AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050444


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050444.t1 MTR_7g109850 95.413 218 8 1 1 218 1 216 4.40e-151 418
MS.gene050444.t1 MTR_8g038785 86.567 134 16 1 1 134 1 132 6.48e-74 234
MS.gene050444.t1 MTR_2g005900 42.308 156 84 3 66 216 68 222 9.97e-30 110
MS.gene050444.t1 MTR_2g036690 37.267 161 99 2 51 210 71 230 7.53e-24 95.5
MS.gene050444.t1 MTR_2g036690 44.248 113 59 2 51 160 71 182 7.89e-20 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050444.t1 AT4G01940 67.157 204 53 4 25 218 32 231 7.92e-89 261
MS.gene050444.t1 AT5G49940 35.897 195 109 5 27 216 51 234 2.22e-26 102
MS.gene050444.t1 AT4G25910 33.180 217 128 6 12 212 11 226 7.93e-24 95.5
MS.gene050444.t1 AT5G49940 53.165 79 35 1 71 149 85 161 1.76e-21 87.8

Find 44 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAACCACAACTATGAAAA+TGG 0.150095 7.1:-4682821 MS.gene050444:CDS
CACTTGCACGATATCTTTAA+TGG 0.162531 7.1:+4682762 None:intergenic
CGTGTTCTTAAGGAGAAATT+TGG 0.227866 7.1:-4682790 MS.gene050444:CDS
TTCGTTGGTATTGAACAAAT+TGG 0.356289 7.1:+4683156 None:intergenic
ATCCCGGAGAAGACTGGTTC+TGG 0.389633 7.1:+4683007 None:intergenic
AAGGTAACATTGAGAATATC+TGG 0.389748 7.1:+4681712 None:intergenic
CTGGTTCTGGTTAGCGGTAG+AGG 0.412467 7.1:+4683020 None:intergenic
GGGAATCGAACGTGTTCTTA+AGG 0.422078 7.1:-4682800 MS.gene050444:CDS
TAACCAGAACCAGTCTTCTC+CGG 0.444988 7.1:-4683010 MS.gene050444:CDS
TCAACCACAACTATGAAAAT+GGG 0.480712 7.1:-4682820 MS.gene050444:CDS
AGTATAATCCCGGAGAAGAC+TGG 0.483617 7.1:+4683001 None:intergenic
GGACCTGAGTCCATTGGATC+AGG 0.493608 7.1:-4681763 MS.gene050444:CDS
AACGAGATCGACGTTTGAAA+CGG 0.497051 7.1:+4682957 None:intergenic
AAATTCAAATTCAGTTTCGT+TGG 0.499228 7.1:+4683141 None:intergenic
AGGTGTTAAAGCTGCGATCA+AGG 0.501612 7.1:-4681743 MS.gene050444:CDS
GATGTTGTATCCGTTGAAAA+CGG 0.506210 7.1:-4682889 MS.gene050444:CDS
TTCATAGTTGTGGTTGAGCT+AGG 0.507201 7.1:+4682826 None:intergenic
AACGGTGAGGTCGAATTTCG+TGG 0.510902 7.1:+4682975 None:intergenic
CCTCCGTCAGAGATGAGGTA+AGG 0.518971 7.1:+4682919 None:intergenic
TATGTTGGACCTGAGTCCAT+TGG 0.522225 7.1:-4681769 MS.gene050444:CDS
CGCCCTTACCTCATCTCTGA+CGG 0.525777 7.1:-4682922 MS.gene050444:CDS
AGAAGACTGGTTCTGGTTAG+CGG 0.534911 7.1:+4683014 None:intergenic
AACCAGAACCAGTCTTCTCC+GGG 0.537520 7.1:-4683009 MS.gene050444:CDS
TTCGTGGCGGAGTATAATCC+CGG 0.541925 7.1:+4682991 None:intergenic
GTCGTTTCTCTTAAGCTACA+AGG 0.546334 7.1:-4682865 MS.gene050444:CDS
AATTGCTACCTAGGTGGAGA+AGG 0.556964 7.1:+4681693 None:intergenic
