AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCCTGTATGCCAAGTTTA+TGG 0.217464 5.2:-36981293 MS.gene064000:CDS
AACAAATAGCTTCTCTCTTC+AGG 0.222642 5.2:+36981803 None:intergenic
GATTTCCTATGGAATCTTCT+AGG 0.252745 5.2:-36981631 MS.gene064000:CDS
CACTTCTAGCTTACCTGCTT+TGG 0.255243 5.2:-36981315 MS.gene064000:CDS
TAAAGAGGTAGTTAAAAGTA+TGG 0.329448 5.2:-36981669 MS.gene064000:CDS
GTCACTTCAATTTGTAGTAA+TGG 0.360788 5.2:-36981843 MS.gene064000:CDS
TTCTAGGACTGTTCGTGGTT+CGG 0.375535 5.2:-36981615 MS.gene064000:CDS
AAGTATGGAATTTGTGGACT+TGG 0.383614 5.2:-36981654 MS.gene064000:CDS
AATTTGTAGTAATGGAATCT+TGG 0.385979 5.2:-36981835 MS.gene064000:CDS
TCATTGATTGATTTGAAGCT+AGG 0.417700 5.2:-36981440 MS.gene064000:CDS
GACGATAACTTTAGCTGTCT+TGG 0.422044 5.2:+36981205 None:intergenic
TTAGTAGATTGTCAAGGTGT+GGG 0.426117 5.2:-36981413 MS.gene064000:CDS
TTCTTGAATTAGGTTCCATC+TGG 0.429111 5.2:-36980619 MS.gene064000:intron
GCTAGAAGTGCGGGATCTCT+TGG 0.433355 5.2:+36981328 None:intergenic
TGTGGACTTGGGATTTCCTA+TGG 0.435441 5.2:-36981642 MS.gene064000:CDS
TGGATTTAATTCAGATAAAG+AGG 0.438758 5.2:-36981684 MS.gene064000:CDS
GCTAACACGCTTTGATGAAT+CGG 0.443304 5.2:+36981350 None:intergenic
TAGAAAACCCTTAGTTGAAT+GGG 0.448095 5.2:-36981738 MS.gene064000:CDS
AGTTAAAAGTATGGAATTTG+TGG 0.448427 5.2:-36981660 MS.gene064000:CDS
CAACCATAAACTTGGCATAC+AGG 0.455845 5.2:+36981290 None:intergenic
GTAGAAAACCCTTAGTTGAA+TGG 0.471526 5.2:-36981739 MS.gene064000:CDS
AGTATGGAATTTGTGGACTT+GGG 0.478417 5.2:-36981653 MS.gene064000:CDS
ACAAATAGCTTCTCTCTTCA+GGG 0.479898 5.2:+36981804 None:intergenic
AAAAGCAATAACATGGATAG+AGG 0.481057 5.2:+36981538 None:intergenic
CCATGCTACAACCATAAACT+TGG 0.490263 5.2:+36981282 None:intergenic
TCATGTAACTTTGAGCGAGA+TGG 0.496792 5.2:-36981704 MS.gene064000:CDS
CCTCGAAAGATTACCACAAA+AGG 0.498780 5.2:-36981250 MS.gene064000:CDS
GAATCTTCTAGGACTGTTCG+TGG 0.500953 5.2:-36981620 MS.gene064000:CDS
ACAGCTAAAGTTATCGTCAA+TGG 0.504384 5.2:-36981200 MS.gene064000:CDS
CATTGATTGATTTGAAGCTA+GGG 0.508340 5.2:-36981439 MS.gene064000:CDS
AATCAAACTGAGGTTTCCTT+CGG 0.512482 5.2:+36980535 None:intergenic
AGCAGGTAAGCTAGAAGTGC+GGG 0.516979 5.2:+36981319 None:intergenic
ATGGTAAGCGCAGTTGTCGC+AGG 0.518129 5.2:-36980581 MS.gene064000:CDS
TCAGACATCTAGCTGTGAGC+TGG 0.532209 5.2:-36981591 MS.gene064000:CDS
