AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene33048

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33048.t1 MTR_1g015275 86.450 369 45 3 1 366 1 367 1.16e-168 475
MS.gene33048.t1 MTR_3g104880 44.146 410 140 15 1 366 1 365 2.15e-54 183
MS.gene33048.t1 MTR_8g019660 40.334 419 173 13 1 367 1 394 6.57e-35 132
MS.gene33048.t1 MTR_4g125620 33.609 363 183 15 17 366 15 332 1.11e-21 95.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33048.t1 AT3G13980 37.250 400 156 15 4 367 5 345 4.08e-38 140
MS.gene33048.t1 AT1G54200 36.973 403 159 14 4 367 13 359 5.40e-33 126
MS.gene33048.t1 AT5G12050 32.250 400 170 14 16 364 7 356 5.92e-17 81.6
MS.gene33048.t1 AT3G42800 31.795 195 110 5 186 364 140 327 5.04e-13 69.7

Find 61 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGCTTGTTCTAACCGGTTT+TGG 0.272024 1.1:+6567741 None:intergenic
ATCTGCTTCTTCGTCTTTGT+TGG 0.273644 1.1:+6567459 None:intergenic
CGTCGATGGAACGGTAAATT+TGG 0.311193 1.1:+6568075 None:intergenic
CAGTTCCACTTCAATTTCTT+CGG 0.312323 1.1:-6567853 MS.gene33048:CDS
CAAGCGTGTCGGCATCATTT+AGG 0.345034 1.1:-6567725 MS.gene33048:CDS
TAGGCTTGAAAAGGAGAAAC+AGG 0.345846 1.1:-6567706 MS.gene33048:CDS
TCCGACACAGATTCATTATA+CGG 0.352790 1.1:-6567804 MS.gene33048:CDS
TTGGATCATTTGAGTGTGTT+TGG 0.380923 1.1:-6567123 MS.gene33048:CDS
GGAAGAGGGTAGGGCTAAGG+TGG 0.392720 1.1:-6567301 MS.gene33048:CDS
GCCGACACGCTTGTTCTAAC+CGG 0.412919 1.1:+6567735 None:intergenic
AGAGGGTAGGGCTAAGGTGG+AGG 0.421619 1.1:-6567298 MS.gene33048:CDS
GTTGGTTTGTTTAAAATCGT+TGG 0.424352 1.1:+6567999 None:intergenic
TTGTGGAGTGGAAGAGGGTA+GGG 0.431294 1.1:-6567310 MS.gene33048:CDS
AGTGGAAGAGGGTAGGGCTA+AGG 0.442934 1.1:-6567304 MS.gene33048:CDS
TGTGAGGAGCTTCCTGTGTA+TGG 0.451538 1.1:-6567087 MS.gene33048:CDS
CATTCCACCTAGGCCAAAAC+CGG 0.453832 1.1:-6567754 MS.gene33048:CDS
ATTTCTTCGGATTCTAGCTC+CGG 0.469115 1.1:-6567840 MS.gene33048:CDS
AACGGTAAATTTGGTCTAAG+AGG 0.473989 1.1:+6568084 None:intergenic
GGCATCATTTAGGCTTGAAA+AGG 0.486316 1.1:-6567715 MS.gene33048:CDS
AAGAGGGTGGAAGAGAATGA+AGG 0.489820 1.1:+6568101 None:intergenic
TTTGTGGAGTGGAAGAGGGT+AGG 0.496413 1.1:-6567311 MS.gene33048:CDS
TGAGTGTGTTTGGAGATAGT+AGG 0.500314 1.1:-6567113 MS.gene33048:CDS
TTTCTCCTTCGTCGATGGAA+CGG 0.507353 1.1:+6568066 None:intergenic
TCTTCTTCTTGTTATAACAT+TGG 0.508602 1.1:+6567247 None:intergenic
ATCATTTCTACCACAAAATG+AGG 0.508732 1.1:+6567350 None:intergenic
AGAAAATCACGGCGAGGAAG+CGG 0.522094 1.1:-6567631 MS.gene33048:CDS
GTGAAGCAACCGATTTCGCC+AGG 0.534045 1.1:-6567555 MS.gene33048:CDS