GACTGTGTTGTGGAATATGT+TGG 0.562518 7.1:-4681784 MS.gene050444:CDS
AGCAAGGGAAACAACGGTTG+AGG 0.563035 7.1:-4682725 MS.gene050444:intron
TGAAGGTGGTGACTGTGTTG+TGG 0.573198 7.1:-4681794 MS.gene050444:CDS
AGCTTTAACACCTGATCCAA+TGG 0.583998 7.1:+4681753 None:intergenic
CTCCGTCAGAGATGAGGTAA+GGG 0.586257 7.1:+4682920 None:intergenic
CGTTTCCTCCGTCAGAGATG+AGG 0.588496 7.1:+4682914 None:intergenic
CAATGTTACCTTCTCCACCT+AGG 0.589162 7.1:-4681701 None:intergenic
GGTTAGCGGTAGAGGATGAA+CGG 0.599940 7.1:+4683028 None:intergenic
TGTTTGATGATGATCAAGCA+AGG 0.620834 7.1:-4682741 MS.gene050444:CDS
GTTTGATGATGATCAAGCAA+GGG 0.625912 7.1:-4682740 MS.gene050444:CDS
CCTTACCTCATCTCTGACGG+AGG 0.627247 7.1:-4682919 MS.gene050444:CDS
TCATCTAGAGATACTGAGAC+CGG 0.630070 7.1:-4681857 MS.gene050444:CDS
ACACCTGATCCAATGGACTC+AGG 0.634250 7.1:+4681760 None:intergenic
GAATTGAATTGCTACCTAGG+TGG 0.663541 7.1:+4681687 None:intergenic
TGATCAAGCAAGGGAAACAA+CGG 0.689446 7.1:-4682731 MS.gene050444:CDS
GATCGACGTTTGAAACGGTG+AGG 0.719915 7.1:+4682962 None:intergenic
AGAGGATGAACGGATTACTG+TGG 0.730832 7.1:+4683038 None:intergenic
GGTGAGGTCGAATTTCGTGG+CGG 0.777998 7.1:+4682978 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTACTATTATTTATCTTTTA+TGG - chr7.1:4682199-4682218 MS.gene050444:intron 10.0%
!!! AATGTTTTTATAACCTATAT+TGG - chr7.1:4682480-4682499 MS.gene050444:intron 15.0%
!! AATAGTAAATGCAAAAAGTA+AGG + chr7.1:4682187-4682206 None:intergenic 20.0%
!! ATAGTAAATGCAAAAAGTAA+GGG + chr7.1:4682186-4682205 None:intergenic 20.0%
!! ATATTAGTTAACATCATGAA+AGG + chr7.1:4682345-4682364 None:intergenic 20.0%
!! TTGGATAAATAACTTATTTG+CGG - chr7.1:4682380-4682399 MS.gene050444:intron 20.0%
!!! TGATATTGTGAAATTGATTT+TGG + chr7.1:4682847-4682866 None:intergenic 20.0%
! AAATTCAAATTCAGTTTCGT+TGG + chr7.1:4681735-4681754 None:intergenic 25.0%
! TAGTAAATGCAAAAAGTAAG+GGG + chr7.1:4682185-4682204 None:intergenic 25.0%
! TGAAACCAAACATAAACTTA+GGG + chr7.1:4682602-4682621 None:intergenic 25.0%
! TGTTAACTAATATAGCAACT+AGG - chr7.1:4682352-4682371 MS.gene050444:intron 25.0%
! TTAGAATCAGTGTATGTTAT+TGG + chr7.1:4682903-4682922 None:intergenic 25.0%
!! ATGAATGTTAGTTGATGTTT+GGG - chr7.1:4682968-4682987 MS.gene050444:CDS 25.0%
!! CTTTTATGGTTGTTAATGAT+TGG - chr7.1:4682213-4682232 MS.gene050444:intron 25.0%
!! GAATTTCTTGAATTTTGCTT+TGG + chr7.1:4681813-4681832 None:intergenic 25.0%
!!! TTCCTTTTTAAGCTAGAAAT+TGG - chr7.1:4682717-4682736 MS.gene050444:intron 25.0%
AAGGTAACATTGAGAATATC+TGG + chr7.1:4683164-4683183 None:intergenic 30.0%
AGACCGGCAATTAAAAATTA+CGG - chr7.1:4683032-4683051 MS.gene050444:CDS 30.0%
