AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene024056

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024056.t1 MTR_7g080390 99.231 130 1 0 1 130 1 130 4.37e-93 265
MS.gene024056.t1 MTR_7g080760 52.066 121 48 3 10 129 7 118 1.58e-35 119
MS.gene024056.t1 MTR_4g133928 51.948 77 37 0 54 130 47 123 3.38e-21 82.8
MS.gene024056.t1 MTR_0446s0010 58.929 56 23 0 54 109 47 102 4.84e-16 68.9
MS.gene024056.t1 MTR_8g099920 41.772 79 44 2 53 130 61 138 4.42e-11 57.0
MS.gene024056.t1 MTR_8g099920 41.772 79 44 2 53 130 59 136 4.58e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024056.t1 AT1G65290 72.180 133 27 3 1 130 1 126 6.42e-60 181
MS.gene024056.t1 AT2G44620 53.488 129 52 4 1 129 1 121 6.07e-36 120
MS.gene024056.t1 AT5G47630 37.097 124 71 3 10 130 8 127 1.35e-19 79.0
MS.gene024056.t1 AT5G47630 37.097 124 71 3 10 130 8 127 1.35e-19 79.0
MS.gene024056.t1 AT5G47630 37.097 124 71 3 10 130 8 127 1.35e-19 79.0

Find 36 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTAGAAGGATCAACTTTC+TGG 0.153197 7.1:-24041204 None:intergenic
ATCTTGTCTGCTTCATTATC+AGG 0.242778 7.1:-24042817 None:intergenic
TATCCAATCCAAGGTCATTC+TGG 0.280875 7.1:-24042738 None:intergenic
GAAGCGACGAAGGAAGAAAT+TGG 0.307444 7.1:-24041107 None:intergenic
CCAGAAAGTTGATCCTTCTA+AGG 0.310928 7.1:+24041204 MS.gene024056:CDS
TGACCTTGGATTGGATAGTT+TGG 0.330609 7.1:+24042744 MS.gene024056:CDS
ATGGCTCTTGAGGAAGAGTT+TGG 0.348440 7.1:+24042784 MS.gene024056:CDS
TCGCTTCAGCGAAGAGGTTA+GGG 0.350830 7.1:+24041123 MS.gene024056:CDS
GTCGCTTCAGCGAAGAGGTT+AGG 0.351899 7.1:+24041122 MS.gene024056:CDS
AAGAATGAATATACCTTAGA+AGG 0.357646 7.1:-24041217 None:intergenic
TGGCTCTTGAGGAAGAGTTT+GGG 0.415460 7.1:+24042785 MS.gene024056:CDS
ACAATGGCGGCGAGAAGAAC+CGG 0.444859 7.1:+24041007 None:intergenic
TTTCCAGAATGACCTTGGAT+TGG 0.459097 7.1:+24042735 MS.gene024056:CDS
CTTCATTGCATCTCATCCTC+AGG 0.467249 7.1:+24042864 MS.gene024056:CDS
GTAATTGATCAGAGGTAAAC+CGG 0.471092 7.1:-24041026 None:intergenic
GAAGAAGACGGAAAGGAGAT+TGG 0.486541 7.1:-24041084 None:intergenic
AAGCGACGAAGGAAGAAATT+GGG 0.487963 7.1:-24041106 None:intergenic
CCTTCGTCGCTTCAGCGAAG+AGG 0.501144 7.1:+24041117 MS.gene024056:CDS
GCTCATTTCCAGAATGACCT+TGG 0.503501 7.1:+24042730 MS.gene024056:CDS
TCATTCTGGAAATGAGCACT+TGG 0.522843 7.1:-24042724 None:intergenic
