AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96949


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96949.t1 MTR_7g098290 98.571 140 2 0 1 140 1 140 3.93e-98 278
MS.gene96949.t1 MTR_1g069585 98.571 140 2 0 1 140 1 140 3.93e-98 278
MS.gene96949.t1 MTR_7g098290 98.400 125 2 0 16 140 1 125 8.58e-87 249
MS.gene96949.t1 MTR_1g026090 81.481 135 10 1 2 136 42 161 3.07e-71 212
MS.gene96949.t1 MTR_5g054560 68.800 125 15 1 16 140 1 101 1.78e-53 164
MS.gene96949.t1 MTR_5g464620 89.796 49 5 0 14 62 16 64 3.73e-25 91.7
MS.gene96949.t1 MTR_2g070580 92.683 41 3 0 100 140 87 127 2.62e-21 83.2
MS.gene96949.t1 MTR_1779s0020 36.522 115 65 3 26 136 8 118 3.65e-16 70.1
MS.gene96949.t1 MTR_4g051390 36.522 115 65 3 26 136 8 118 4.98e-16 69.7
MS.gene96949.t1 MTR_2g087550 36.792 106 60 2 26 128 8 109 1.55e-14 67.8
MS.gene96949.t1 MTR_0002s0780 34.426 122 73 3 23 140 132 250 1.92e-14 68.2
MS.gene96949.t1 MTR_4g017930 80.556 36 5 1 104 139 13 46 1.09e-11 58.5
MS.gene96949.t1 MTR_4g066540 72.500 40 7 1 100 139 54 89 7.28e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96949.t1 AT3G04400 98.571 140 2 0 1 140 1 140 1.65e-98 279
MS.gene96949.t1 AT2G33370 98.571 140 2 0 1 140 1 140 1.65e-98 279
MS.gene96949.t1 AT1G04480 98.571 140 2 0 1 140 1 140 1.65e-98 279
MS.gene96949.t1 AT3G04400 100.000 125 0 0 16 140 1 125 4.64e-88 252
MS.gene96949.t1 AT2G33370 100.000 125 0 0 16 140 1 125 4.64e-88 252
MS.gene96949.t1 ATCG00780 34.783 115 67 3 26 136 8 118 4.97e-15 67.0

Find 50 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACCTTTCATTTCTCCTT+TGG 0.232028 7.4:-12072601 None:intergenic
TTACCTTTCATTTCTCCTTT+GGG 0.290146 7.4:-12072600 None:intergenic
ATTCTTAGCTCCGGTGTTAT+CGG 0.357276 7.4:-12072252 None:intergenic
ACATGAAAACACCGTCCTTT+CGG 0.371684 7.4:-12072433 None:intergenic
GATCCGCGGGTAACAAGTTC+AGG 0.386005 7.4:+12072189 MS.gene96949:CDS
GGAAGGAGTGTGCTGATCTA+TGG 0.394494 7.4:+12073027 MS.gene96949:CDS
CCTTCCTTTGATACCTTTGA+CGG 0.396996 7.4:-12072288 None:intergenic
AGCACCTTCTTACGGAGATC+AGG 0.422915 7.4:-12072374 None:intergenic
TTCTGCTTGCGTTGGTGACA+TGG 0.443666 7.4:+12072325 MS.gene96949:CDS
CAATTCACCGTCGCCGCCAC+TGG 0.459295 7.4:-12072227 None:intergenic
TTAGCAGCACTTGCAATCCT+AGG 0.471348 7.4:-12073050 None:intergenic
CTCTACATCATTTCCGTCAA+AGG 0.478393 7.4:+12072275 MS.gene96949:CDS
GGTGATGGCCACCGTGAAGA+AGG 0.480460 7.4:+12072346 MS.gene96949:CDS
CGTTTGCCTTCTGCTTGCGT+TGG 0.482632 7.4:+12072317 MS.gene96949:CDS
TCTGCTATCACTGGTCCAAT+CGG 0.485775 7.4:+12073005 MS.gene96949:CDS