CCTATATTGGAGAACTTATA+AGG - chr7.1:4682493-4682512 MS.gene050444:intron 30.0%
CCTTATAAGTTCTCCAATAT+AGG + chr7.1:4682496-4682515 None:intergenic 30.0%
GCTTAAAAAGGAATCAATTC+TGG + chr7.1:4682710-4682729 None:intergenic 30.0%
GTGAAACCAAACATAAACTT+AGG + chr7.1:4682603-4682622 None:intergenic 30.0%
TAAAAAGGAATCAATTCTGG+AGG + chr7.1:4682707-4682726 None:intergenic 30.0%
TCAACCACAACTATGAAAAT+GGG - chr7.1:4682053-4682072 MS.gene050444:intron 30.0%
! GATGAATGTTAGTTGATGTT+TGG - chr7.1:4682967-4682986 MS.gene050444:CDS 30.0%
! TTCGTTGGTATTGAACAAAT+TGG + chr7.1:4681720-4681739 None:intergenic 30.0%
! TTTGGTTAAAAGTGAGTTGA+AGG + chr7.1:4682829-4682848 None:intergenic 30.0%
!! CAAAAGTGATTTTAAAGGTG+TGG - chr7.1:4682635-4682654 MS.gene050444:intron 30.0%
!! CTCCAATTTCTAGCTTAAAA+AGG + chr7.1:4682722-4682741 None:intergenic 30.0%
!!! CACACCTTTAAAATCACTTT+TGG + chr7.1:4682637-4682656 None:intergenic 30.0%
!!! TGAGATTGTGTTGTTTTTGT+TGG + chr7.1:4681764-4681783 None:intergenic 30.0%
ATATAGCAACTAGGTCTGTT+TGG - chr7.1:4682361-4682380 MS.gene050444:intron 35.0%
CACTTGCACGATATCTTTAA+TGG + chr7.1:4682114-4682133 None:intergenic 35.0%
CGTGTTCTTAAGGAGAAATT+TGG - chr7.1:4682083-4682102 MS.gene050444:intron 35.0%
CTCAACCACAACTATGAAAA+TGG - chr7.1:4682052-4682071 MS.gene050444:intron 35.0%
GATGTTGTATCCGTTGAAAA+CGG - chr7.1:4681984-4682003 MS.gene050444:intron 35.0%
GTTGAAGGTAAACTGAATGA+TGG + chr7.1:4682814-4682833 None:intergenic 35.0%
! ATGTTTGGTTTCACTTCTAG+AGG - chr7.1:4682609-4682628 MS.gene050444:intron 35.0%
! GATTCCCATTTTCATAGTTG+TGG + chr7.1:4682060-4682079 None:intergenic 35.0%
! TGTTTGGTTTCACTTCTAGA+GGG - chr7.1:4682610-4682629 MS.gene050444:intron 35.0%
!! CAAGTTTTATCTGTTGAAGG+TGG - chr7.1:4683065-4683084 MS.gene050444:CDS 35.0%
!! CCTCCGTAATTTTTAATTGC+CGG + chr7.1:4683038-4683057 None:intergenic 35.0%
!! GTGCAAGTTTTATCTGTTGA+AGG - chr7.1:4683062-4683081 MS.gene050444:CDS 35.0%
!! GTTTGATGATGATCAAGCAA+GGG - chr7.1:4682133-4682152 MS.gene050444:intron 35.0%
!! TGTTTGATGATGATCAAGCA+AGG - chr7.1:4682132-4682151 MS.gene050444:intron 35.0%
AACGAGATCGACGTTTGAAA+CGG + chr7.1:4681919-4681938 None:intergenic 40.0%
AACTTAGGGCCAGTTTGAAT+TGG + chr7.1:4682588-4682607 None:intergenic 40.0%
ACTGGCCCTAAGTTTATGTT+TGG - chr7.1:4682594-4682613 MS.gene050444:intron 40.0%
CCGGCAATTAAAAATTACGG+AGG - chr7.1:4683035-4683054 MS.gene050444:CDS 40.0%
GACTGTGTTGTGGAATATGT+TGG - chr7.1:4683089-4683108 MS.gene050444:CDS 40.0%
GTCGTTTCTCTTAAGCTACA+AGG - chr7.1:4682008-4682027 MS.gene050444:intron 40.0%
TCAGATACGCCAATTCAAAC+TGG - chr7.1:4682576-4682595 MS.gene050444:intron 40.0%
