AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280008597.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008597.01.T01 MTR_2g045280 95.833 192 5 1 5 196 12 200 5.92e-133 371
MsG0280008597.01.T01 MTR_4g124190 86.413 184 25 0 13 196 3 186 6.32e-119 335
MsG0280008597.01.T01 MTR_1g081550 76.730 159 37 0 38 196 11 169 2.24e-88 257
MsG0280008597.01.T01 MTR_1g081420 62.179 156 52 3 38 192 12 161 2.67e-63 196
MsG0280008597.01.T01 MTR_1g081450 51.295 193 53 3 37 194 29 215 9.85e-60 186
MsG0280008597.01.T01 MTR_3g005755 47.561 164 50 3 30 193 69 196 3.90e-36 128
MsG0280008597.01.T01 MTR_1g081440 66.129 62 15 1 38 99 18 73 4.96e-22 85.9
MsG0280008597.01.T01 MTR_4g012000 42.000 100 57 1 41 140 855 953 2.56e-16 77.0
MsG0280008597.01.T01 MTR_4g012000 42.000 100 57 1 41 140 855 953 2.66e-16 77.0
MsG0280008597.01.T01 MTR_4g012000 42.000 100 57 1 41 140 1048 1146 3.80e-16 76.3
MsG0280008597.01.T01 MTR_4g012000 42.000 100 57 1 41 140 1048 1146 3.87e-16 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008597.01.T01 AT5G28050 82.222 180 32 0 17 196 111 290 5.87e-111 319
MsG0280008597.01.T01 AT5G28050 82.222 180 32 0 17 196 6 185 6.27e-111 315
MsG0280008597.01.T01 AT5G28050 81.667 180 33 0 17 196 25 204 1.78e-110 314
MsG0280008597.01.T01 AT3G05300 66.087 115 36 1 81 195 1 112 6.51e-50 157
MsG0280008597.01.T01 AT1G68720 43.000 100 56 1 41 140 1110 1208 1.33e-18 83.6

Find 43 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATGTAGAGGTTGGTTTA+TGG 0.196375 2:+34605681 MsG0280008597.01.T01:intron
TTCGCATTCTACACCTTTAT+AGG 0.197891 2:-34605068 None:intergenic
AAACACTTCTTCAGCAATTA+TGG 0.210407 2:-34605823 None:intergenic
ATTATTTAAACTGATTATTA+TGG 0.233838 2:+34604445 MsG0280008597.01.T01:exon
TTGTTTGTGGAGGATCAAAA+TGG 0.374746 2:+34605977 MsG0280008597.01.T01:three_prime_UTR
TATTGTGTTATTAGCTATCA+AGG 0.396477 2:+34605006 MsG0280008597.01.T01:intron
GCTGAGGCAGCAATTGCAAT+TGG 0.405341 2:+34605711 MsG0280008597.01.T01:CDS
TATCCACCTTTCACGTGTTA+AGG 0.408310 2:+34605389 MsG0280008597.01.T01:CDS
TGCGAAGATGGAGGTCCATT+TGG 0.413628 2:+34605085 MsG0280008597.01.T01:CDS
AATATTTGAATCATAGAAGT+TGG 0.414352 2:+34606095 MsG0280008597.01.T01:three_prime_UTR
GCAGTTGAAGAAGCCTATAA+AGG 0.442236 2:+34605055 MsG0280008597.01.T01:CDS
GTTGTCACAACATGGTTCTA+AGG 0.442612 2:+34605143 MsG0280008597.01.T01:CDS
GCTGATGCATTACGAGGAAC+TGG 0.446579 2:+34605750 MsG0280008597.01.T01:CDS