CCTCTTCGCTGAAGCGACGA+AGG 0.533871 7.1:-24041117 None:intergenic
CATTCTGGAAATGAGCACTT+GGG 0.569313 7.1:-24042723 None:intergenic
GATCAATTACTTGAGAGTGC+AGG 0.571679 7.1:+24041039 MS.gene024056:CDS
CTCATCCTCAGGCAAAGTAG+TGG 0.581931 7.1:+24042875 MS.gene024056:CDS
AAATTGGGAAGAAGACGGAA+AGG 0.582954 7.1:-24041091 None:intergenic
AAAGGAGATTGGTGGTTCAG+TGG 0.588384 7.1:-24041073 None:intergenic
GAAGACGGAAAGGAGATTGG+TGG 0.596794 7.1:-24041081 None:intergenic
AGAGATTGTGATGGCTCTTG+AGG 0.598690 7.1:+24042774 MS.gene024056:CDS
GGATGCTGTAGAGATTGTGA+TGG 0.619499 7.1:+24042765 MS.gene024056:CDS
GAATTCCACTACTTTGCCTG+AGG 0.625155 7.1:-24042880 None:intergenic
GGAAGAAATTGGGAAGAAGA+CGG 0.626548 7.1:-24041096 None:intergenic
CATCCAAACTATCCAATCCA+AGG 0.636485 7.1:-24042747 None:intergenic
TACGTTTCTCGACAAATCTG+AGG 0.640218 7.1:+24041147 MS.gene024056:CDS
ATTCTGGAAATGAGCACTTG+GGG 0.645151 7.1:-24042722 None:intergenic
ACTCTCAAGTAATTGATCAG+AGG 0.661217 7.1:-24041034 None:intergenic
CGCTTCAGCGAAGAGGTTAG+GGG 0.670708 7.1:+24041124 MS.gene024056:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAATAAATCAAGAAATAA+TGG - chr7.1:24041347-24041366 None:intergenic 15.0%
!!! AAAAGTTATTTCAGATAATT+AGG + chr7.1:24041380-24041399 MS.gene024056:intron 15.0%
!!! ATTGTTTTCATATAAGTTAT+AGG + chr7.1:24041482-24041501 MS.gene024056:intron 15.0%
!!! TAAACTAGATTATTTTCTTA+AGG - chr7.1:24041806-24041825 None:intergenic 15.0%
!!! TAAGAAAATAATCTAGTTTA+TGG + chr7.1:24041806-24041825 MS.gene024056:intron 15.0%
!!! TTCATTTTATCTTTAGTTAT+AGG - chr7.1:24041457-24041476 None:intergenic 15.0%
!!! TTGTTTTCATATAAGTTATA+GGG + chr7.1:24041483-24041502 MS.gene024056:intron 15.0%
!! AAAATGATATTTGAGAATTG+AGG - chr7.1:24042100-24042119 None:intergenic 20.0%
!! AAATGATATTTGAGAATTGA+GGG - chr7.1:24042099-24042118 None:intergenic 20.0%
!! AACTAAAACAATGTTACTAT+CGG - chr7.1:24042157-24042176 None:intergenic 20.0%
!! ATATAAACTTCAGACTAATT+GGG - chr7.1:24042506-24042525 None:intergenic 20.0%
!! ATATAATCCTTGTATTTGAT+TGG + chr7.1:24042017-24042036 MS.gene024056:intron 20.0%
!!! AGAAATAATGGAAAATAATC+CGG - chr7.1:24041335-24041354 None:intergenic 20.0%
!!! GCTATTTTTATAAGCTATAT+TGG + chr7.1:24041638-24041657 MS.gene024056:intron 20.0%
! AAACATTTCATAAGCTACTT+TGG + chr7.1:24041777-24041796 MS.gene024056:intron 25.0%