AGTTGTCGCAGGCGTCTAGC+TGG 0.532617 5.2:-36980570 MS.gene064000:CDS
TAGTAGATTGTCAAGGTGTG+GGG 0.537134 5.2:-36981412 MS.gene064000:CDS
AAGATTCTTCAGTCATATCA+AGG 0.537497 5.2:-36980492 MS.gene064000:CDS
CCAAGTTTATGGTTGTAGCA+TGG 0.562642 5.2:-36981282 MS.gene064000:CDS
ATTAGTAGATTGTCAAGGTG+TGG 0.566271 5.2:-36981414 MS.gene064000:CDS
CTGGACACAATGAGCGCCGA+AGG 0.574137 5.2:-36980551 MS.gene064000:CDS
TGGCATACAGGAGCCAAAGC+AGG 0.579602 5.2:+36981302 None:intergenic
CGTCGAACTCAGTTACCAGA+TGG 0.604322 5.2:+36980604 None:intergenic
ATGAATCAAAAGCAATAACA+TGG 0.620760 5.2:+36981531 None:intergenic
CTAGTCATGTAATCAAACTG+AGG 0.623999 5.2:+36980525 None:intergenic
TCGTCAATGGTGTTGAACAG+AGG 0.637850 5.2:-36981187 MS.gene064000:CDS
ACAGTCCTAGAAGATTCCAT+AGG 0.645968 5.2:+36981626 None:intergenic
GGGAGATTAGTAGATTGTCA+AGG 0.666785 5.2:-36981419 MS.gene064000:CDS
CTGGTAACTGAGTTCGACGA+TGG 0.666961 5.2:-36980600 MS.gene064000:CDS
AAGCAGGTAAGCTAGAAGTG+CGG 0.678203 5.2:+36981318 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATCTTAGAATTGTTAA+TGG - chr5.2:36981622-36981641 MS.gene064000:CDS 15.0%
!!! CGTATTATTTTACTTTCTTA+TGG - chr5.2:36981407-36981426 MS.gene064000:CDS 20.0%
!!! CTTATTTTTGTTCTTGAATT+AGG - chr5.2:36981709-36981728 MS.gene064000:CDS 20.0%
! ATGAATCAAAAGCAATAACA+TGG + chr5.2:36980810-36980829 None:intergenic 25.0%
! GAATTGTCAAATAAACTAGA+CGG + chr5.2:36981487-36981506 None:intergenic 25.0%
! TAAAGAGGTAGTTAAAAGTA+TGG - chr5.2:36980669-36980688 MS.gene064000:intron 25.0%
! TATGAAATATACATTCTGCT+AGG - chr5.2:36981869-36981888 MS.gene064000:CDS 25.0%
! TCATAGTCTAAATTCTAACA+TGG - chr5.2:36981599-36981618 MS.gene064000:CDS 25.0%
! TGGATTTAATTCAGATAAAG+AGG - chr5.2:36980654-36980673 MS.gene064000:intron 25.0%
!! AATTTGTAGTAATGGAATCT+TGG - chr5.2:36980503-36980522 MS.gene064000:CDS 25.0%
!! ACTTTCTTATGGTTTTCTTA+GGG - chr5.2:36981418-36981437 MS.gene064000:CDS 25.0%
!! AGTTAAAAGTATGGAATTTG+TGG - chr5.2:36980678-36980697 MS.gene064000:intron 25.0%
!! ATATCAAAGAAGTACAAGAA+TGG + chr5.2:36981311-36981330 None:intergenic 25.0%
!! TACTTTCTTATGGTTTTCTT+AGG - chr5.2:36981417-36981436 MS.gene064000:CDS 25.0%
!! TATCAAAGAAGTACAAGAAT+GGG + chr5.2:36981310-36981329 None:intergenic 25.0%
!!! AATAATACGAGAAGTATTGA+TGG + chr5.2:36981396-36981415 None:intergenic 25.0%
!!! CTATTTGTTTTCTGATGAAA+TGG - chr5.2:36980549-36980568 MS.gene064000:CDS 25.0%
