCTGGTTG+AGG 0.434519 2.2:+12061787 None:intergenic
GAAAGGGATTGAAGCAGTGT+TGG 0.454932 2.2:+12061918 None:intergenic
ATTTGGTGAACTCCATTTCA+AGG 0.460735 2.2:-12061841 MS.gene84318:CDS
TCTTGCAGAAACTCATCATC+AGG 0.462826 2.2:+12061309 None:intergenic
AAGACTCGGACTCTTTGATC+TGG 0.485201 2.2:+12061781 None:intergenic
CAATAGCAAGGCATACCAAC+AGG 0.489567 2.2:-12061713 MS.gene84318:CDS
CTCCTCCCATTTCAAGCATA+GGG 0.493217 2.2:-12061473 MS.gene84318:CDS
GGGTGTCAAAGATGTGTTGT+AGG 0.504528 2.2:+12061955 None:intergenic
ATTTCAAGCATAGGGAGGAC+TGG 0.507716 2.2:-12061465 MS.gene84318:CDS
GTCCTCCCTATGCTTGAAAT+GGG 0.513543 2.2:+12061468 None:intergenic
TAGGCTGTCACAGGTTGCCA+TGG 0.514804 2.2:+12061974 None:intergenic
CCTCCTCCCATTTCAAGCAT+AGG 0.517066 2.2:-12061474 MS.gene84318:CDS
TCGGTATCCTTACCTCTTCG+AGG 0.517417 2.2:+12061394 None:intergenic
ATAGAGAATGTAGGAGGTCA+AGG 0.517866 2.2:-12061509 MS.gene84318:CDS
TTCACCAAATATCTCAGTAA+AGG 0.527789 2.2:+12061854 None:intergenic
TTTCAAGCATAGGGAGGACT+GGG 0.533628 2.2:-12061464 MS.gene84318:CDS
AGCATGCATCTTTGCACCGA+AGG 0.535589 2.2:-12061651 MS.gene84318:CDS
GAGGACTCTATGGATTTCAC+TGG 0.537192 2.2:+12061879 None:intergenic
CCTATGCTTGAAATGGGAGG+AGG 0.541240 2.2:+12061474 None:intergenic
CTGCGTGCTTATAGAGAGGA+TGG 0.545087 2.2:-12061360 MS.gene84318:CDS
GATTTGTCCTCGAAGAGGTA+AGG 0.546648 2.2:-12061401 MS.gene84318:CDS
ACTCTCAAAACCAAGACCTT+CGG 0.553557 2.2:+12061635 None:intergenic
TTTCAATTACACCAATAGCA+AGG 0.571241 2.2:-12061725 MS.gene84318:CDS
ACCAAATATCTCAGTAAAGG+AGG 0.572346 2.2:+12061857 None:intergenic
AGAAGACATGGCAAAAGAAG+AGG 0.576952 2.2:-12061241 MS.gene84318:CDS
TGAGAGTTCAGACGATGTCG+AGG 0.585948 2.2:-12061619 MS.gene84318:CDS
TGATCTGGTTGAGGTTTGTG+TGG 0.587869 2.2:+12061796 None:intergenic
ATCATTCTTATAGAGAATGT+AGG 0.592656 2.2:-12061518 MS.gene84318:CDS
AAATATCTCAGTAAAGGAGG+AGG 0.599938 2.2:+12061860 None:intergenic
CTATGCTTGAAATGGGAGGA+GGG 0.601586 2.2:+12061475 None:intergenic
AGCTGAGGAAGGAGAAGACA+TGG 0.613301 2.2:-12061253 MS.gene84318:CDS
TGCAGAAACTCATCATCAGG+AGG 0.618671 2.2:+12061312 None:intergenic
TAGAGAATGTAGGAGGTCAA+GGG 0.619517 2.2:-12061508 MS.gene84318:CDS
GATGTGTTGTAGGCTGTCAC+AGG 0.621992 2.2:+12061965 None:intergenic
GATGTCGAGGACTCAAAGAG+TGG 0.622521 2.2:-12061606 MS.gene84318:CDS
ATAGGAAGCATAGCTGAGGA+AGG 0.623879 2.2:-12061264 MS.gene84318:CDS
TTGGATAGTGTCAAAAGACT+CGG 0.624073 2.2:+12061767 None:intergenic
ATTCTTATAGAGAATGTAGG+AGG 0.628375 2.2:-12061515 MS.gene84318:CDS
CTCCCTATGCTTGAAATGGG+AGG 0.629607 2.2:+12061471 None:intergenic
AGAGGTAAGGATACCGACAC+AGG 0.634664 2.2:-12061388 MS.gene84318:CDS