! AAAGTAGCTTATGAAATGTT+TGG - chr7.1:24041778-24041797 None:intergenic 25.0%
! AAGAAGTTAAAAACAGCTTA+TGG + chr7.1:24042451-24042470 MS.gene024056:intron 25.0%
! AAGAATGAATATACCTTAGA+AGG - chr7.1:24041220-24041239 None:intergenic 25.0%
! CAATAATTAGGAGATTGAAA+AGG - chr7.1:24041261-24041280 None:intergenic 25.0%
! CATATAAACTTCAGACTAAT+TGG - chr7.1:24042507-24042526 None:intergenic 25.0%
! CGATGAATGAAACAATAATT+AGG - chr7.1:24041273-24041292 None:intergenic 25.0%
! GGAATAAACATTTATGCTAT+TGG - chr7.1:24041436-24041455 None:intergenic 25.0%
! GTTAACATGATGTTATTGTT+AGG + chr7.1:24041292-24041311 MS.gene024056:intron 25.0%
! TACATACGCTACTTATATAA+AGG + chr7.1:24041579-24041598 MS.gene024056:intron 25.0%
! TCAGATAATTAGGTAATGTT+TGG + chr7.1:24041390-24041409 MS.gene024056:intron 25.0%
! TTAAAATAGTACACAATAGC+TGG - chr7.1:24042645-24042664 None:intergenic 25.0%
!! AAGTGAATACTTCATTTTAG+AGG + chr7.1:24042266-24042285 MS.gene024056:intron 25.0%
!! ATTTCTGTATTGCATTTTAG+TGG - chr7.1:24041993-24042012 None:intergenic 25.0%
!!! AACATTGTTTTAGTTACATG+AGG + chr7.1:24042162-24042181 MS.gene024056:intron 25.0%
!!! TACTTCATTTTAGAGGATTA+AGG + chr7.1:24042273-24042292 MS.gene024056:intron 25.0%
AAAGTGGGTAGCAATATTAA+AGG - chr7.1:24041928-24041947 None:intergenic 30.0%
AACACAACCAATCAAATACA+AGG - chr7.1:24042027-24042046 None:intergenic 30.0%
AATTGAGGGTAATTCTTACA+TGG - chr7.1:24042085-24042104 None:intergenic 30.0%
ACAAATAAACCAAACCAAAC+AGG + chr7.1:24042534-24042553 MS.gene024056:intron 30.0%
CAAATAAACCAAACCAAACA+GGG + chr7.1:24042535-24042554 MS.gene024056:intron 30.0%
CAATTCCTTTATGAAGCTAA+AGG + chr7.1:24041965-24041984 MS.gene024056:intron 30.0%
TTAGGTAATGTTTGGATCAA+CGG + chr7.1:24041398-24041417 MS.gene024056:intron 30.0%
! TTGTATTTGATTGGTTGTGT+TGG + chr7.1:24042026-24042045 MS.gene024056:intron 30.0%
ACTCTCAAGTAATTGATCAG+AGG - chr7.1:24041037-24041056 None:intergenic 35.0%
AGCTTATGAAATGTTTGGCT+TGG - chr7.1:24041773-24041792 None:intergenic 35.0%
ATAAAGGAATTGCTCATCGA+TGG - chr7.1:24041957-24041976 None:intergenic 35.0%
ATCTTGTCTGCTTCATTATC+AGG - chr7.1:24042820-24042839 None:intergenic 35.0%
GTAATTGATCAGAGGTAAAC+CGG - chr7.1:24041029-24041048 None:intergenic 35.0%
TAAGCATTCAGACATTGTTC+AGG - chr7.1:24041861-24041880 None:intergenic 35.0%