TCATCTAGAGATACTGAGAC+CGG - chr7.1:4683016-4683035 MS.gene050444:CDS 40.0%
TGATCAAGCAAGGGAAACAA+CGG - chr7.1:4682142-4682161 MS.gene050444:intron 40.0%
TTCATAGTTGTGGTTGAGCT+AGG + chr7.1:4682050-4682069 None:intergenic 40.0%
! AGCTTTAACACCTGATCCAA+TGG + chr7.1:4683123-4683142 None:intergenic 40.0%
! GGGGCCAAAAGTGATTTTAA+AGG - chr7.1:4682630-4682649 MS.gene050444:intron 40.0%
! GTTAGTTGATGTTTGGGTGT+GGG - chr7.1:4682974-4682993 MS.gene050444:CDS 40.0%
! GTTTGGTTTCACTTCTAGAG+GGG - chr7.1:4682611-4682630 MS.gene050444:intron 40.0%
! TGTTAGTTGATGTTTGGGTG+TGG - chr7.1:4682973-4682992 MS.gene050444:CDS 40.0%
!!! TGTTTGGGTGTGGGTTTTTT+AGG - chr7.1:4682983-4683002 MS.gene050444:CDS 40.0%
AGGTGTTAAAGCTGCGATCA+AGG - chr7.1:4683130-4683149 MS.gene050444:CDS 45.0%
AGTATAATCCCGGAGAAGAC+TGG + chr7.1:4681875-4681894 None:intergenic 45.0%
GAGCTCATCAATTGGCGTTT+GGG + chr7.1:4682558-4682577 None:intergenic 45.0%
GCGTATCTGAGCTCATCAAT+TGG + chr7.1:4682566-4682585 None:intergenic 45.0%
GGGAATCGAACGTGTTCTTA+AGG - chr7.1:4682073-4682092 MS.gene050444:intron 45.0%
TAACCAGAACCAGTCTTCTC+CGG - chr7.1:4681863-4681882 MS.gene050444:CDS 45.0%
TATGTTGGACCTGAGTCCAT+TGG - chr7.1:4683104-4683123 MS.gene050444:CDS 45.0%
TGAGCTCATCAATTGGCGTT+TGG + chr7.1:4682559-4682578 None:intergenic 45.0%
!! AGAAACGACGCCGTTTTCAA+CGG + chr7.1:4681997-4682016 None:intergenic 45.0%
!! AGAAGACTGGTTCTGGTTAG+CGG + chr7.1:4681862-4681881 None:intergenic 45.0%
!! AGAGGATGAACGGATTACTG+TGG + chr7.1:4681838-4681857 None:intergenic 45.0%
!!! TTGGGTGTGGGTTTTTTAGG+CGG - chr7.1:4682986-4683005 MS.gene050444:CDS 45.0%
AACCAGAACCAGTCTTCTCC+GGG - chr7.1:4681864-4681883 MS.gene050444:CDS 50.0%
AACGGTGAGGTCGAATTTCG+TGG + chr7.1:4681901-4681920 None:intergenic 50.0%
AGCAAGGGAAACAACGGTTG+AGG - chr7.1:4682148-4682167 MS.gene050444:intron 50.0%
CTCCGTCAGAGATGAGGTAA+GGG + chr7.1:4681956-4681975 None:intergenic 50.0%
GGTTAGCGGTAGAGGATGAA+CGG + chr7.1:4681848-4681867 None:intergenic 50.0%
TGAAGGTGGTGACTGTGTTG+TGG - chr7.1:4683079-4683098 MS.gene050444:CDS 50.0%
! ACACCTGATCCAATGGACTC+AGG + chr7.1:4683116-4683135 None:intergenic 50.0%
! GATCGACGTTTGAAACGGTG+AGG + chr7.1:4681914-4681933 None:intergenic 50.0%
! TTCGTGGCGGAGTATAATCC+CGG + chr7.1:4681885-4681904 None:intergenic 50.0%
CCTCCGTCAGAGATGAGGTA+AGG + chr7.1:4681957-4681976 None:intergenic 55.0%
CCTTACCTCATCTCTGACGG+AGG - chr7.1:4681954-4681973 MS.gene050444:intron 55.0%
CGCCCTTACCTCATCTCTGA+CGG - chr7.1:4681951-4681970 MS.gene050444:intron 55.0%
CGTTTCCTCCGTCAGAGATG+AGG + chr7.1:4681962-4681981 None:intergenic 55.0%