TTTCTGCAAGATGAGGATGA+AGG 0.644075 2.2:-12061297 MS.gene84318:CDS
CTCCCATTTCAAGCATAGGG+AGG 0.649676 2.2:-12061470 MS.gene84318:CDS
ATAGACCTGAAATAAACCCA+AGG 0.650033 2.2:+12061438 None:intergenic
GCACGCAGGACCTCCTGTGT+CGG 0.651046 2.2:+12061375 None:intergenic
TGGAAGATTTGTCCTCGAAG+AGG 0.651915 2.2:-12061406 MS.gene84318:CDS
GTGCTTATAGAGAGGATGGA+AGG 0.652178 2.2:-12061356 MS.gene84318:CDS
GGTCCTGCGTGCTTATAGAG+AGG 0.655010 2.2:-12061364 MS.gene84318:CDS
TGATATAGGAAGCATAGCTG+AGG 0.669846 2.2:-12061268 MS.gene84318:CDS
GCAGAAACTCATCATCAGGA+GGG 0.670033 2.2:+12061313 None:intergenic
CATCCTCTCTATAAGCACGC+AGG 0.674324 2.2:+12061361 None:intergenic
TGATGAGTTTCTGCAAGATG+AGG 0.689997 2.2:-12061304 MS.gene84318:CDS
GGTAAGGATACCGACACAGG+AGG 0.697117 2.2:-12061385 MS.gene84318:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATTTTGTTAAATGAAA+GGG + chr2.2:12061267-12061286 None:intergenic 10.0%
!!! GTTTAATTTTGTTAAATGAA+AGG + chr2.2:12061268-12061287 None:intergenic 15.0%
! ATCATTCTTATAGAGAATGT+AGG - chr2.2:12061648-12061667 MS.gene84318:CDS 25.0%
!!! TTGATAATGATTCCTTGAAA+TGG + chr2.2:12061340-12061359 None:intergenic 25.0%
ATTCTTATAGAGAATGTAGG+AGG - chr2.2:12061651-12061670 MS.gene84318:CDS 30.0%
ATTGAAAAAGAAGCTGAAGA+TGG + chr2.2:12061428-12061447 None:intergenic 30.0%
TTCACCAAATATCTCAGTAA+AGG + chr2.2:12061315-12061334 None:intergenic 30.0%
TTCAGGTCTATTAGGAATAA+TGG - chr2.2:12061740-12061759 MS.gene84318:CDS 30.0%
TTTCAATTACACCAATAGCA+AGG - chr2.2:12061441-12061460 MS.gene84318:CDS 30.0%
AAATATCTCAGTAAAGGAGG+AGG + chr2.2:12061309-12061328 None:intergenic 35.0%
ACCAAATATCTCAGTAAAGG+AGG + chr2.2:12061312-12061331 None:intergenic 35.0%
ATAGACCTGAAATAAACCCA+AGG + chr2.2:12061731-12061750 None:intergenic 35.0%
GATGAAGGAGAGAATGATAT+AGG - chr2.2:12061884-12061903 MS.gene84318:CDS 35.0%
TCCTCCTTTACTGAGATATT+TGG - chr2.2:12061308-12061327 MS.gene84318:CDS 35.0%
TTGGATAGTGTCAAAAGACT+CGG + chr2.2:12061402-12061421 None:intergenic 35.0%
! ATTTGGTGAACTCCATTTCA+AGG - chr2.2:12061325-12061344 MS.gene84318:CDS 35.0%
! GGGTTTATTTCAGGTCTATT+AGG - chr2.2:12061732-12061751 MS.gene84318:CDS 35.0%
!! GCAATCTCTTTTTCGTCATT+TGG + chr2.2:12061971-12061990 None:intergenic 35.0%
!! TGTTGGATTTTCTGGCAATA+GGG + chr2.2:12061234-12061253 None:intergenic 35.0%
AAGAAGCTGAAGATGGAGTT+TGG + chr2.2:12061421-12061440 None:intergenic 40.0%
ACTCTCAAAACCAAGACCTT+CGG + chr2.2:12061534-12061553 None:intergenic 40.0%
AGAAGACATGGCAAAAGAAG+AGG - chr2.2:12061925-12061944 MS.gene84318:CDS 40.0%
ATAGAGAATGTAGGAGGTCA+AGG - chr2.2:12061657-12061676 MS.gene84318:CDS 40.0%
TAGAGAATGTAGGAGGTCAA+GGG - chr2.2:12061658-12061677 MS.gene84318:CDS 40.0%