GAACCATGCCCAATGTGCTT+TGG 0.452969 2:+34605363 MsG0280008597.01.T01:CDS
GGATAGCACCAAAGCACATT+GGG 0.453339 2:-34605371 None:intergenic
AGAGTTAATCACAATGACTT+AGG 0.491851 2:-34605894 None:intergenic
TTATAATGTAGTACTATGTA+TGG 0.494852 2:+34604293 None:intergenic
ATATTTGAATCATAGAAGTT+GGG 0.495533 2:+34606096 MsG0280008597.01.T01:three_prime_UTR
AACTCTTATTGATATAGAAA+AGG 0.500839 2:-34606119 None:intergenic
AAAACTATAACAGCACCAAA+TGG 0.503753 2:-34605100 None:intergenic
GTGACTTCAGCATGAGCAGA+AGG 0.538349 2:-34605175 None:intergenic
AAAGGTGTAGAATGCGAAGA+TGG 0.542521 2:+34605073 MsG0280008597.01.T01:CDS
TCTCATAGAAGTATTGTTTG+TGG 0.550760 2:+34605964 MsG0280008597.01.T01:three_prime_UTR
TTGGAGATTAAAAGAGCTGA+TGG 0.558816 2:+34605792 MsG0280008597.01.T01:CDS
CCAGTGGTGCAAAACAAGGA+TGG 0.571547 2:+34604506 MsG0280008597.01.T01:CDS
TATTAGAAATATACAATACA+AGG 0.575825 2:-34606043 None:intergenic
TGGATAGCACCAAAGCACAT+TGG 0.576743 2:-34605372 None:intergenic
TCTTCCAGTGGTGCAAAACA+AGG 0.581267 2:+34604502 MsG0280008597.01.T01:CDS
CAGAAACAATACCTTGCTTG+TGG 0.592546 2:-34604559 None:intergenic
TATTGCTAGTTGTCACAACA+TGG 0.593501 2:+34605135 MsG0280008597.01.T01:CDS
TACTTCTATGAGACACATGA+TGG 0.594487 2:-34605954 None:intergenic
CATAGAAGTATTGTTTGTGG+AGG 0.597271 2:+34605967 MsG0280008597.01.T01:three_prime_UTR
GCACCAAAGCACATTGGGCA+TGG 0.599892 2:-34605366 None:intergenic
CAACCTTAACACGTGAAAGG+TGG 0.611123 2:-34605392 None:intergenic
TTACAACCTTAACACGTGAA+AGG 0.623769 2:-34605395 None:intergenic
GTTCAATAGCTGTGTACCGA+CGG 0.626178 2:+34604315 MsG0280008597.01.T01:five_prime_UTR
TTTATAGCTGATGCATTACG+AGG 0.630911 2:+34605744 MsG0280008597.01.T01:CDS
AGAAGTGTTTGAGAAAACAA+AGG 0.641403 2:+34605836 MsG0280008597.01.T01:CDS
TAAAAGAGCTGATGGCAATG+AGG 0.644473 2:+34605800 MsG0280008597.01.T01:CDS
TGACTTCAGCATGAGCAGAA+GGG 0.653823 2:-34605174 None:intergenic
GGTGTAGAATGCGAAGATGG+AGG 0.660099 2:+34605076 MsG0280008597.01.T01:CDS
GGTTTATGGAGCAAAAGCTG+AGG 0.686000 2:+34605695 MsG0280008597.01.T01:CDS
TGAAGTCACAGCAATAAGAG+AGG 0.692221 2:+34605189 MsG0280008597.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTTAAACTGATTATTA+TGG + Chr2:34604445-34604464 MsG0280008597.01.T01:exon 10.0%
!!! GTTTTTTTTTTTTTTTTTGT+TGG - Chr2:34604835-34604854 None:intergenic 10.0%
!!! TTATACTTATTTGTTAATTT+TGG - Chr2:34604698-34604717 None:intergenic 10.0%
!! AACTAATGCAAAAAAAATTA+AGG - Chr2:34605249-34605268 None:intergenic 15.0%