TGGTAGAAATGATTACAAAA+CGG 0.535489 1.1:-6567340 MS.gene33048:CDS
CGAAGAAGCAGATGAACACA+TGG 0.541264 1.1:-6567449 MS.gene33048:CDS
AACTGAAGAACAGAGCATCT+TGG 0.545134 1.1:+6567871 None:intergenic
TGGAGATAGTAGGTATTGTG+AGG 0.545793 1.1:-6567103 MS.gene33048:CDS
AGAGGGTGGAAGAGAATGAA+GGG 0.557335 1.1:+6568102 None:intergenic
TAATGAATCTGTGTCGGAGG+AGG 0.558404 1.1:+6567809 None:intergenic
CGTCGTGCTTCATTCCACCT+AGG 0.568549 1.1:-6567764 MS.gene33048:CDS
AGAATCCGAAGAAATTGAAG+TGG 0.585201 1.1:+6567848 None:intergenic
AAGGGTTTATGAACCTCTCG+TGG 0.590814 1.1:+6568120 None:intergenic
TCTTCGGATTCTAGCTCCGG+TGG 0.592579 1.1:-6567837 MS.gene33048:CDS
TCCGTATAATGAATCTGTGT+CGG 0.592790 1.1:+6567803 None:intergenic
ACGGTAAATTTGGTCTAAGA+GGG 0.594369 1.1:+6568085 None:intergenic
GAACACATGGGAGACTCATG+AGG 0.596864 1.1:-6567436 MS.gene33048:CDS
GTCGGAGGAGGAGAATCCAC+CGG 0.606459 1.1:+6567821 None:intergenic
CTTGGTCGTGATCACGTAGG+TGG 0.607856 1.1:+6567889 None:intergenic
AATAAAGAACAAATCAAGAG+CGG 0.611789 1.1:-6567604 MS.gene33048:CDS
AAACAAAGCACAGAAAATCA+CGG 0.616367 1.1:-6567642 MS.gene33048:CDS
GTAAATTTGGTCTAAGAGGG+TGG 0.617354 1.1:+6568088 None:intergenic
AGGCTTGAAAAGGAGAAACA+GGG 0.627580 1.1:-6567705 MS.gene33048:CDS
TATTAGCAAATAGAGTGTTG+AGG 0.629706 1.1:+6567514 None:intergenic
GGATGAAGATGATGATGATG+TGG 0.631674 1.1:-6567175 MS.gene33048:CDS
ATTTACCGTTCCATCGACGA+AGG 0.641766 1.1:-6568071 MS.gene33048:CDS
CGAAGAAGCAGATGAACACG+TGG 0.648153 1.1:+6567401 None:intergenic
ACCGGTTAGAACAAGCGTGT+CGG 0.655186 1.1:-6567736 MS.gene33048:CDS
GGCTTGAAAAGGAGAAACAG+GGG 0.655509 1.1:-6567704 MS.gene33048:CDS
ATTTCTACCACAAAATGAGG+CGG 0.655870 1.1:+6567353 None:intergenic
AAGCAACCGATTTCGCCAGG+TGG 0.662604 1.1:-6567552 MS.gene33048:CDS
GTATAATGAATCTGTGTCGG+AGG 0.665395 1.1:+6567806 None:intergenic
AACACATGGGAGACTCATGA+GGG 0.677376 1.1:-6567435 MS.gene33048:CDS
ACACGAGTAGTTCCATACAC+AGG 0.691654 1.1:+6567075 None:intergenic
AGAGATCAACAAACCACGAG+AGG 0.700583 1.1:-6568133 MS.gene33048:CDS
AAGCACAGAAAATCACGGCG+AGG 0.718569 1.1:-6567637 MS.gene33048:CDS
CATCTTGGTCGTGATCACGT+AGG 0.729154 1.1:+6567886 None:intergenic
GAAGAAGCAGATGAACACAT+GGG 0.731435 1.1:-6567448 MS.gene33048:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATGATTTAGTTTTATTAA+AGG - chr1.1:6567991-6568010 MS.gene33048:CDS 15.0%
!! TATTAATCAAAAAGAAGAAG+AGG - chr1.1:6568021-6568040 MS.gene33048:CDS 20.0%
! AATAAAGAACAAATCAAGAG+CGG - chr1.1:6567613-6567632 MS.gene33048:CDS 25.0%
! TGGTAGAAATGATTACAAAA+CGG - chr1.1:6567877-6567896 MS.gene33048:CDS 25.0%
