AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene26949

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene26949.t1 MTR_1g009110 72.348 264 67 3 31 290 118 379 4.59e-130 374
MS.gene26949.t1 MTR_1g022105 69.198 237 28 4 31 267 127 318 7.02e-105 308
MS.gene26949.t1 MTR_1g023400 42.435 271 134 9 29 289 94 352 1.03e-56 186
MS.gene26949.t1 MTR_1g022200 40.468 299 154 9 9 290 79 370 1.28e-55 184
MS.gene26949.t1 MTR_4g080200 41.852 270 141 7 29 289 87 349 3.66e-55 182
MS.gene26949.t1 MTR_1g037540 41.065 263 125 14 49 289 146 400 5.24e-42 149
MS.gene26949.t1 MTR_1g023430 47.368 133 69 1 158 290 42 173 1.11e-33 121
MS.gene26949.t1 MTR_1g024125 51.923 104 46 2 161 260 38 141 4.08e-29 108
MS.gene26949.t1 MTR_1g008000 42.553 141 66 8 159 290 135 269 4.66e-15 73.9
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 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAGTATGATAAATGTTTA+TGG 0.150614 1.1:+2268173 MS.gene26949:CDS
GTCCTGTCCGGTTAGAAATT+TGG 0.176280 1.1:+2267975 MS.gene26949:CDS
AAATATGATGATTCCTTATA+TGG 0.185379 1.1:+2267578 MS.gene26949:CDS
TTGTTAACTACGTTTATTAT+TGG 0.195963 1.1:+2267786 MS.gene26949:CDS
CACATGGCAATTGCAATTAA+TGG 0.267597 1.1:+2267437 MS.gene26949:CDS
GGGTTCACTTGCTTATGTTT+TGG 0.277483 1.1:+2267937 MS.gene26949:CDS
ATGAGGGTGCAGGAGGGATA+TGG 0.328189 1.1:-2267544 None:intergenic
AAAGTATGATAAATGTTTAT+GGG 0.339753 1.1:+2268174 MS.gene26949:CDS
TATTGGAATTCAACAAATCT+TGG 0.344030 1.1:+2267482 MS.gene26949:CDS
CCGGTTAGAAATTTGGATTA+TGG 0.356395 1.1:+2267982 MS.gene26949:CDS
GAAGGAGGAGGGTGATGGAC+AGG 0.358181 1.1:-2267722 None:intergenic
AAGCCGATGCTTTATGCTTC+GGG 0.360072 1.1:+2267662 MS.gene26949:CDS
GAAGCCGATGCTTTATGCTT+CGG 0.376318 1.1:+2267661 MS.gene26949:CDS
AAAGGCACAGAAACCATATA+AGG 0.408235 1.1:-2267591 None:intergenic
AACTTTGAAATTATTTCTAA+AGG 0.414378 1.1:-2267609 None:intergenic
TGAAAACATCGTCGAGATCA+AGG 0.419509 1.1:+2267916 MS.gene26949:CDS
ATGTGATTCAATGTTGTGTA+TGG 0.428693 1.1:-2267419 None:intergenic
ATAACTGTGATCCGGTTAGA+AGG 0.432134 1.1:-2267740 None:intergenic
ATCACCCTCCTCCTTCTAAC+CGG 0.446237 1.1:+2267729 MS.gene26949:CDS
CCATAATCCAAATTTCTAAC+CGG 0.447165 1.1:-2267982 None:intergenic
TAATAAACGTAGTTAACAAC+TGG 0.454507 1.1:-2267782 None:intergenic
TTTATTATTAGCAGGAAAGA+GGG 0.459387 1.1:-2267395 None:intergenic