TCTTGCAGAAACTCATCATC+AGG + chr2.2:12061860-12061879 None:intergenic 40.0%
TGATGAGTTTCTGCAAGATG+AGG - chr2.2:12061862-12061881 MS.gene84318:CDS 40.0%
TTTCTGCAAGATGAGGATGA+AGG - chr2.2:12061869-12061888 MS.gene84318:CDS 40.0%
! AAAGCAGTGACAGCTTTTCA+TGG - chr2.2:12061480-12061499 MS.gene84318:CDS 40.0%
! TGATATAGGAAGCATAGCTG+AGG - chr2.2:12061898-12061917 MS.gene84318:CDS 40.0%
!! GTGTTGGATTTTCTGGCAAT+AGG + chr2.2:12061235-12061254 None:intergenic 40.0%
!! TGAAGCAGTGTTGGATTTTC+TGG + chr2.2:12061242-12061261 None:intergenic 40.0%
AAGACTCGGACTCTTTGATC+TGG + chr2.2:12061388-12061407 None:intergenic 45.0%
AGTAAAGGAGGAGGACTCTA+TGG + chr2.2:12061300-12061319 None:intergenic 45.0%
AGTCCTCCCTATGCTTGAAA+TGG + chr2.2:12061702-12061721 None:intergenic 45.0%
ATTTCAAGCATAGGGAGGAC+TGG - chr2.2:12061701-12061720 MS.gene84318:CDS 45.0%
CAATAGCAAGGCATACCAAC+AGG - chr2.2:12061453-12061472 MS.gene84318:CDS 45.0%
CTATGCTTGAAATGGGAGGA+GGG + chr2.2:12061694-12061713 None:intergenic 45.0%
CTCCTCCCATTTCAAGCATA+GGG - chr2.2:12061693-12061712 MS.gene84318:CDS 45.0%
GAAAGGGATTGAAGCAGTGT+TGG + chr2.2:12061251-12061270 None:intergenic 45.0%
GAGGACTCTATGGATTTCAC+TGG + chr2.2:12061290-12061309 None:intergenic 45.0%
GATTTGTCCTCGAAGAGGTA+AGG - chr2.2:12061765-12061784 MS.gene84318:CDS 45.0%
GCAGAAACTCATCATCAGGA+GGG + chr2.2:12061856-12061875 None:intergenic 45.0%
GGAAGCCTTGGGTTTATTTC+AGG - chr2.2:12061723-12061742 MS.gene84318:CDS 45.0%
GGGTGTCAAAGATGTGTTGT+AGG + chr2.2:12061214-12061233 None:intergenic 45.0%
GTCCTCCCTATGCTTGAAAT+GGG + chr2.2:12061701-12061720 None:intergenic 45.0%
GTGCTTATAGAGAGGATGGA+AGG - chr2.2:12061810-12061829 MS.gene84318:CDS 45.0%
TGATCTGGTTGAGGTTTGTG+TGG + chr2.2:12061373-12061392 None:intergenic 45.0%
TGCAGAAACTCATCATCAGG+AGG + chr2.2:12061857-12061876 None:intergenic 45.0%
TGGAAGATTTGTCCTCGAAG+AGG - chr2.2:12061760-12061779 MS.gene84318:CDS 45.0%
TTTCAAGCATAGGGAGGACT+GGG - chr2.2:12061702-12061721 MS.gene84318:CDS 45.0%
! ATAGGAAGCATAGCTGAGGA+AGG - chr2.2:12061902-12061921 MS.gene84318:CDS 45.0%
! CTGTTGGTATGCCTTGCTAT+TGG + chr2.2:12061455-12061474 None:intergenic 45.0%
AGAGGTAAGGATACCGACAC+AGG - chr2.2:12061778-12061797 MS.gene84318:CDS 50.0%
AGCATGCATCTTTGCACCGA+AGG - chr2.2:12061515-12061534 MS.gene84318:CDS 50.0%
AGCTGAGGAAGGAGAAGACA+TGG - chr2.2:12061913-12061932 MS.gene84318:CDS 50.0%
CATCCTCTCTATAAGCACGC+AGG + chr2.2:12061808-12061827 None:intergenic 50.0%
CATCTTTGCACCGAAGGTCT+TGG - chr2.2:12061521-12061540 MS.gene84318:CDS 50.0%
CCTATGCTTGAAATGGGAGG+AGG + chr2.2:12061695-12061714 None:intergenic 50.0%