!! GTTATTGTTATGTTTTCTGT+CGG + chr1.1:6567246-6567265 None:intergenic 25.0%
!! TCTTCTTCTTGTTATAACAT+TGG + chr1.1:6567973-6567992 None:intergenic 25.0%
!!! GAAACAGTTTTTTCGATTTT+TGG + chr1.1:6567278-6567297 None:intergenic 25.0%
!!! GTAAAATTTTGTTGATTCAG+TGG + chr1.1:6567186-6567205 None:intergenic 25.0%
AAACAAAGCACAGAAAATCA+CGG - chr1.1:6567575-6567594 MS.gene33048:CDS 30.0%
ATCATTTCTACCACAAAATG+AGG + chr1.1:6567870-6567889 None:intergenic 30.0%
!! GTTGGTTTGTTTAAAATCGT+TGG + chr1.1:6567221-6567240 None:intergenic 30.0%
!! TATTAGCAAATAGAGTGTTG+AGG + chr1.1:6567706-6567725 None:intergenic 30.0%
!!! AAGTTCTGATCTTTTTGAGT+TGG - chr1.1:6568075-6568094 MS.gene33048:CDS 30.0%
AACGGTAAATTTGGTCTAAG+AGG + chr1.1:6567136-6567155 None:intergenic 35.0%
ACGGTAAATTTGGTCTAAGA+GGG + chr1.1:6567135-6567154 None:intergenic 35.0%
AGAATCCGAAGAAATTGAAG+TGG + chr1.1:6567372-6567391 None:intergenic 35.0%
ATTTCTACCACAAAATGAGG+CGG + chr1.1:6567867-6567886 None:intergenic 35.0%
CAGTTCCACTTCAATTTCTT+CGG - chr1.1:6567364-6567383 MS.gene33048:CDS 35.0%
TCCGACACAGATTCATTATA+CGG - chr1.1:6567413-6567432 MS.gene33048:CDS 35.0%
TCCGTATAATGAATCTGTGT+CGG + chr1.1:6567417-6567436 None:intergenic 35.0%
TTGGATCATTTGAGTGTGTT+TGG - chr1.1:6568094-6568113 MS.gene33048:CDS 35.0%
! TACAAAACGGTACGTTTTTG+TGG - chr1.1:6567890-6567909 MS.gene33048:CDS 35.0%
! TAGGTGGAATTTTCTGTTGT+CGG + chr1.1:6567315-6567334 None:intergenic 35.0%
!! TTATGTTTTCTGTCGGTTGT+TGG + chr1.1:6567239-6567258 None:intergenic 35.0%
AGGCTTGAAAAGGAGAAACA+GGG - chr1.1:6567512-6567531 MS.gene33048:CDS 40.0%
ATCTGCTTCTTCGTCTTTGT+TGG + chr1.1:6567761-6567780 None:intergenic 40.0%
GAAGAAGCAGATGAACACAT+GGG - chr1.1:6567769-6567788 MS.gene33048:CDS 40.0%
GGCATCATTTAGGCTTGAAA+AGG - chr1.1:6567502-6567521 MS.gene33048:CDS 40.0%
GTAAATTTGGTCTAAGAGGG+TGG + chr1.1:6567132-6567151 None:intergenic 40.0%
GTATAATGAATCTGTGTCGG+AGG + chr1.1:6567414-6567433 None:intergenic 40.0%
TAGGCTTGAAAAGGAGAAAC+AGG - chr1.1:6567511-6567530 MS.gene33048:CDS 40.0%
TGAGTGTGTTTGGAGATAGT+AGG - chr1.1:6568104-6568123 MS.gene33048:CDS 40.0%
! AACTGAAGAACAGAGCATCT+TGG + chr1.1:6567349-6567368 None:intergenic 40.0%
! GGATGAAGATGATGATGATG+TGG - chr1.1:6568042-6568061 MS.gene33048:CDS 40.0%
! TGGAGATAGTAGGTATTGTG+AGG - chr1.1:6568114-6568133 MS.gene33048:CDS 40.0%
!! ATTTCTTCGGATTCTAGCTC+CGG - chr1.1:6567377-6567396 MS.gene33048:CDS 40.0%
!! TTTTGTTTCTCCTTCGTCGA+TGG + chr1.1:6567159-6567178 None:intergenic 40.0%
AACACATGGGAGACTCATGA+GGG - chr1.1:6567782-6567801 MS.gene33048:CDS 45.0%