CTACAACACGTCCACTCAAC+CGG 0.459439 1.1:-2268040 None:intergenic
AAGTTTGAGATTTGCTATGC+AGG 0.475011 1.1:-2268144 None:intergenic
TTCAACATGAGGTTGTCGTT+GGG 0.478589 1.1:+2267639 MS.gene26949:CDS
CTTCAACATGAGGTTGTCGT+TGG 0.499378 1.1:+2267638 MS.gene26949:CDS
ATTTCTAACCGGACAGGACT+AGG 0.503309 1.1:-2267971 None:intergenic
ATCATCTTCCTAGTCCTGTC+CGG 0.513742 1.1:+2267963 MS.gene26949:CDS
GCTAGCTAGCTAGGTTGACA+AGG 0.514125 1.1:-2268224 None:intergenic
CTGACTTCGTATGAAGATCA+AGG 0.526393 1.1:+2268118 MS.gene26949:CDS
GATTATAAATAACTGTGATC+CGG 0.527165 1.1:-2267748 None:intergenic
CGGCGCCGACGATGAGGAGG+TGG 0.528618 1.1:+2267354 None:intergenic
ATCTTGGTCACTTGATTCTG+TGG 0.533610 1.1:+2267498 MS.gene26949:CDS
AAGGAGGAGGGTGATGGACA+GGG 0.542016 1.1:-2267721 None:intergenic
ATCCAAATTTCTAACCGGAC+AGG 0.542204 1.1:-2267977 None:intergenic
GGTTAGAAGGAGGAGGGTGA+TGG 0.546100 1.1:-2267727 None:intergenic
TTAACAACTGGTGTATAAGC+AGG 0.547126 1.1:-2267770 None:intergenic
TCAAAGAATGAGGGTGCAGG+AGG 0.547678 1.1:-2267551 None:intergenic
GAGTCAAAGAATGAGGGTGC+AGG 0.549550 1.1:-2267554 None:intergenic
GTGATCCGGTTAGAAGGAGG+AGG 0.550362 1.1:-2267734 None:intergenic
TTTGGATTATGGATCAAAGT+GGG 0.554416 1.1:+2267993 MS.gene26949:CDS
ATAACATTGGTCCGGTTGAG+TGG 0.557869 1.1:+2268029 MS.gene26949:CDS
GAAAACATCGTCGAGATCAA+GGG 0.557945 1.1:+2267917 MS.gene26949:CDS
ATATTTAGAGTCAAAGAATG+AGG 0.562684 1.1:-2267561 None:intergenic
ACGATCTAAGCACTCAGTCA+TGG 0.566417 1.1:+2267696 MS.gene26949:CDS
AAGTATGATAAATGTTTATG+GGG 0.574545 1.1:+2268175 MS.gene26949:CDS
ATTTGGATTATGGATCAAAG+TGG 0.575328 1.1:+2267992 MS.gene26949:CDS
TGACGGCGCCGACGATGAGG+AGG 0.608116 1.1:+2267351 None:intergenic
GATTATGGATCAAAGTGGGT+GGG 0.612527 1.1:+2267997 MS.gene26949:CDS
AGGAGGAGGGTGATGGACAG+GGG 0.614131 1.1:-2267720 None:intergenic
GGATTATGGATCAAAGTGGG+TGG 0.615476 1.1:+2267996 MS.gene26949:CDS
CTAGCTAGCTAGGTTGACAA+GGG 0.623600 1.1:-2268223 None:intergenic
GCTCCCGAAGCATAAAGCAT+CGG 0.629012 1.1:-2267665 None:intergenic
TATTTAGAGTCAAAGAATGA+GGG 0.639125 1.1:-2267560 None:intergenic
AGTTGTTAGACTTCAACATG+AGG 0.650334 1.1:+2267628 MS.gene26949:CDS
ACTGTGATCCGGTTAGAAGG+AGG 0.659902 1.1:-2267737 None:intergenic
ATACACAACATTGAATCACA+TGG 0.666706 1.1:+2267421 MS.gene26949:CDS