CCTCCTCCCATTTCAAGCAT+AGG - chr2.2:12061692-12061711 MS.gene84318:CDS 50.0%
CGGACTCTTTGATCTGGTTG+AGG + chr2.2:12061382-12061401 None:intergenic 50.0%
CTCCCATTTCAAGCATAGGG+AGG - chr2.2:12061696-12061715 MS.gene84318:CDS 50.0%
CTCCCTATGCTTGAAATGGG+AGG + chr2.2:12061698-12061717 None:intergenic 50.0%
CTGCGTGCTTATAGAGAGGA+TGG - chr2.2:12061806-12061825 MS.gene84318:CDS 50.0%
GATGTCGAGGACTCAAAGAG+TGG - chr2.2:12061560-12061579 MS.gene84318:CDS 50.0%
GATGTGTTGTAGGCTGTCAC+AGG + chr2.2:12061204-12061223 None:intergenic 50.0%
TCGGTATCCTTACCTCTTCG+AGG + chr2.2:12061775-12061794 None:intergenic 50.0%
TGAGAGTTCAGACGATGTCG+AGG - chr2.2:12061547-12061566 MS.gene84318:CDS 50.0%
!! GTCACTGCTTTTGTGCCTGT+TGG + chr2.2:12061471-12061490 None:intergenic 50.0%
GGTAAGGATACCGACACAGG+AGG - chr2.2:12061781-12061800 MS.gene84318:CDS 55.0%
GGTCCTGCGTGCTTATAGAG+AGG - chr2.2:12061802-12061821 MS.gene84318:CDS 55.0%
AGGGAGGACTGGGAAGCCTT+GGG - chr2.2:12061712-12061731 MS.gene84318:CDS 60.0%
TAGGGAGGACTGGGAAGCCT+TGG - chr2.2:12061711-12061730 MS.gene84318:CDS 60.0%
GCACGCAGGACCTCCTGTGT+CGG + chr2.2:12061794-12061813 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 12061194 12061994 12061194 ID=MS.gene84318
chr2.2 mRNA 12061194 12061994 12061194 ID=MS.gene84318.t1;Parent=MS.gene84318
chr2.2 exon 12061194 12061994 12061194 ID=MS.gene84318.t1.exon1;Parent=MS.gene84318.t1
chr2.2 CDS 12061194 12061994 12061194 ID=cds.MS.gene84318.t1;Parent=MS.gene84318.t1
Gene Sequence

>MS.gene84318

ATGGCAACCTGTGACAGCCTACAACACATCTTTGACACCCTATTGCCAGAAAATCCAACACTGCTTCAATCCCTTTCATTTAACAAAATTAAACCAGTGAAATCCATAGAGTCCTCCTCCTTTACTGAGATATTTGGTGAACTCCATTTCAAGGAATCATTATCAACAGAGATAAACCACACAAACCTCAACCAGATCAAAGAGTCCGAGTCTTTTGACACTATCCAAACTCCATCTTCAGCTTCTTTTTCAATTACACCAATAGCAAGGCATACCAACAGGCACAAAAGCAGTGACAGCTTTTCATGGCTGAATTCTGAAAGCATGCATCTTTGCACCGAAGGTCTTGGTTTTGAGAGTTCAGACGATGTCGAGGACTCAAAGAGTGGAGCGAATGAATCTTTACAAATTGATCAAAATGAGAAACGTGTCGAACATCATTTATCTTCAAGACATCATTCTTATAGAGAATGTAGGAGGTCAAGGGTAAGCGAGTACCCTCCTCCCATTTCAAGCATAGGGAGGACTGGGAAGCCTTGGGTTTATTTCAGGTCTATTAGGAATAATGGAAGATTTGTCCTCGAAGAGGTAAGGATACCGACACAGGAGGTCCTGCGTGCTTATAGAGAGGATGGAAGGCTCAAGCTGCAGTTTGTTCACCCTCCTGATGATGAGTTTCTGCAAGATGAGGATGAAGGAGAGAATGATATAGGAAGCATAGCTGAGGAAGGAGAAGACATGGCAAAAGAAGAGGACGATTGTGTAACACATCATCCAAATGACGAAAAAGAGATTGCTTGA
Protein sequence

>MS.gene84318.t1

MATCDSLQHIFDTLLPENPTLLQSLSFNKIKPVKSIESSSFTEIFGELHFKESLSTEINHTNLNQIKESESFDTIQTPSSASFSITPIARHTNRHKSSDSFSWLNSESMHLCTEGLGFESSDDVEDSKSGANESLQIDQNEKRVEHHLSSRHHSYRECRRSRVSEYPPPISSIGRTGKPWVYFRSIRNNGRFVLEEVRIPTQEVLRAYREDGRLKLQFVHPPDDEFLQDEDEGENDIGSIAEEGEDMAKEEDDCVTHHPNDEKEIA