AAGAGGGTGGAAGAGAATGA+AGG + chr1.1:6567119-6567138 None:intergenic 45.0%
AAGGGTTTATGAACCTCTCG+TGG + chr1.1:6567100-6567119 None:intergenic 45.0%
ACACGAGTAGTTCCATACAC+AGG + chr1.1:6568145-6568164 None:intergenic 45.0%
AGAGATCAACAAACCACGAG+AGG - chr1.1:6567084-6567103 MS.gene33048:CDS 45.0%
AGAGGGTGGAAGAGAATGAA+GGG + chr1.1:6567118-6567137 None:intergenic 45.0%
ATTTACCGTTCCATCGACGA+AGG - chr1.1:6567146-6567165 MS.gene33048:CDS 45.0%
CGAAGAAGCAGATGAACACA+TGG - chr1.1:6567768-6567787 MS.gene33048:CDS 45.0%
CGTCGATGGAACGGTAAATT+TGG + chr1.1:6567145-6567164 None:intergenic 45.0%
GGCTTGAAAAGGAGAAACAG+GGG - chr1.1:6567513-6567532 MS.gene33048:CDS 45.0%
TAATGAATCTGTGTCGGAGG+AGG + chr1.1:6567411-6567430 None:intergenic 45.0%
TTTCTCCTTCGTCGATGGAA+CGG + chr1.1:6567154-6567173 None:intergenic 45.0%
! AAACTCGTGAGTTTTCCACC+TGG + chr1.1:6567683-6567702 None:intergenic 45.0%
! AACGGTACGTTTTTGTGGAG+TGG - chr1.1:6567895-6567914 MS.gene33048:CDS 45.0%
! ACGTTTTTGTGGAGTGGAAG+AGG - chr1.1:6567901-6567920 MS.gene33048:CDS 45.0%
! AGCAAAACCGCCTCATTTTG+TGG - chr1.1:6567857-6567876 MS.gene33048:CDS 45.0%
! AGTTTTCCACCTGGCGAAAT+CGG + chr1.1:6567674-6567693 None:intergenic 45.0%
! CATCTGCTTCTTCGTTTTCG+CGG - chr1.1:6567825-6567844 MS.gene33048:CDS 45.0%
! CGTTTTTGTGGAGTGGAAGA+GGG - chr1.1:6567902-6567921 MS.gene33048:CDS 45.0%
!! ACGCTTGTTCTAACCGGTTT+TGG + chr1.1:6567479-6567498 None:intergenic 45.0%
AAGCACAGAAAATCACGGCG+AGG - chr1.1:6567580-6567599 MS.gene33048:CDS 50.0%
ACCGGTTAGAACAAGCGTGT+CGG - chr1.1:6567481-6567500 MS.gene33048:CDS 50.0%
AGAAAATCACGGCGAGGAAG+CGG - chr1.1:6567586-6567605 MS.gene33048:CDS 50.0%
CATCTTGGTCGTGATCACGT+AGG + chr1.1:6567334-6567353 None:intergenic 50.0%
CATTCCACCTAGGCCAAAAC+CGG - chr1.1:6567463-6567482 MS.gene33048:CDS 50.0%
CGAAGAAGCAGATGAACACG+TGG + chr1.1:6567819-6567838 None:intergenic 50.0%
GAACACATGGGAGACTCATG+AGG - chr1.1:6567781-6567800 MS.gene33048:CDS 50.0%
TGTGAGGAGCTTCCTGTGTA+TGG - chr1.1:6568130-6568149 MS.gene33048:CDS 50.0%
TTGTGGAGTGGAAGAGGGTA+GGG - chr1.1:6567907-6567926 MS.gene33048:CDS 50.0%
TTTGTGGAGTGGAAGAGGGT+AGG - chr1.1:6567906-6567925 MS.gene33048:CDS 50.0%
! AGGGGAATCACGTTTTCGAC+AGG - chr1.1:6567531-6567550 MS.gene33048:CDS 50.0%
! CAAGCGTGTCGGCATCATTT+AGG - chr1.1:6567492-6567511 MS.gene33048:CDS 50.0%
!! GTTCTAACCGGTTTTGGCCT+AGG + chr1.1:6567473-6567492 None:intergenic 50.0%
AGTGGAAGAGGGTAGGGCTA+AGG - chr1.1:6567913-6567932 MS.gene33048:CDS 55.0%
CGTCGTGCTTCATTCCACCT+AGG - chr1.1:6567453-6567472 MS.gene33048:CDS 55.0%