TAACAAGTTCAGGATGTCAC+TGG 0.500497 7.4:+12072199 MS.gene96949:CDS
CGGCAGGAAGCACCTTCTTA+CGG 0.502055 7.4:-12072382 None:intergenic
ATCAGGCTTACCCTTCTTCA+CGG 0.504036 7.4:-12072357 None:intergenic
CTCAGGTCGCGGAGGATCCG+CGG 0.504873 7.4:+12072175 MS.gene96949:intron
CTGCTATCACTGGTCCAATC+GGG 0.511052 7.4:+12073006 MS.gene96949:CDS
TTGTATTGTGCAGACAATGC+TGG 0.531818 7.4:+12072564 MS.gene96949:intron
ATTGTAGGGTCTGCTATCAC+TGG 0.534637 7.4:+12072996 MS.gene96949:intron
CAACGCAAGCAGAAGGCAAA+CGG 0.538758 7.4:-12072316 None:intergenic
TCAGCACACTCCTTCCCGAT+TGG 0.539409 7.4:-12073020 None:intergenic
CGCTGACGAACGATGACGGC+AGG 0.540043 7.4:-12072398 None:intergenic
ACACCGTCCTTTCGGCGCCA+TGG 0.550488 7.4:-12072425 None:intergenic
CCGTCAAAGGTATCAAAGGA+AGG 0.551618 7.4:+12072288 MS.gene96949:CDS
TCAGGTCGCGGAGGATCCGC+GGG 0.560803 7.4:+12072176 MS.gene96949:intron
AGTGTGCTGATCTATGGCCT+AGG 0.561029 7.4:+12073033 MS.gene96949:CDS
GGTGTTATTGTTAATCCCAA+AGG 0.565013 7.4:+12072585 MS.gene96949:CDS
TAAGCCTGATCTCCGTAAGA+AGG 0.569085 7.4:+12072370 MS.gene96949:CDS
ATTTCCGTCAAAGGTATCAA+AGG 0.575410 7.4:+12072284 MS.gene96949:CDS
GGGTCTACCAGTGGCGGCGA+CGG 0.576990 7.4:+12072220 MS.gene96949:CDS
GTGATGGCCACCGTGAAGAA+GGG 0.579374 7.4:+12072347 MS.gene96949:CDS
TTGCGTTGGTGACATGGTGA+TGG 0.588839 7.4:+12072331 MS.gene96949:CDS
GATGTAGAGATTCTTAGCTC+CGG 0.596136 7.4:-12072261 None:intergenic
AAACCATGGCGCCGAAAGGA+CGG 0.604162 7.4:+12072422 MS.gene96949:CDS
AACAAGTTCAGGATGTCACT+GGG 0.607031 7.4:+12072200 MS.gene96949:CDS
ATGTCACCAACGCAAGCAGA+AGG 0.609870 7.4:-12072323 None:intergenic
GCGTAAACCATGGCGCCGAA+AGG 0.610086 7.4:+12072418 MS.gene96949:CDS
GTCACTGGGTCTACCAGTGG+CGG 0.621290 7.4:+12072214 MS.gene96949:CDS
GTGAATTGCGCCGATAACAC+CGG 0.624326 7.4:+12072242 MS.gene96949:CDS
AATCCCAAAGGAGAAATGAA+AGG 0.624552 7.4:+12072597 MS.gene96949:CDS
TTTACGCTGACGAACGATGA+CGG 0.626909 7.4:-12072402 None:intergenic
GCAGCAGCAATGTCGAAGAG+AGG 0.651240 7.4:+12072047 None:intergenic
GATGTCACTGGGTCTACCAG+TGG 0.653286 7.4:+12072211 MS.gene96949:CDS
TCGTTCGTCAGCGTAAACCA+TGG 0.671478 7.4:+12072408 MS.gene96949:CDS
TATCACTGGTCCAATCGGGA+AGG 0.675150 7.4:+12073010 MS.gene96949:CDS
CATCCTGAACTTGTTACCCG+CGG 0.683379 7.4:-12072192 None:intergenic
AGGCTTACCCTTCTTCACGG+TGG 0.718796 7.4:-12072354 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATAATCAGTATTAAAAT+TGG + chr7.4:12072874-12072893 MS.gene96949:intron 10.0%
!! TAATCAGTATTAAAATTGGT+TGG + chr7.4:12072878-12072897 MS.gene96949:intron 20.0%
!! TGATTCTTACTTAATATTTC+TGG + chr7.4:12072540-12072559 MS.gene96949:intron 20.0%