TGATCCGGTTAGAAGGAGGA+GGG 0.681484 1.1:-2267733 None:intergenic
CAAAGAATGAGGGTGCAGGA+GGG 0.683552 1.1:-2267550 None:intergenic
TAATGTTCAACAGCAATACG+CGG 0.694168 1.1:-2267890 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTATGATAAATGTTTAT+GGG + chr1.1:2268174-2268193 MS.gene26949:CDS 15.0%
!! TAAAGTATGATAAATGTTTA+TGG + chr1.1:2268173-2268192 MS.gene26949:CDS 15.0%
!!! AACTTTGAAATTATTTCTAA+AGG - chr1.1:2267612-2267631 None:intergenic 15.0%
!!! TCTTTTTAAAAGCTTTTTAT+TGG + chr1.1:2267465-2267484 MS.gene26949:CDS 15.0%
!! AAATATGATGATTCCTTATA+TGG + chr1.1:2267578-2267597 MS.gene26949:CDS 20.0%
!! AAGTATGATAAATGTTTATG+GGG + chr1.1:2268175-2268194 MS.gene26949:CDS 20.0%
!! TTGTTAACTACGTTTATTAT+TGG + chr1.1:2267786-2267805 MS.gene26949:CDS 20.0%
! GATTATAAATAACTGTGATC+CGG - chr1.1:2267751-2267770 None:intergenic 25.0%
! TAATAAACGTAGTTAACAAC+TGG - chr1.1:2267785-2267804 None:intergenic 25.0%
! TATTGGAATTCAACAAATCT+TGG + chr1.1:2267482-2267501 MS.gene26949:CDS 25.0%
! TTTATTATTAGCAGGAAAGA+GGG - chr1.1:2267398-2267417 None:intergenic 25.0%
!! ATATTTAGAGTCAAAGAATG+AGG - chr1.1:2267564-2267583 None:intergenic 25.0%
!! TATTTAGAGTCAAAGAATGA+GGG - chr1.1:2267563-2267582 None:intergenic 25.0%
!! TTTTATTATTAGCAGGAAAG+AGG - chr1.1:2267399-2267418 None:intergenic 25.0%
!!! TGTATGGTTTTATTATTAGC+AGG - chr1.1:2267406-2267425 None:intergenic 25.0%
ATACACAACATTGAATCACA+TGG + chr1.1:2267421-2267440 MS.gene26949:CDS 30.0%
ATGTGATTCAATGTTGTGTA+TGG - chr1.1:2267422-2267441 None:intergenic 30.0%
ATTTGGATTATGGATCAAAG+TGG + chr1.1:2267992-2268011 MS.gene26949:CDS 30.0%
CCATAATCCAAATTTCTAAC+CGG - chr1.1:2267985-2268004 None:intergenic 30.0%
TTTGGATTATGGATCAAAGT+GGG + chr1.1:2267993-2268012 MS.gene26949:CDS 30.0%
! GAAAAAGTATAACATTGGTC+CGG + chr1.1:2268021-2268040 MS.gene26949:CDS 30.0%
! TGGGTGAAAAAGTATAACAT+TGG + chr1.1:2268016-2268035 MS.gene26949:CDS 30.0%
AGTTGTTAGACTTCAACATG+AGG + chr1.1:2267628-2267647 MS.gene26949:CDS 35.0%
CACATGGCAATTGCAATTAA+TGG + chr1.1:2267437-2267456 MS.gene26949:CDS 35.0%
CCGGTTAGAAATTTGGATTA+TGG + chr1.1:2267982-2268001 MS.gene26949:CDS 35.0%
TAATGTTCAACAGCAATACG+CGG - chr1.1:2267893-2267912 None:intergenic 35.0%
TTAACAACTGGTGTATAAGC+AGG - chr1.1:2267773-2267792 None:intergenic 35.0%
! AAAGGCACAGAAACCATATA+AGG - chr1.1:2267594-2267613 None:intergenic 35.0%