TATAAGTTATAGGGCGTGTT+TGG + chr7.1:24041492-24041511 MS.gene024056:intron 35.0%
TGGGTAGCAATATTAAAGGA+AGG - chr7.1:24041924-24041943 None:intergenic 35.0%
!! TAGAGGATTAAGGCTTTGTT+TGG + chr7.1:24042283-24042302 MS.gene024056:intron 35.0%
AAATTGGGAAGAAGACGGAA+AGG - chr7.1:24041094-24041113 None:intergenic 40.0%
AACTTCAGACTAATTGGGAG+AGG - chr7.1:24042501-24042520 None:intergenic 40.0%
AAGCGACGAAGGAAGAAATT+GGG - chr7.1:24041109-24041128 None:intergenic 40.0%
ACATTGTTCAGGAGAGCTTA+TGG - chr7.1:24041850-24041869 None:intergenic 40.0%
ACTTCTTTCCTAAGCTCTCT+AGG - chr7.1:24042438-24042457 None:intergenic 40.0%
AGCTTATGCTCTCGTTAACA+TGG + chr7.1:24042669-24042688 MS.gene024056:intron 40.0%
CACACACACTTCAAAGTGTA+AGG - chr7.1:24042593-24042612 None:intergenic 40.0%
CACTTAAGAGATCAAACCCT+CGG - chr7.1:24042251-24042270 None:intergenic 40.0%
CATCCAAACTATCCAATCCA+AGG - chr7.1:24042750-24042769 None:intergenic 40.0%
CCTTAGAAGGATCAACTTTC+TGG - chr7.1:24041207-24041226 None:intergenic 40.0%
CTAGTTTATGGACGTGTCAT+TGG + chr7.1:24041818-24041837 MS.gene024056:intron 40.0%
GATGAAATTATCACTGCCGA+GGG + chr7.1:24042232-24042251 MS.gene024056:intron 40.0%
GGAAGAAATTGGGAAGAAGA+CGG - chr7.1:24041099-24041118 None:intergenic 40.0%
GGTTTAGCTGTTAACTTTGC+CGG + chr7.1:24041313-24041332 MS.gene024056:intron 40.0%
GTTTACACTATAGCCCTGTT+TGG - chr7.1:24042551-24042570 None:intergenic 40.0%
TAAGCTATCCTAGAGAGCTT+AGG + chr7.1:24042427-24042446 MS.gene024056:intron 40.0%
TACGTTTCTCGACAAATCTG+AGG + chr7.1:24041147-24041166 MS.gene024056:CDS 40.0%
TATCCAATCCAAGGTCATTC+TGG - chr7.1:24042741-24042760 None:intergenic 40.0%
TGTGCTTCTTTCCATTTGTC+AGG + chr7.1:24042696-24042715 MS.gene024056:intron 40.0%
TTTCCAGAATGACCTTGGAT+TGG + chr7.1:24042735-24042754 MS.gene024056:CDS 40.0%
! ATTCTGGAAATGAGCACTTG+GGG - chr7.1:24042725-24042744 None:intergenic 40.0%
! CATTCTGGAAATGAGCACTT+GGG - chr7.1:24042726-24042745 None:intergenic 40.0%
! CCAGAAAGTTGATCCTTCTA+AGG + chr7.1:24041204-24041223 MS.gene024056:CDS 40.0%
! GATCAATTACTTGAGAGTGC+AGG + chr7.1:24041039-24041058 MS.gene024056:CDS 40.0%
! TCATTCTGGAAATGAGCACT+TGG - chr7.1:24042727-24042746 None:intergenic 40.0%
! TGACAAATGGAAAGAAGCAC+AGG - chr7.1:24042697-24042716 None:intergenic 40.0%
! TGACCTTGGATTGGATAGTT+TGG + chr7.1:24042744-24042763 MS.gene024056:CDS 40.0%