!! TATTAGAAATATACAATACA+AGG - Chr2:34606046-34606065 None:intergenic 15.0%
!!! ATTTCTTTTTAACATACTTT+TGG + Chr2:34605629-34605648 MsG0280008597.01.T01:intron 15.0%
!!! TAATAGCATGTTAATTTTTA+AGG + Chr2:34606061-34606080 MsG0280008597.01.T01:three_prime_UTR 15.0%
!!! TAGTATTATTTTTTATGTAG+AGG + Chr2:34605670-34605689 MsG0280008597.01.T01:intron 15.0%
!! AAAAAGGAAAATAAATGCAA+AGG - Chr2:34605431-34605450 None:intergenic 20.0%
!! AAAATAAATGCAAAGGAATT+AGG - Chr2:34605424-34605443 None:intergenic 20.0%
!! AACTCTTATTGATATAGAAA+AGG - Chr2:34606122-34606141 None:intergenic 20.0%
!! AATATTTGAATCATAGAAGT+TGG + Chr2:34606095-34606114 MsG0280008597.01.T01:three_prime_UTR 20.0%
!! ATATTTGAATCATAGAAGTT+GGG + Chr2:34606096-34606115 MsG0280008597.01.T01:three_prime_UTR 20.0%
!!! ATTATTTTTTATGTAGAGGT+TGG + Chr2:34605674-34605693 MsG0280008597.01.T01:intron 20.0%
!!! CTGCTTTTCTTAAAAATTTA+TGG - Chr2:34605039-34605058 None:intergenic 20.0%
!!! GCTACAACAATAATAAATTT+TGG - Chr2:34604927-34604946 None:intergenic 20.0%
!!! TTGAAATGATATTTTCATCT+GGG + Chr2:34604970-34604989 MsG0280008597.01.T01:intron 20.0%
!!! TTTTCTATATCAATAAGAGT+TGG + Chr2:34606121-34606140 MsG0280008597.01.T01:three_prime_UTR 20.0%
! AATGAAAGAAAGAGTGAAAT+TGG - Chr2:34604605-34604624 None:intergenic 25.0%
! CTTTCATTATCACATTATGA+AGG + Chr2:34604617-34604636 MsG0280008597.01.T01:intron 25.0%
! TTTGTATGTGTGAGTTATTA+TGG - Chr2:34605473-34605492 None:intergenic 25.0%
!! CTTGAAATGATATTTTCATC+TGG + Chr2:34604969-34604988 MsG0280008597.01.T01:intron 25.0%
!! TATTGTGTTATTAGCTATCA+AGG + Chr2:34605006-34605025 MsG0280008597.01.T01:intron 25.0%
!! TTTAGAGTTCAACAAAATCA+CGG - Chr2:34604782-34604801 None:intergenic 25.0%
!!! ATTTTATCAGAAAGCACAAT+TGG + Chr2:34605773-34605792 MsG0280008597.01.T01:CDS 25.0%
!!! TAGCATGTTAATTTTTAAGG+AGG + Chr2:34606064-34606083 MsG0280008597.01.T01:three_prime_UTR 25.0%
!!! TTTTATTTTTGATCTTCCAG+TGG + Chr2:34604490-34604509 MsG0280008597.01.T01:CDS 25.0%
AAAACTATAACAGCACCAAA+TGG - Chr2:34605103-34605122 None:intergenic 30.0%
AAACACTTCTTCAGCAATTA+TGG - Chr2:34605826-34605845 None:intergenic 30.0%
ACATTATGAAGGCTTGAAAA+CGG + Chr2:34604628-34604647 MsG0280008597.01.T01:intron 30.0%
AGAGTTAATCACAATGACTT+AGG - Chr2:34605897-34605916 None:intergenic 30.0%
GGTCGTTCGATTAAATTAAT+CGG - Chr2:34604906-34604925 None:intergenic 30.0%
!! AGAAGTGTTTGAGAAAACAA+AGG + Chr2:34605836-34605855 MsG0280008597.01.T01:CDS 30.0%