GGACCTGAGTCCATTGGATC+AGG - chr7.1:4683110-4683129 MS.gene050444:CDS 55.0%
GGTGAGGTCGAATTTCGTGG+CGG + chr7.1:4681898-4681917 None:intergenic 55.0%
! ATCCCGGAGAAGACTGGTTC+TGG + chr7.1:4681869-4681888 None:intergenic 55.0%
!! CTGGTTCTGGTTAGCGGTAG+AGG + chr7.1:4681856-4681875 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 4681702 4683193 4681702 ID=MS.gene050444
chr7.1 mRNA 4681702 4683193 4681702 ID=MS.gene050444.t1;Parent=MS.gene050444
chr7.1 exon 4682726 4683193 4682726 ID=MS.gene050444.t1.exon1;Parent=MS.gene050444.t1
chr7.1 CDS 4682726 4683193 4682726 ID=cds.MS.gene050444.t1;Parent=MS.gene050444.t1
chr7.1 exon 4681702 4681890 4681702 ID=MS.gene050444.t1.exon2;Parent=MS.gene050444.t1
chr7.1 CDS 4681702 4681890 4681702 ID=cds.MS.gene050444.t1;Parent=MS.gene050444.t1
Gene Sequence

>MS.gene050444

ATGGCGACTCTAACTCCAATTTGTTCAATACCAACGAAACTGAATTTGAATTTGAGTATCCAACAAAAACAACACAATCTCAACTTCGCACTTTTCAATTTCAAAAATCCAAAGCAAAATTCAAGAAATTCAACCACAGTAATCCGTTCATCCTCTACCGCTAACCAGAACCAGTCTTCTCCGGGATTATACTCCGCCACGAAATTCGACCTCACCGTTTCAAACGTCGATCTCGTTCTCGAAGATGTTCGCCCTTACCTCATCTCTGACGGAGGAAACGTCGATGTTGTATCCGTTGAAAACGGCGTCGTTTCTCTTAAGCTACAAGGTGCATGCGAAAGTTGTCCTAGCTCAACCACAACTATGAAAATGGGAATCGAACGTGTTCTTAAGGAGAAATTTGGAGATTCCATTAAAGATATCGTGCAAGTGTTTGATGATGATCAAGCAAGGGAAACAACGGTTGAGGTCAGTGATTTTCCCCTTACTTTTTGCATTTACTATTATTTATCTTTTATGGTTGTTAATGATTGGATATTAATTTTAGTTAGTCTTATAGAAGTAGTTAGAAGTTAGATGTGATTAGTTGTTGTTAGTTAATTAGTTACATCACATATGAAGTGATCAATTTCAAAATCAACCTTTCATGATGTTAACTAATATAGCAACTAGGTCTGTTTGGATAAATAACTTATTTGCGGTTTATAGCACAATCACTTATAAGCTATTTTTGTAGCAAAAGATAAAATGAAGTTAAATTGTATTTGTATATGCTATAAATGTTTTTATAACCTATATTGGAGAACTTATAAGGTTAAGTTGTAAAAAGCTTATGAAAATTGTCGTAAGTTTTCCCAAACGCCAATTGATGAGCTCAGATACGCCAATTCAAACTGGCCCTAAGTTTATGTTTGGTTTCACTTCTAGAGGGGCCAAAAGTGATTTTAAAGGTGTGGAATTGATTTTGACATGTTTGATTACTCTCTACTATAATTGATTTTGCCTCCAGAATTGATTCCTTTTTAAGCTAGAAATTGGAGTTATAATTATAGAATTGATTTTAGCACTCAAATCTACTGTTCAACTCACTTTTACTTAAATGTAACAAACCATCATTCAGTTTACCTTCAACTCACTTTTAACCAAAATCAATTTCACAATATCAATTCATGCACAATCAATTTATGTCAATGCAAAACCAATAACATACACTGATTCTAATTAATATTCAATTTATCTAATGTGCATAGAAATGAAATGAAAATGATGAATGTTAGTTGATGTTTGGGTGTGGGTTTTTTAGGCGGTGAACAATCATCTAGAGATACTGAGACCGGCAATTAAAAATTACGGAGGTAGTGTGCAAGTTTTATCTGTTGAAGGTGGTGACTGTGTTGTGGAATATGTTGGACCTGAGTCCATTGGATCAGGTGTTAAAGCTGCGATCAAGGAGAAGTTTCCAGATATTCTCAATGTTACCTTCTCCACCTAG

Protein sequence

>MS.gene050444.t1

MATLTPICSIPTKLNLNLSIQQKQHNLNFALFNFKNPKQNSRNSTTVIRSSSTANQNQSSPGLYSATKFDLTVSNVDLVLEDVRPYLISDGGNVDVVSVENGVVSLKLQGACESCPSSTTTMKMGIERVLKEKFGDSIKDIVQVFDDDQARETTVEAVNNHLEILRPAIKNYGGSVQVLSVEGGDCVVEYVGPESIGSGVKAAIKEKFPDILNVTFST