! TGGTGCCTTTAGCTTCATAA+AGG - chr7.1:24041973-24041992 None:intergenic 40.0%
!!! GAAGTGTGTGTGTGTCATTT+TGG + chr7.1:24042601-24042620 MS.gene024056:intron 40.0%
ACTTGGGGTAACCTGACAAA+TGG - chr7.1:24042710-24042729 None:intergenic 45.0%
AGAGATTGTGATGGCTCTTG+AGG + chr7.1:24042774-24042793 MS.gene024056:CDS 45.0%
AGTACACAATAGCTGGCAGA+GGG - chr7.1:24042638-24042657 None:intergenic 45.0%
ATGGCTCTTGAGGAAGAGTT+TGG + chr7.1:24042784-24042803 MS.gene024056:CDS 45.0%
CACTATAGCCCTGTTTGGTT+TGG - chr7.1:24042546-24042565 None:intergenic 45.0%
CATCGATGGCATCGTAAAGT+GGG - chr7.1:24041943-24041962 None:intergenic 45.0%
CGATGAAATTATCACTGCCG+AGG + chr7.1:24042231-24042250 MS.gene024056:intron 45.0%
CTTCATTGCATCTCATCCTC+AGG + chr7.1:24042864-24042883 MS.gene024056:CDS 45.0%
GAAGAAGACGGAAAGGAGAT+TGG - chr7.1:24041087-24041106 None:intergenic 45.0%
GAAGCGACGAAGGAAGAAAT+TGG - chr7.1:24041110-24041129 None:intergenic 45.0%
GCTCATTTCCAGAATGACCT+TGG + chr7.1:24042730-24042749 MS.gene024056:CDS 45.0%
GGATGCTGTAGAGATTGTGA+TGG + chr7.1:24042765-24042784 MS.gene024056:CDS 45.0%
TAGTACACAATAGCTGGCAG+AGG - chr7.1:24042639-24042658 None:intergenic 45.0%
TCATCGATGGCATCGTAAAG+TGG - chr7.1:24041944-24041963 None:intergenic 45.0%
TGGCTCTTGAGGAAGAGTTT+GGG + chr7.1:24042785-24042804 MS.gene024056:CDS 45.0%
! AAAGGAGATTGGTGGTTCAG+TGG - chr7.1:24041076-24041095 None:intergenic 45.0%
!!! GTGTGTGTGTGTCATTTTGG+AGG + chr7.1:24042604-24042623 MS.gene024056:intron 45.0%
GAAGACGGAAAGGAGATTGG+TGG - chr7.1:24041084-24041103 None:intergenic 50.0%
TCGCTTCAGCGAAGAGGTTA+GGG + chr7.1:24041123-24041142 MS.gene024056:CDS 50.0%
CGCTTCAGCGAAGAGGTTAG+GGG + chr7.1:24041124-24041143 MS.gene024056:CDS 55.0%
GTCGCTTCAGCGAAGAGGTT+AGG + chr7.1:24041122-24041141 MS.gene024056:CDS 55.0%
CCTCTTCGCTGAAGCGACGA+AGG - chr7.1:24041120-24041139 None:intergenic 60.0%
CCTTCGTCGCTTCAGCGAAG+AGG + chr7.1:24041117-24041136 MS.gene024056:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 24041010 24042894 24041010 ID=MS.gene024056
chr7.1 mRNA 24041010 24042894 24041010 ID=MS.gene024056.t1;Parent=MS.gene024056
chr7.1 exon 24041010 24041225 24041010 ID=MS.gene024056.t1.exon1;Parent=MS.gene024056.t1
chr7.1 CDS 24041010 24041225 24041010 ID=cds.MS.gene024056.t1;Parent=MS.gene024056.t1