!! TCTCATAGAAGTATTGTTTG+TGG + Chr2:34605964-34605983 MsG0280008597.01.T01:three_prime_UTR 30.0%
!! TTTATGTAGAGGTTGGTTTA+TGG + Chr2:34605681-34605700 MsG0280008597.01.T01:intron 30.0%
!!! CACAATGCTATCATTTTTTC+AGG + Chr2:34605284-34605303 MsG0280008597.01.T01:intron 30.0%
!!! GAACATATTTTTTACACCGT+CGG - Chr2:34604334-34604353 None:intergenic 30.0%
ACACATACAAAGTGAGATGT+CGG + Chr2:34605482-34605501 MsG0280008597.01.T01:intron 35.0%
CGCATATACATGTAGACATT+AGG + Chr2:34604946-34604965 MsG0280008597.01.T01:intron 35.0%
TACTTCTATGAGACACATGA+TGG - Chr2:34605957-34605976 None:intergenic 35.0%
TATAGTGCATGTTTCGATTG+AGG + Chr2:34604732-34604751 MsG0280008597.01.T01:intron 35.0%
TATTGCTAGTTGTCACAACA+TGG + Chr2:34605135-34605154 MsG0280008597.01.T01:CDS 35.0%
TCAATCGAAACATGCACTAT+AGG - Chr2:34604733-34604752 None:intergenic 35.0%
TCGTAGCTCAACTAGTAAAA+AGG - Chr2:34605547-34605566 None:intergenic 35.0%
TGACCTCAAATTAACAGTTG+AGG - Chr2:34604868-34604887 None:intergenic 35.0%
TTACAACCTTAACACGTGAA+AGG - Chr2:34605398-34605417 None:intergenic 35.0%
TTCGCATTCTACACCTTTAT+AGG - Chr2:34605071-34605090 None:intergenic 35.0%
TTGGAGATTAAAAGAGCTGA+TGG + Chr2:34605792-34605811 MsG0280008597.01.T01:CDS 35.0%
TTGTTTGTGGAGGATCAAAA+TGG + Chr2:34605977-34605996 MsG0280008597.01.T01:three_prime_UTR 35.0%
TTTATAGCTGATGCATTACG+AGG + Chr2:34605744-34605763 MsG0280008597.01.T01:CDS 35.0%
! TTATGGCTTTGCCATTTCAT+CGG - Chr2:34605456-34605475 None:intergenic 35.0%
!! CATAGAAGTATTGTTTGTGG+AGG + Chr2:34605967-34605986 MsG0280008597.01.T01:three_prime_UTR 35.0%
!!! TTCCTTTTTTCCCGATGAAA+TGG + Chr2:34605442-34605461 MsG0280008597.01.T01:intron 35.0%
ACATACAAAGTGAGATGTCG+GGG + Chr2:34605484-34605503 MsG0280008597.01.T01:intron 40.0%
ACTAGTTGAGCTACGACTTA+TGG + Chr2:34605551-34605570 MsG0280008597.01.T01:intron 40.0%
CACATACAAAGTGAGATGTC+GGG + Chr2:34605483-34605502 MsG0280008597.01.T01:intron 40.0%
CAGAAACAATACCTTGCTTG+TGG - Chr2:34604562-34604581 None:intergenic 40.0%
CTAGTTGAGCTACGACTTAT+GGG + Chr2:34605552-34605571 MsG0280008597.01.T01:intron 40.0%
GCAGTTGAAGAAGCCTATAA+AGG + Chr2:34605055-34605074 MsG0280008597.01.T01:CDS 40.0%
GGCTTGAAAACGGTACTTTA+AGG + Chr2:34604638-34604657 MsG0280008597.01.T01:intron 40.0%
TAAAAGAGCTGATGGCAATG+AGG + Chr2:34605800-34605819 MsG0280008597.01.T01:CDS 40.0%
TATCCACCTTTCACGTGTTA+AGG + Chr2:34605389-34605408 MsG0280008597.01.T01:CDS 40.0%
TGAAGTCACAGCAATAAGAG+AGG + Chr2:34605189-34605208 MsG0280008597.01.T01:CDS 40.0%