!! AAGTTTGAGATTTGCTATGC+AGG - chr1.1:2268147-2268166 None:intergenic 35.0%
!! TTGTAGACGTAGTTTTTGGA+AGG + chr1.1:2268057-2268076 MS.gene26949:CDS 35.0%
ATAACTGTGATCCGGTTAGA+AGG - chr1.1:2267743-2267762 None:intergenic 40.0%
ATCCAAATTTCTAACCGGAC+AGG - chr1.1:2267980-2267999 None:intergenic 40.0%
ATCTTGGTCACTTGATTCTG+TGG + chr1.1:2267498-2267517 MS.gene26949:CDS 40.0%
CTGACTTCGTATGAAGATCA+AGG + chr1.1:2268118-2268137 MS.gene26949:CDS 40.0%
GAAAACATCGTCGAGATCAA+GGG + chr1.1:2267917-2267936 MS.gene26949:CDS 40.0%
GATTATGGATCAAAGTGGGT+GGG + chr1.1:2267997-2268016 MS.gene26949:CDS 40.0%
TGAAAACATCGTCGAGATCA+AGG + chr1.1:2267916-2267935 MS.gene26949:CDS 40.0%
TTCAACATGAGGTTGTCGTT+GGG + chr1.1:2267639-2267658 MS.gene26949:CDS 40.0%
! CGTGTTGTAGACGTAGTTTT+TGG + chr1.1:2268053-2268072 MS.gene26949:CDS 40.0%
! GGGTTCACTTGCTTATGTTT+TGG + chr1.1:2267937-2267956 MS.gene26949:CDS 40.0%
!! AGACGTAGTTTTTGGAAGGA+TGG + chr1.1:2268061-2268080 MS.gene26949:CDS 40.0%
AAGCCGATGCTTTATGCTTC+GGG + chr1.1:2267662-2267681 MS.gene26949:CDS 45.0%
ACGATCTAAGCACTCAGTCA+TGG + chr1.1:2267696-2267715 MS.gene26949:CDS 45.0%
ATAACATTGGTCCGGTTGAG+TGG + chr1.1:2268029-2268048 MS.gene26949:CDS 45.0%
ATCATCTTCCTAGTCCTGTC+CGG + chr1.1:2267963-2267982 MS.gene26949:CDS 45.0%
ATTTCTAACCGGACAGGACT+AGG - chr1.1:2267974-2267993 None:intergenic 45.0%
CTTCAACATGAGGTTGTCGT+TGG + chr1.1:2267638-2267657 MS.gene26949:CDS 45.0%
GAAGCCGATGCTTTATGCTT+CGG + chr1.1:2267661-2267680 MS.gene26949:CDS 45.0%
GGATTATGGATCAAAGTGGG+TGG + chr1.1:2267996-2268015 MS.gene26949:CDS 45.0%
GTCCTGTCCGGTTAGAAATT+TGG + chr1.1:2267975-2267994 MS.gene26949:CDS 45.0%
! AAGGATGGCGATCGAGTTTT+TGG + chr1.1:2268076-2268095 MS.gene26949:CDS 45.0%
!! CGAGTTTTTGGAGGAAAGGT+TGG + chr1.1:2268088-2268107 MS.gene26949:CDS 45.0%
!! CGATCGAGTTTTTGGAGGAA+AGG + chr1.1:2268084-2268103 MS.gene26949:CDS 45.0%
ACTGTGATCCGGTTAGAAGG+AGG - chr1.1:2267740-2267759 None:intergenic 50.0%
ATCACCCTCCTCCTTCTAAC+CGG + chr1.1:2267729-2267748 MS.gene26949:CDS 50.0%
CTACAACACGTCCACTCAAC+CGG - chr1.1:2268043-2268062 None:intergenic 50.0%
GCTCCCGAAGCATAAAGCAT+CGG - chr1.1:2267668-2267687 None:intergenic 50.0%
TGATCCGGTTAGAAGGAGGA+GGG - chr1.1:2267736-2267755 None:intergenic 50.0%