!!! TAATTTTCATTTTGTTTCTC+AGG + chr7.4:12072158-12072177 MS.gene96949:intron 20.0%
!!! TTATTAAAACGCAATTTTGT+AGG - chr7.4:12072141-12072160 None:intergenic 20.0%
! TGAAAATGAAAACGAAAATG+AGG - chr7.4:12072079-12072098 None:intergenic 25.0%
!! AATGATTGGTGTTTAATAAG+TGG + chr7.4:12072706-12072725 MS.gene96949:intron 25.0%
ATGATAATATCGATGTAGGT+GGG + chr7.4:12072673-12072692 MS.gene96949:intron 30.0%
ATTAAAATTGGTTGGAGGAT+CGG + chr7.4:12072886-12072905 MS.gene96949:intron 30.0%
CACAACATCAAAACCAAAAA+CGG - chr7.4:12072938-12072957 None:intergenic 30.0%
TCAGTATTAAAATTGGTTGG+AGG + chr7.4:12072881-12072900 MS.gene96949:intron 30.0%
TGGGTAATCTATGTAATGAT+TGG + chr7.4:12072692-12072711 MS.gene96949:intron 30.0%
TTACCTTTCATTTCTCCTTT+GGG - chr7.4:12072603-12072622 None:intergenic 30.0%
TTTACCTTTCATTTCTCCTT+TGG - chr7.4:12072604-12072623 None:intergenic 30.0%
!! TATGTTTTTATCGCCGTTTT+TGG + chr7.4:12072922-12072941 MS.gene96949:intron 30.0%
!! TCGTGTTGATTGTAATTGTA+GGG + chr7.4:12072982-12073001 MS.gene96949:intron 30.0%
!! TTCGTGTTGATTGTAATTGT+AGG + chr7.4:12072981-12073000 MS.gene96949:intron 30.0%
AATCCCAAAGGAGAAATGAA+AGG + chr7.4:12072597-12072616 MS.gene96949:CDS 35.0%
ACTGCTGTGTCTTCAATAAT+TGG + chr7.4:12072788-12072807 MS.gene96949:intron 35.0%
CACGATGATAATATCGATGT+AGG + chr7.4:12072669-12072688 MS.gene96949:intron 35.0%
CTACATCGATATTATCATCG+TGG - chr7.4:12072671-12072690 None:intergenic 35.0%
GATGATAATATCGATGTAGG+TGG + chr7.4:12072672-12072691 MS.gene96949:intron 35.0%
TTAAAATTGGTTGGAGGATC+GGG + chr7.4:12072887-12072906 MS.gene96949:intron 35.0%
!! ATTTCCGTCAAAGGTATCAA+AGG + chr7.4:12072284-12072303 MS.gene96949:CDS 35.0%
!! GGTGTTATTGTTAATCCCAA+AGG + chr7.4:12072585-12072604 MS.gene96949:CDS 35.0%
!! GGTTTTGATGTTGTGCTTTT+TGG + chr7.4:12072943-12072962 MS.gene96949:intron 35.0%
AACAAGTTCAGGATGTCACT+GGG + chr7.4:12072200-12072219 MS.gene96949:CDS 40.0%
ACATGAAAACACCGTCCTTT+CGG - chr7.4:12072436-12072455 None:intergenic 40.0%
CCTTCCTTTGATACCTTTGA+CGG - chr7.4:12072291-12072310 None:intergenic 40.0%
CTCTACATCATTTCCGTCAA+AGG + chr7.4:12072275-12072294 MS.gene96949:CDS 40.0%
GATGTAGAGATTCTTAGCTC+CGG - chr7.4:12072264-12072283 None:intergenic 40.0%
TAACAAGTTCAGGATGTCAC+TGG + chr7.4:12072199-12072218 MS.gene96949:CDS 40.0%
TTGTATTGTGCAGACAATGC+TGG + chr7.4:12072564-12072583 MS.gene96949:intron 40.0%
! GGTGTTTTCATGTACTTCGA+AGG + chr7.4:12072443-12072462 MS.gene96949:CDS 40.0%
!! ATTCTTAGCTCCGGTGTTAT+CGG - chr7.4:12072255-12072274 None:intergenic 40.0%