!!! GGTATATTTTTTGGTTTCTT+AGG - chr5.2:36981193-36981212 MS.gene064000:CDS 25.0%
AAAAGCAATAACATGGATAG+AGG + chr5.2:36980803-36980822 None:intergenic 30.0%
AAGATTCTTCAGTCATATCA+AGG - chr5.2:36981846-36981865 MS.gene064000:CDS 30.0%
ATACTTCTCTTACAATCAGA+TGG - chr5.2:36981234-36981253 MS.gene064000:CDS 30.0%
CTCTGATCAATTTGTGTATA+TGG - chr5.2:36981513-36981532 MS.gene064000:CDS 30.0%
GTCACTTCAATTTGTAGTAA+TGG - chr5.2:36980495-36980514 MS.gene064000:CDS 30.0%
TAGAAAACCCTTAGTTGAAT+GGG - chr5.2:36980600-36980619 MS.gene064000:CDS 30.0%
TAGACTATGAATGACTACTT+TGG + chr5.2:36981589-36981608 None:intergenic 30.0%
! ATCAAAGAAGTACAAGAATG+GGG + chr5.2:36981309-36981328 None:intergenic 30.0%
! TTGTTTTCCCATTCAACTAA+GGG + chr5.2:36980610-36980629 None:intergenic 30.0%
!! CATTGATTGATTTGAAGCTA+GGG - chr5.2:36980899-36980918 MS.gene064000:intron 30.0%
!! TCATTGATTGATTTGAAGCT+AGG - chr5.2:36980898-36980917 MS.gene064000:intron 30.0%
!! TGAGAAAACTCTTACTTTTC+TGG + chr5.2:36981362-36981381 None:intergenic 30.0%
!! TGCTTTTGATTCATCTTTTG+CGG - chr5.2:36980816-36980835 MS.gene064000:intron 30.0%
!! TTTGTTTTCCCATTCAACTA+AGG + chr5.2:36980611-36980630 None:intergenic 30.0%
AACAAATAGCTTCTCTCTTC+AGG + chr5.2:36980538-36980557 None:intergenic 35.0%
AAGTATGGAATTTGTGGACT+TGG - chr5.2:36980684-36980703 MS.gene064000:intron 35.0%
AATCAAACTGAGGTTTCCTT+CGG + chr5.2:36981806-36981825 None:intergenic 35.0%
ACAAATAGCTTCTCTCTTCA+GGG + chr5.2:36980537-36980556 None:intergenic 35.0%
ACAGCTAAAGTTATCGTCAA+TGG - chr5.2:36981138-36981157 MS.gene064000:intron 35.0%
AGTATGGAATTTGTGGACTT+GGG - chr5.2:36980685-36980704 MS.gene064000:intron 35.0%
ATTAGTAGATTGTCAAGGTG+TGG - chr5.2:36980924-36980943 MS.gene064000:intron 35.0%
CAAATAAACTAGACGGCATT+TGG + chr5.2:36981480-36981499 None:intergenic 35.0%
CTAGTCATGTAATCAAACTG+AGG + chr5.2:36981816-36981835 None:intergenic 35.0%
GATTTCCTATGGAATCTTCT+AGG - chr5.2:36980707-36980726 MS.gene064000:intron 35.0%
GTAGAAAACCCTTAGTTGAA+TGG - chr5.2:36980599-36980618 MS.gene064000:CDS 35.0%
TTAGTAGATTGTCAAGGTGT+GGG - chr5.2:36980925-36980944 MS.gene064000:intron 35.0%
TTCTTGAATTAGGTTCCATC+TGG - chr5.2:36981719-36981738 MS.gene064000:CDS 35.0%
! CACAAACTTTATGCCTTTTG+TGG + chr5.2:36981104-36981123 None:intergenic 35.0%
!!! AGTGCAGCAGGTATATTTTT+TGG - chr5.2:36981184-36981203 MS.gene064000:CDS 35.0%