chr7.1 exon 24042718 24042894 24042718 ID=MS.gene024056.t1.exon2;Parent=MS.gene024056.t1
chr7.1 CDS 24042718 24042894 24042718 ID=cds.MS.gene024056.t1;Parent=MS.gene024056.t1
Gene Sequence

>MS.gene024056

ATGGCGGCGAGAAGAACCGGTTTACCTCTGATCAATTACTTGAGAGTGCAGGTTGATTCTCGTCCACTGAACCACCAATCTCCTTTCCGTCTTCTTCCCAATTTCTTCCTTCGTCGCTTCAGCGAAGAGGTTAGGGGTACGTTTCTCGACAAATCTGAGGTCACAGATCGCGTCGTTTCTTGCGTCAAAAACTTCCAGAAAGTTGATCCTTCTAAGGTATATTCATTCTTCTATTATTATCATTCGTTCCTTTTCAATCTCCTAATTATTGTTTCATTCATCGTTAACATGATGTTATTGTTAGGTTTAGCTGTTAACTTTGCCGGATTATTTTCCATTATTTCTTGATTTATTTTCACTTATTTTTCAAAAAAGTTATTTCAGATAATTAGGTAATGTTTGGATCAACGGATTAATTAAGCACCAATAGCATAAATGTTTATTCCTATAACTAAAGATAAAATGAATTTACATTGTTTTCATATAAGTTATAGGGCGTGTTTGGATAAACAGCTTATTTGCAGCATATAGCATAGCATGATAAGTGCATAATTGCATATGTATAAGCTTACATACGCTACTTATATAAAGGTTAAATAAATTTAAATAATTTTTGTATATGCTATAAGCTATTTTTATAAGCTATATTGGTGAAATTTTGAAAATAAGCTGAAAAAAGCTTATGAAAATTGTCTTAAGCTGTTTTCATAAGTTCTCTCGAGTCTCACAAAACTTATGTCAGTATATAAGCTCAAATAAGCCAAGCCAAACATTTCATAAGCTACTTTGGTGACCTTAAGAAAATAATCTAGTTTATGGACGTGTCATTGGTTGTTTCCATAAGCTCTCCTGAACAATGTCTGAATGCTTACGCGAGTAGATGAGCTCAAATAAATCAAACAGATTCATGACCTTCCTTTAATATTGCTACCCACTTTACGATGCCATCGATGAGCAATTCCTTTATGAAGCTAAAGGCACCACTAAAATGCAATACAGAAATATATATATAATCCTTGTATTTGATTGGTTGTGTTGGTAGATTTTTTCTAAAGTTCTGTAGATATTGCATCCATGTAAGAATTACCCTCAATTCTCAAATATCATTTTTAAGCTACACTTGTTTGTAGACATCATATAGCAACCGATAGTAACATTGTTTTAGTTACATGAGGTGCATTCTATGCTAGAATCTTTCATCAAAATAAACATTACTGTTTGCGATGAAATTATCACTGCCGAGGGTTTGATCTCTTAAGTGAATACTTCATTTTAGAGGATTAAGGCTTTGTTTGGATAAATTTGCTGCTTAATTAATTGATTATCATATAAGTGCTTAAGTATAAGCAATTTCTATCACATGAGATGAAATAAAGATGAAATAAAGTTGAACTGTTTTCAAACAAGATATTCGCTGTAAGCTATCCTAGAGAGCTTAGGAAAGAAGTTAAAAACAGCTTATGGACACGTCGTAAGCTGTTTAAATAACCTCTCCCAATTAGTCTGAAGTTTATATGCTAGTATACAAATAAACCAAACCAAACAGGGCTATAGTGTAAACTTGCACAACTGTTAAATAACCTTACACTTTGAAGTGTGTGTGTGTCATTTTGGAGGATTCAAATCCCTCTGCCAGCTATTGTGTACTATTTTAATTTTAGCTTATGCTCTCGTTAACATGGAGCCTGTGCTTCTTTCCATTTGTCAGGTTACCCCAAGTGCTCATTTCCAGAATGACCTTGGATTGGATAGTTTGGATGCTGTAGAGATTGTGATGGCTCTTGAGGAAGAGTTTGGGTTTGAGATTCCTGATAATGAAGCAGACAAGATCAACTCTGTTAATCTTGCAATTGACTTCATTGCATCTCATCCTCAGGCAAAGTAG
Protein sequence

>MS.gene024056.t1

MAARRTGLPLINYLRVQVDSRPLNHQSPFRLLPNFFLRRFSEEVRGTFLDKSEVTDRVVSCVKNFQKVDPSKVTPSAHFQNDLGLDSLDAVEIVMALEEEFGFEIPDNEADKINSVNLAIDFIASHPQAK