CTTGGTCGTGATCACGTAGG+TGG + chr1.1:6567331-6567350 None:intergenic 55.0%
GCCGACACGCTTGTTCTAAC+CGG + chr1.1:6567485-6567504 None:intergenic 55.0%
! AAGCAACCGATTTCGCCAGG+TGG - chr1.1:6567665-6567684 MS.gene33048:CDS 55.0%
! GTGAAGCAACCGATTTCGCC+AGG - chr1.1:6567662-6567681 MS.gene33048:CDS 55.0%
!! CTAACCGGTTTTGGCCTAGG+TGG + chr1.1:6567470-6567489 None:intergenic 55.0%
!! TCTTCGGATTCTAGCTCCGG+TGG - chr1.1:6567380-6567399 MS.gene33048:CDS 55.0%
AGAGGGTAGGGCTAAGGTGG+AGG - chr1.1:6567919-6567938 MS.gene33048:CDS 60.0%
GGAAGAGGGTAGGGCTAAGG+TGG - chr1.1:6567916-6567935 MS.gene33048:CDS 60.0%
GTCGGAGGAGGAGAATCCAC+CGG + chr1.1:6567399-6567418 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 6567068 6568171 6567068 ID=MS.gene33048
chr1.1 mRNA 6567068 6568171 6567068 ID=MS.gene33048.t1;Parent=MS.gene33048
chr1.1 exon 6567068 6568171 6567068 ID=MS.gene33048.t1.exon1;Parent=MS.gene33048.t1
chr1.1 CDS 6567068 6568171 6567068 ID=cds.MS.gene33048.t1;Parent=MS.gene33048.t1
Gene Sequence

>MS.gene33048

ATGTACAAGTATGAGAAGAGATCAACAAACCACGAGAGGTTCATAAACCCTTCATTCTCTTCCACCCTCTTAGACCAAATTTACCGTTCCATCGACGAAGGAGAAACAAAATTAACCACTGAATCAACAAAATTTTACAGAGAGCAAAAACCAACGATTTTAAACAAACCAACAACCGACAGAAAACATAACAATAACAACAACAAACCAAAAATCGAAAAAACTGTTTCTGTCGCGAAAGAAACCGACAACAGAAAATTCCACCTACGTGATCACGACCAAGATGCTCTGTTCTTCAGTTCCACTTCAATTTCTTCGGATTCTAGCTCCGGTGGATTCTCCTCCTCCGACACAGATTCATTATACGGAACGAAGTCACATGCTTCGTCGTGCTTCATTCCACCTAGGCCAAAACCGGTTAGAACAAGCGTGTCGGCATCATTTAGGCTTGAAAAGGAGAAACAGGGGAATCACGTTTTCGACAGGTTTTGTCGAAGTTCTCAAAACAAACAAAGCACAGAAAATCACGGCGAGGAAGCGGTTTTAATAAAGAACAAATCAAGAGCGGTTAAGATTTACAATAACTTGAAGAAAGTGAAGCAACCGATTTCGCCAGGTGGAAAACTCACGAGTTTCCTCAACACTCTATTTGCTAATAGTAACAATGAGAAGAAAACGAAGACAGAGAATCCAACAAAGACGAAGAAGCAGATGAACACATGGGAGACTCATGAGGGAAAAGTAGCTTCCACGTGTTCATCTGCTTCTTCGTTTTCGCGGTCTTGTTTGAGCAAAACCGCCTCATTTTGTGGTAGAAATGATTACAAAACGGTACGTTTTTGTGGAGTGGAAGAGGGTAGGGCTAAGGTGGAGGAAGCTACTAGAAAGTTTTTGAATGAGTACCAATGTTATAACAAGAAGAAGAATGATTTAGTTTTATTAAAGGATTTGTGTATTAATCAAAAAGAAGAAGAGGATGAAGATGATGATGATGTGGCAAGTTGTGCAAGTTCTGATCTTTTTGAGTTGGATCATTTGAGTGTGTTTGGAGATAGTAGGTATTGTGAGGAGCTTCCTGTGTATGGAACTACTCGTGTTAATTAG
Protein sequence

>MS.gene33048.t1

MYKYEKRSTNHERFINPSFSSTLLDQIYRSIDEGETKLTTESTKFYREQKPTILNKPTTDRKHNNNNNKPKIEKTVSVAKETDNRKFHLRDHDQDALFFSSTSISSDSSSGGFSSSDTDSLYGTKSHASSCFIPPRPKPVRTSVSASFRLEKEKQGNHVFDRFCRSSQNKQSTENHGEEAVLIKNKSRAVKIYNNLKKVKQPISPGGKLTSFLNTLFANSNNEKKTKTENPTKTKKQMNTWETHEGKVASTCSSASSFSRSCLSKTASFCGRNDYKTVRFCGVEEGRAKVEEATRKFLNEYQCYNKKKNDLVLLKDLCINQKEEEDEDDDDVASCASSDLFELDHLSVFGDSRYCEELPVYGTTRVN