ACAGTCCTAGAAGATTCCAT+AGG + chr5.2:36980715-36980734 None:intergenic 40.0%
CAACCATAAACTTGGCATAC+AGG + chr5.2:36981051-36981070 None:intergenic 40.0%
CAAGACTGGACATTTACAAG+TGG + chr5.2:36981649-36981668 None:intergenic 40.0%
CCAAGTTTATGGTTGTAGCA+TGG - chr5.2:36981056-36981075 MS.gene064000:intron 40.0%
CCATGCTACAACCATAAACT+TGG + chr5.2:36981059-36981078 None:intergenic 40.0%
CCTCGAAAGATTACCACAAA+AGG - chr5.2:36981088-36981107 MS.gene064000:intron 40.0%
GACGATAACTTTAGCTGTCT+TGG + chr5.2:36981136-36981155 None:intergenic 40.0%
GCTAACACGCTTTGATGAAT+CGG + chr5.2:36980991-36981010 None:intergenic 40.0%
GGGAGATTAGTAGATTGTCA+AGG - chr5.2:36980919-36980938 MS.gene064000:intron 40.0%
TAGTAGATTGTCAAGGTGTG+GGG - chr5.2:36980926-36980945 MS.gene064000:intron 40.0%
TCATGTAACTTTGAGCGAGA+TGG - chr5.2:36980634-36980653 MS.gene064000:intron 40.0%
! CCTTTTGTGGTAATCTTTCG+AGG + chr5.2:36981091-36981110 None:intergenic 40.0%
AAGCAGGTAAGCTAGAAGTG+CGG + chr5.2:36981023-36981042 None:intergenic 45.0%
GCTCCTGTATGCCAAGTTTA+TGG - chr5.2:36981045-36981064 MS.gene064000:intron 45.0%
TACAGAGCAGTTTGCAAGAC+TGG + chr5.2:36981663-36981682 None:intergenic 45.0%
TGTGGACTTGGGATTTCCTA+TGG - chr5.2:36980696-36980715 MS.gene064000:intron 45.0%
! TCGTCAATGGTGTTGAACAG+AGG - chr5.2:36981151-36981170 MS.gene064000:intron 45.0%
!! CACTTCTAGCTTACCTGCTT+TGG - chr5.2:36981023-36981042 MS.gene064000:intron 45.0%
!! GAATCTTCTAGGACTGTTCG+TGG - chr5.2:36980718-36980737 MS.gene064000:intron 45.0%
!! TTCTAGGACTGTTCGTGGTT+CGG - chr5.2:36980723-36980742 MS.gene064000:intron 45.0%
CGTCGAACTCAGTTACCAGA+TGG + chr5.2:36981737-36981756 None:intergenic 50.0%
CTGGTAACTGAGTTCGACGA+TGG - chr5.2:36981738-36981757 MS.gene064000:CDS 50.0%
TCAGACATCTAGCTGTGAGC+TGG - chr5.2:36980747-36980766 MS.gene064000:intron 50.0%
! AGCAGGTAAGCTAGAAGTGC+GGG + chr5.2:36981022-36981041 None:intergenic 50.0%
ATGGTAAGCGCAGTTGTCGC+AGG - chr5.2:36981757-36981776 MS.gene064000:CDS 55.0%
TGGCATACAGGAGCCAAAGC+AGG + chr5.2:36981039-36981058 None:intergenic 55.0%
! GCTAGAAGTGCGGGATCTCT+TGG + chr5.2:36981013-36981032 None:intergenic 55.0%
!! GGTTTTGTCAGCAGTGCAGC+AGG - chr5.2:36981172-36981191 MS.gene064000:CDS 55.0%
AGTTGTCGCAGGCGTCTAGC+TGG - chr5.2:36981768-36981787 MS.gene064000:CDS 60.0%