! CAAAGAATGAGGGTGCAGGA+GGG - chr1.1:2267553-2267572 None:intergenic 50.0%
! GAGTCAAAGAATGAGGGTGC+AGG - chr1.1:2267557-2267576 None:intergenic 50.0%
! TCAAAGAATGAGGGTGCAGG+AGG - chr1.1:2267554-2267573 None:intergenic 50.0%
!! GATGGCGATCGAGTTTTTGG+AGG + chr1.1:2268079-2268098 MS.gene26949:CDS 50.0%
GGTTAGAAGGAGGAGGGTGA+TGG - chr1.1:2267730-2267749 None:intergenic 55.0%
GTGATCCGGTTAGAAGGAGG+AGG - chr1.1:2267737-2267756 None:intergenic 55.0%
! ATGAGGGTGCAGGAGGGATA+TGG - chr1.1:2267547-2267566 None:intergenic 55.0%
!! AAGGAGGAGGGTGATGGACA+GGG - chr1.1:2267724-2267743 None:intergenic 55.0%
!! AGGAGGAGGGTGATGGACAG+GGG - chr1.1:2267723-2267742 None:intergenic 60.0%
!! GAAGGAGGAGGGTGATGGAC+AGG - chr1.1:2267725-2267744 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 2267365 2268237 2267365 ID=MS.gene26949
chr1.1 mRNA 2267365 2268237 2267365 ID=MS.gene26949.t1;Parent=MS.gene26949
chr1.1 exon 2267365 2268237 2267365 ID=MS.gene26949.t1.exon1;Parent=MS.gene26949.t1
chr1.1 CDS 2267365 2268237 2267365 ID=cds.MS.gene26949.t1;Parent=MS.gene26949.t1
Gene Sequence

>MS.gene26949

ATGAGGAGGTGGAGCGCATCTGCTTCTACTCCCTCTTTCCTGCTAATAATAAAACCATACACAACATTGAATCACATGGCAATTGCAATTAATGGTGTTTTCTTTTTAAAAGCTTTTTATTGGAATTCAACAAATCTTGGTCACTTGATTCTGTGGAACACAACAGTTAAACAAGTTCACCATATCCCTCCTGCACCCTCATTCTTTGACTCTAAATATGATGATTCCTTATATGGTTTCTGTGCCTTTAGAAATAATTTCAAAGTTGTTAGACTTCAACATGAGGTTGTCGTTGGGAAGCCGATGCTTTATGCTTCGGGAGCAGAAGTTTACGATCTAAGCACTCAGTCATGGACCCCTGTCCATCACCCTCCTCCTTCTAACCGGATCACAGTTATTTATAATCCTGCTTATACACCAGTTGTTAACTACGTTTATTATTGGATTACGACTGTCAATTTTTCTACTATTTCAAACATTCTTTGTTTCGACTTTTGCAACATTCAGTTTTACGAACTCAAAGCTCCGCGTATTGCTGTTGAACATTATATTGAAAACATCGTCGAGATCAAGGGTTCACTTGCTTATGTTTTGGAGTATCATCTTCCTAGTCCTGTCCGGTTAGAAATTTGGATTATGGATCAAAGTGGGTGGGTGAAAAAGTATAACATTGGTCCGGTTGAGTGGACGTGTTGTAGACGTAGTTTTTGGAAGGATGGCGATCGAGTTTTTGGAGGAAAGGTTGGACAACTGCTGACTTCGTATGAAGATCAAGGAAACCTGCATAGCAAATCTCAAACTTATCTATTAAAGTATGATAAATGTTTATGGGGTCATGAGTATTTGCAGAGCATAACTCCCTTGTCAACCTAG
Protein sequence

>MS.gene26949.t1

MRRWSASASTPSFLLIIKPYTTLNHMAIAINGVFFLKAFYWNSTNLGHLILWNTTVKQVHHIPPAPSFFDSKYDDSLYGFCAFRNNFKVVRLQHEVVVGKPMLYASGAEVYDLSTQSWTPVHHPPPSNRITVIYNPAYTPVVNYVYYWITTVNFSTISNILCFDFCNIQFYELKAPRIAVEHYIENIVEIKGSLAYVLEYHLPSPVRLEIWIMDQSGWVKKYNIGPVEWTCCRRSFWKDGDRVFGGKVGQLLTSYEDQGNLHSKSQTYLLKYDKCLWGHEYLQSITPLST