TGTTAAGTCAACGTCATGAC+CGG - Chr2:34605517-34605536 None:intergenic 40.0%
! AAAGGTGTAGAATGCGAAGA+TGG + Chr2:34605073-34605092 MsG0280008597.01.T01:CDS 40.0%
! CGACCTCAACTGTTAATTTG+AGG + Chr2:34604862-34604881 MsG0280008597.01.T01:intron 40.0%
! GTTGTCACAACATGGTTCTA+AGG + Chr2:34605143-34605162 MsG0280008597.01.T01:CDS 40.0%
! TATGGCTTTGCCATTTCATC+GGG - Chr2:34605455-34605474 None:intergenic 40.0%
! TGCCATTTCATCGGGAAAAA+AGG - Chr2:34605447-34605466 None:intergenic 40.0%
CAACCTTAACACGTGAAAGG+TGG - Chr2:34605395-34605414 None:intergenic 45.0%
GGATAGCACCAAAGCACATT+GGG - Chr2:34605374-34605393 None:intergenic 45.0%
GGTTTATGGAGCAAAAGCTG+AGG + Chr2:34605695-34605714 MsG0280008597.01.T01:CDS 45.0%
GTGAGTTTCGCGGGATATAT+TGG + Chr2:34604754-34604773 MsG0280008597.01.T01:intron 45.0%
GTTAAGTCAACGTCATGACC+GGG - Chr2:34605516-34605535 None:intergenic 45.0%
GTTCAATAGCTGTGTACCGA+CGG + Chr2:34604315-34604334 MsG0280008597.01.T01:five_prime_UTR 45.0%
TCTTCCAGTGGTGCAAAACA+AGG + Chr2:34604502-34604521 MsG0280008597.01.T01:CDS 45.0%
TGACTTCAGCATGAGCAGAA+GGG - Chr2:34605177-34605196 None:intergenic 45.0%
TGGATAGCACCAAAGCACAT+TGG - Chr2:34605375-34605394 None:intergenic 45.0%
TTAAGTCAACGTCATGACCG+GGG - Chr2:34605515-34605534 None:intergenic 45.0%
TTCGATTGAGGTGAGTTTCG+CGG + Chr2:34604744-34604763 MsG0280008597.01.T01:intron 45.0%
!!! TTATTTTTGTTATTTTTATT+TGG + Chr2:34605582-34605601 MsG0280008597.01.T01:intron 5.0%
CCAGTGGTGCAAAACAAGGA+TGG + Chr2:34604506-34604525 MsG0280008597.01.T01:CDS 50.0%
GAACCATGCCCAATGTGCTT+TGG + Chr2:34605363-34605382 MsG0280008597.01.T01:CDS 50.0%
GCTGAGGCAGCAATTGCAAT+TGG + Chr2:34605711-34605730 MsG0280008597.01.T01:CDS 50.0%
GCTGATGCATTACGAGGAAC+TGG + Chr2:34605750-34605769 MsG0280008597.01.T01:CDS 50.0%
GGTGTAGAATGCGAAGATGG+AGG + Chr2:34605076-34605095 MsG0280008597.01.T01:CDS 50.0%
GTGACTTCAGCATGAGCAGA+AGG - Chr2:34605178-34605197 None:intergenic 50.0%
TCGATTGAGGTGAGTTTCGC+GGG + Chr2:34604745-34604764 MsG0280008597.01.T01:intron 50.0%
TGCGAAGATGGAGGTCCATT+TGG + Chr2:34605085-34605104 MsG0280008597.01.T01:CDS 50.0%
!! ACGGTACTTTAAGGTCGTCG+AGG + Chr2:34604647-34604666 MsG0280008597.01.T01:intron 50.0%
!! GCAGTAGCTTCTGCTTTTGC+TGG + Chr2:34604536-34604555 MsG0280008597.01.T01:CDS 50.0%
!! TACTTTAAGGTCGTCGAGGC+TGG + Chr2:34604651-34604670 MsG0280008597.01.T01:intron 50.0%
!!! CCATCCTTGTTTTGCACCAC+TGG - Chr2:34604509-34604528 None:intergenic 50.0%