!! TCATTTTGTTTCTCAGGTCG+CGG + chr7.4:12072164-12072183 MS.gene96949:intron 40.0%
ATCAGGCTTACCCTTCTTCA+CGG - chr7.4:12072360-12072379 None:intergenic 45.0%
ATTGTAGGGTCTGCTATCAC+TGG + chr7.4:12072996-12073015 MS.gene96949:intron 45.0%
TAAGCCTGATCTCCGTAAGA+AGG + chr7.4:12072370-12072389 MS.gene96949:CDS 45.0%
TCTGCTATCACTGGTCCAAT+CGG + chr7.4:12073005-12073024 MS.gene96949:CDS 45.0%
TTAGCAGCACTTGCAATCCT+AGG - chr7.4:12073053-12073072 None:intergenic 45.0%
TTTACGCTGACGAACGATGA+CGG - chr7.4:12072405-12072424 None:intergenic 45.0%
!! CCGTCAAAGGTATCAAAGGA+AGG + chr7.4:12072288-12072307 MS.gene96949:CDS 45.0%
AGCACCTTCTTACGGAGATC+AGG - chr7.4:12072377-12072396 None:intergenic 50.0%
ATGTCACCAACGCAAGCAGA+AGG - chr7.4:12072326-12072345 None:intergenic 50.0%
CAACGCAAGCAGAAGGCAAA+CGG - chr7.4:12072319-12072338 None:intergenic 50.0%
CTGCTATCACTGGTCCAATC+GGG + chr7.4:12073006-12073025 MS.gene96949:CDS 50.0%
TATCACTGGTCCAATCGGGA+AGG + chr7.4:12073010-12073029 MS.gene96949:CDS 50.0%
TCGTTCGTCAGCGTAAACCA+TGG + chr7.4:12072408-12072427 MS.gene96949:CDS 50.0%
! AGTGTGCTGATCTATGGCCT+AGG + chr7.4:12073033-12073052 MS.gene96949:CDS 50.0%
! GGAAGGAGTGTGCTGATCTA+TGG + chr7.4:12073027-12073046 MS.gene96949:CDS 50.0%
! GTGAATTGCGCCGATAACAC+CGG + chr7.4:12072242-12072261 MS.gene96949:CDS 50.0%
!! CATCCTGAACTTGTTACCCG+CGG - chr7.4:12072195-12072214 None:intergenic 50.0%
!! TTCTGCTTGCGTTGGTGACA+TGG + chr7.4:12072325-12072344 MS.gene96949:CDS 50.0%
!! TTGCGTTGGTGACATGGTGA+TGG + chr7.4:12072331-12072350 MS.gene96949:CDS 50.0%
!! TTTTGTTTCTCAGGTCGCGG+AGG + chr7.4:12072167-12072186 MS.gene96949:intron 50.0%
AGGCTTACCCTTCTTCACGG+TGG - chr7.4:12072357-12072376 None:intergenic 55.0%
CGTTTGCCTTCTGCTTGCGT+TGG + chr7.4:12072317-12072336 MS.gene96949:CDS 55.0%
GATCCGCGGGTAACAAGTTC+AGG + chr7.4:12072189-12072208 MS.gene96949:CDS 55.0%
GATGTCACTGGGTCTACCAG+TGG + chr7.4:12072211-12072230 MS.gene96949:CDS 55.0%
GTGATGGCCACCGTGAAGAA+GGG + chr7.4:12072347-12072366 MS.gene96949:CDS 55.0%
TCAGCACACTCCTTCCCGAT+TGG - chr7.4:12073023-12073042 None:intergenic 55.0%
! AAACCATGGCGCCGAAAGGA+CGG + chr7.4:12072422-12072441 MS.gene96949:CDS 55.0%
!! CGGCAGGAAGCACCTTCTTA+CGG - chr7.4:12072385-12072404 None:intergenic 55.0%
GTCACTGGGTCTACCAGTGG+CGG + chr7.4:12072214-12072233 MS.gene96949:CDS 60.0%
! GCGTAAACCATGGCGCCGAA+AGG + chr7.4:12072418-12072437 MS.gene96949:CDS 60.0%
! GGTGATGGCCACCGTGAAGA+AGG + chr7.4:12072346-12072365 MS.gene96949:CDS 60.0%
ACACCGTCCTTTCGGCGCCA+TGG - chr7.4:12072428-12072447 None:intergenic 65.0%