!! CTGGACACAATGAGCGCCGA+AGG - chr5.2:36981787-36981806 MS.gene064000:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 36980470 36981890 36980470 ID=MS.gene064000
chr5.2 mRNA 36980470 36981890 36980470 ID=MS.gene064000.t1;Parent=MS.gene064000
chr5.2 exon 36981167 36981890 36981167 ID=MS.gene064000.t1.exon1;Parent=MS.gene064000.t1
chr5.2 CDS 36981167 36981890 36981167 ID=cds.MS.gene064000.t1;Parent=MS.gene064000.t1
chr5.2 exon 36980470 36980629 36980470 ID=MS.gene064000.t1.exon2;Parent=MS.gene064000.t1
chr5.2 CDS 36980470 36980629 36980470 ID=cds.MS.gene064000.t1;Parent=MS.gene064000.t1
Gene Sequence

>MS.gene064000

GTTTCTTCACTATTTCAGTGTTTCTGTCACTTCAATTTGTAGTAATGGAATCTTGGAGTTATATCCCTGAAGAGAGAAGCTATTTGTTTTCTGATGAAATGGATTTTTCACTTGATGCTTTTATGAGAAGTAGAAAACCCTTAGTTGAATGGGAAAACAAATCTTCATGTAACTTTGAGCGAGATGGATTTAATTCAGATAAAGAGGTAGTTAAAAGTATGGAATTTGTGGACTTGGGATTTCCTATGGAATCTTCTAGGACTGTTCGTGGTTCGGTTCAGACATCTAGCTGTGAGCTGGATAGTAATAATTCTAGTAAAAGAGAGAATTCCTCTATCCATGTTATTGCTTTTGATTCATCTTTTGCGGAAGAAGATTCTGAGTCAAAGCATTTAAGTTCTCTAGTTGAATCGAAAAATCATGATTCTTCATTGATTGATTTGAAGCTAGGGAGATTAGTAGATTGTCAAGGTGTGGGGAGTGATAGAGATGCAAAAACATTCGCTTCTGAATCTATGCCGATTCATCAAAGCGTGTTAGCCAAGAGATCCCGCACTTCTAGCTTACCTGCTTTGGCTCCTGTATGCCAAGTTTATGGTTGTAGCATGGATCTTAGCTCCTCGAAAGATTACCACAAAAGGCATAAAGTTTGTGACGTTCACTCCAAGACAGCTAAAGTTATCGTCAATGGTGTTGAACAGAGGTTTTGTCAGCAGTGCAGCAGGTATATTTTTTGGTTTCTTAGGAATTAAAATTACATTTCTATACTTCTCTTACAATCAGATGGTCATCTTCTAACTATATAAGATCATTATATTTGTTCGATTATTGACATACCCCATTCTTGTACTTCTTTGATATATTTAAACAAGAAATGTTGTTAGTAAAACCAGAAAAGTAAGAGTTTTCTCAAATCAGACAAGCCATCAATACTTCTCGTATTATTTTACTTTCTTATGGTTTTCTTAGGGCTACTATTGATAAAATGATTTAAGAGTTTTCTTTCTCCAAATGCCGTCTAGTTTATTTGACAATTCACAATGCTCTGATCAATTTGTGTATATGGTATTGATATAGAATAGATATGTTGAAATCTCACATTCGCTAAATATATGACCAAAGTAGTCATTCATAGTCTAAATTCTAACATGGTAATATCTTAGAATTGTTAATGGACCACTTGTAAATGTCCAGTCTTGCAAACTGCTCTGTATATCTTACATTTGTTACTTAATTATGCTTATTTTTGTTCTTGAATTAGGTTCCATCTGGTAACTGAGTTCGACGATGGTAAGCGCAGTTGTCGCAGGCGTCTAGCTGGACACAATGAGCGCCGAAGGAAACCTCAGTTTGATTACATGACTAGTAAACAACACAAGATTCTTCAGTCATATCAAGGTATGAAATATACATTCTGCTAG
Protein sequence

>MS.gene064000.t1

VSSLFQCFCHFNLUUWNLGVISLKREAICFLMKWIFHLMLLUEVENPULNGKTNLHVTLSEMDLIQIKRULKVWNLWTWDFLWNLLGLFVVRFRHLAVSWIVIILVKERIPLSMLLLLIHLLRKKILSQSIUVLULNRKIMILHULIUSUGDUUIVKVWGVIEMQKHSLLNLCRFIKACUPRDPALLAYLLWLLYAKFMVVAWILAPRKITTKGIKFVTFTPRQLKLSSMVLNRGFVSSAAGSIWULSSTMVSAVVAGVULDTMSAEGNLSLITULVNNTRFFSHIKVUNIHSA