GCACCAAAGCACATTGGGCA+TGG - Chr2:34605369-34605388 None:intergenic 55.0%
! GCTTTTGCTGGCCACAAGCA+AGG + Chr2:34604548-34604567 MsG0280008597.01.T01:CDS 55.0%
GAGATGTCGGGGTTCGACCC+CGG + Chr2:34605495-34605514 MsG0280008597.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr2 gene 34604308 34606153 34604308 ID=MsG0280008597.01;Name=MsG0280008597.01
Chr2 mRNA 34604308 34606153 34604308 ID=MsG0280008597.01.T01;Parent=MsG0280008597.01;Name=MsG0280008597.01.T01;_AED=0.25;_eAED=0.25;_QI=156|1|1|1|1|1|4|275|196
Chr2 exon 34604308 34604569 34604308 ID=MsG0280008597.01.T01:exon:15232;Parent=MsG0280008597.01.T01
Chr2 exon 34605020 34605210 34605020 ID=MsG0280008597.01.T01:exon:15233;Parent=MsG0280008597.01.T01
Chr2 exon 34605306 34605410 34605306 ID=MsG0280008597.01.T01:exon:15234;Parent=MsG0280008597.01.T01
Chr2 exon 34605690 34606153 34605690 ID=MsG0280008597.01.T01:exon:15235;Parent=MsG0280008597.01.T01
Chr2 five_prime_UTR 34604308 34604463 34604308 ID=MsG0280008597.01.T01:five_prime_utr;Parent=MsG0280008597.01.T01
Chr2 CDS 34604464 34604569 34604464 ID=MsG0280008597.01.T01:cds;Parent=MsG0280008597.01.T01
Chr2 CDS 34605020 34605210 34605020 ID=MsG0280008597.01.T01:cds;Parent=MsG0280008597.01.T01
Chr2 CDS 34605306 34605410 34605306 ID=MsG0280008597.01.T01:cds;Parent=MsG0280008597.01.T01
Chr2 CDS 34605690 34605878 34605690 ID=MsG0280008597.01.T01:cds;Parent=MsG0280008597.01.T01
Chr2 three_prime_UTR 34605879 34606153 34605879 ID=MsG0280008597.01.T01:three_prime_utr;Parent=MsG0280008597.01.T01
Gene Sequence

>MsG0280008597.01.T01

ATGGCATTATTTATGATTTATTTTTATTTTATTTTTGATCTTCCAGTGGTGCAAAACAAGGATGGAACTGTTGCAGTAGCTTCTGCTTTTGCTGGCCACAAGCAAGCTATCAAGGATAGAGACCATAAATTTTTAAGAAAAGCAGTTGAAGAAGCCTATAAAGGTGTAGAATGCGAAGATGGAGGTCCATTTGGTGCTGTTATAGTTTTGAATGATGAAGTTATTGCTAGTTGTCACAACATGGTTCTAAGGAACACTGACCCTTCTGCTCATGCTGAAGTCACAGCAATAAGAGAGGCTTGTAAAAAGCTGAAGCAGATAGAACTTTCTGAATGTGAAATATATGCTTCTTGTGAACCATGCCCAATGTGCTTTGGTGCTATCCACCTTTCACGTGTTAAGAGGTTGGTTTATGGAGCAAAAGCTGAGGCAGCAATTGCAATTGGTTTTGATGATTTTATAGCTGATGCATTACGAGGAACTGGATTTTATCAGAAAGCACAATTGGAGATTAAAAGAGCTGATGGCAATGAGGCCATAATTGCTGAAGAAGTGTTTGAGAAAACAAAGGAAAAATTTCGAATGTATTAA
Protein sequence

>MsG0280008597.01.T01

MALFMIYFYFIFDLPVVQNKDGTVAVASAFAGHKQAIKDRDHKFLRKAVEEAYKGVECEDGGPFGAVIVLNDEVIASCHNMVLRNTDPSAHAEVTAIREACKKLKQIELSECEIYASCEPCPMCFGAIHLSRVKRLVYGAKAEAAIAIGFDDFIADALRGTGFYQKAQLEIKRADGNEAIIAEEVFEKTKEKFRMY*