CAATTCACCGTCGCCGCCAC+TGG - chr7.4:12072230-12072249 None:intergenic 65.0%
TGGAGGATCGGGCGAGTGTG+TGG + chr7.4:12072898-12072917 MS.gene96949:intron 65.0%
! CGCTGACGAACGATGACGGC+AGG - chr7.4:12072401-12072420 None:intergenic 65.0%
CTCAGGTCGCGGAGGATCCG+CGG + chr7.4:12072175-12072194 MS.gene96949:intron 70.0%
GGGTCTACCAGTGGCGGCGA+CGG + chr7.4:12072220-12072239 MS.gene96949:CDS 70.0%
TCAGGTCGCGGAGGATCCGC+GGG + chr7.4:12072176-12072195 MS.gene96949:intron 70.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 12072056 12073085 12072056 ID=MS.gene96949
chr7.4 mRNA 12072056 12073085 12072056 ID=MS.gene96949.t1;Parent=MS.gene96949
chr7.4 exon 12072056 12072068 12072056 ID=MS.gene96949.t1.exon1;Parent=MS.gene96949.t1
chr7.4 CDS 12072056 12072068 12072056 ID=cds.MS.gene96949.t1;Parent=MS.gene96949.t1
chr7.4 exon 12072180 12072464 12072180 ID=MS.gene96949.t1.exon2;Parent=MS.gene96949.t1
chr7.4 CDS 12072180 12072464 12072180 ID=cds.MS.gene96949.t1;Parent=MS.gene96949.t1
chr7.4 exon 12072577 12072618 12072577 ID=MS.gene96949.t1.exon3;Parent=MS.gene96949.t1
chr7.4 CDS 12072577 12072618 12072577 ID=cds.MS.gene96949.t1;Parent=MS.gene96949.t1
chr7.4 exon 12073003 12073085 12073003 ID=MS.gene96949.t1.exon4;Parent=MS.gene96949.t1
chr7.4 CDS 12073003 12073085 12073003 ID=cds.MS.gene96949.t1;Parent=MS.gene96949.t1
Gene Sequence

>MS.gene96949

ATGTCGAAGAGAGGTTCGTTCCTCATTTTCGTTTTCATTTTCATTTTCATTTTCAGATTCTTAGATCAATTAATCACTTTTACCTACAAAATTGCGTTTTAATAATTTTCATTTTGTTTCTCAGGTCGCGGAGGATCCGCGGGTAACAAGTTCAGGATGTCACTGGGTCTACCAGTGGCGGCGACGGTGAATTGCGCCGATAACACCGGAGCTAAGAATCTCTACATCATTTCCGTCAAAGGTATCAAAGGAAGGTTGAACCGTTTGCCTTCTGCTTGCGTTGGTGACATGGTGATGGCCACCGTGAAGAAGGGTAAGCCTGATCTCCGTAAGAAGGTGCTTCCTGCCGTCATCGTTCGTCAGCGTAAACCATGGCGCCGAAAGGACGGTGTTTTCATGTACTTCGAAGGTATATTCACATTCTTCATTTTTTTTTGTTTCAAAATTGAGATTAATCTTAATTTGATGTATATGTTAGTGTGAATGATTCTTACTTAATATTTCTGGTTTGTATTGTGCAGACAATGCTGGTGTTATTGTTAATCCCAAAGGAGAAATGAAAGGTAAAAATTCTATATATCTCTTATTAGTTTTGATTCTATATTATTAAATCCACGATGATAATATCGATGTAGGTGGGTAATCTATGTAATGATTGGTGTTTAATAAGTGGAATTAGAGCTTAGTAGCTTAGTATATTGAAATTAGAGTTAATAGTTTAGAATTAATAACACTGCTGTGTCTTCAATAATTGGAATTAGAGTTTAGTAACTTAGTGTTAAAATTGAAATTAGAGTTTAATACTTGATAGTTTAGTATTAATAATCAGTATTAAAATTGGTTGGAGGATCGGGCGAGTGTGTGGCTATGTTTTTATCGCCGTTTTTGGTTTTGATGTTGTGCTTTTTGGTTCTTCTCTTGATATTTCGTGTTGATTGTAATTGTAGGGTCTGCTATCACTGGTCCAATCGGGAAGGAGTGTGCTGATCTATGGCCTAGGATTGCAAGTGCTGCTAATGCTATCGTTTAA

Protein sequence

>MS.gene96949.t1

MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVLPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV