AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280008593.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008593.01.T01 MTR_2g045020 77.540 187 29 2 48 234 1 174 7.74e-94 273
MsG0280008593.01.T01 MTR_3g437790 63.855 166 54 5 73 235 12 174 3.23e-59 185
MsG0280008593.01.T01 MTR_8g022970 50.867 173 78 5 67 235 8 177 3.04e-45 149
MsG0280008593.01.T01 MTR_3g109930 50.000 158 74 4 79 235 7 160 6.42e-41 138
MsG0280008593.01.T01 MTR_2g105290 36.196 163 90 7 74 228 5 161 1.15e-16 75.5
MsG0280008593.01.T01 MTR_7g028448 33.088 136 77 3 94 228 31 153 1.26e-16 75.1
MsG0280008593.01.T01 MTR_4g036915 33.088 136 77 3 94 228 31 153 1.26e-16 75.1
MsG0280008593.01.T01 MTR_8g086290 35.849 159 91 7 74 228 10 161 7.71e-15 70.5
MsG0280008593.01.T01 MTR_5g053390 30.864 162 105 6 67 225 2 159 7.24e-13 66.2
MsG0280008593.01.T01 MTR_2g030740 33.728 169 91 7 67 225 2 159 1.00e-12 65.9
MsG0280008593.01.T01 MTR_8g043650 34.783 161 81 8 75 222 7 156 1.09e-12 65.9
MsG0280008593.01.T01 MTR_1g106070 34.568 162 86 8 75 225 7 159 1.37e-12 64.7
MsG0280008593.01.T01 MTR_3g052920 33.333 162 88 6 75 225 7 159 2.30e-12 64.7
MsG0280008593.01.T01 MTR_1g105910 31.677 161 99 6 67 222 2 156 3.50e-12 64.3
MsG0280008593.01.T01 MTR_2g085280 30.460 174 93 8 75 233 7 167 1.30e-11 62.8
MsG0280008593.01.T01 MTR_2g085250 30.460 174 93 8 75 233 7 167 1.34e-11 62.8
MsG0280008593.01.T01 MTR_1g012570 29.878 164 104 6 67 225 2 159 1.99e-11 62.4
MsG0280008593.01.T01 MTR_3g080940 29.448 163 94 7 76 228 11 162 6.32e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008593.01.T01 AT2G24840 28.289 152 105 4 76 225 65 214 3.64e-13 67.4
MsG0280008593.01.T01 AT5G60440 31.875 160 91 7 76 225 9 160 9.22e-13 66.6

Find 35 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCTGGCTCGAGTTCTTT+CGG 0.207843 2:+34488909 MsG0280008593.01.T01:CDS
ACTCTGGCTCGAGTTCTTTC+GGG 0.227438 2:+34488910 MsG0280008593.01.T01:CDS
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2:+34490562 MsG0280008593.01.T01:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2:-34490412 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2:-34490514 None:intergenic
CTCGAGTTCTTTCGGGGTGG+TGG 0.399097 2:+34488917 MsG0280008593.01.T01:CDS
TGATGTTGAATGAAACAAAC+TGG 0.408161 2:+34490033 MsG0280008593.01.T01:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2:-34490411 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2:-34490287 None:intergenic
GTCTGAAAAGATTACTGCTA+GGG 0.453546 2:+34490082 MsG0280008593.01.T01:CDS
GTGATGTCAATTTCCATGAT+TGG 0.461626 2:+34490501 MsG0280008593.01.T01:CDS
ACGATGAATGACAGCATCAC+AGG 0.499770 2:-34490321 None:intergenic
GACATATGATGGTCGACGAT+GGG 0.514442 2:+34490354 MsG0280008593.01.T01:CDS
GTTTCTGACATAAAGAATGC+TGG 0.527461 2:+34490104 MsG0280008593.01.T01:CDS
ATGAAATTGCTGAAACCCTA+AGG 0.533334 2:+34490396 MsG0280008593.01.T01:CDS
GAAGAAGTGACGCATGCGAA+AGG 0.537155 2:+34488975 MsG0280008593.01.T01:CDS
ATCGTCGACCATCATATGTC+CGG 0.542227 2:-34490351 None:intergenic
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2:+34490197 MsG0280008593.01.T01:CDS
TGTCTGAAAAGATTACTGCT+AGG 0.558102 2:+34490081 MsG0280008593.01.T01:CDS
TCTTGTCCGGCGATTTGACG+AGG 0.561634 2:-34490274 None:intergenic
GGACATATGATGGTCGACGA+TGG 0.562958 2:+34490353 MsG0280008593.01.T01:CDS
TGCACTCCTCGTCAAATCGC+CGG 0.565424 2:+34490268 MsG0280008593.01.T01:CDS
CTTTATATGAATGAGAACTC+TGG 0.571730 2:+34488894 None:intergenic
CTCTGGCTCGAGTTCTTTCG+GGG 0.582888 2:+34488911 MsG0280008593.01.T01:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2:+34490599 MsG0280008593.01.T01:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2:-34490320 None:intergenic
GGGGTGGTGGAGACTAATGT+AGG 0.595483 2:+34488930 MsG0280008593.01.T01:CDS
ATGTCAATTTCCATGATTGG+TGG 0.630551 2:+34490504 MsG0280008593.01.T01:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2:+34490293 MsG0280008593.01.T01:CDS
GAACAAAACTGAACAACACA+CGG 0.651271 2:+34490126 MsG0280008593.01.T01:CDS
TGGCTCGAGTTCTTTCGGGG+TGG 0.655988 2:+34488914 MsG0280008593.01.T01:CDS
GTGGTGGAGACTAATGTAGG+AGG 0.676177 2:+34488933 MsG0280008593.01.T01:CDS
GAAAGCTGTCAAAGTCACCA+AGG 0.688984 2:+34490469 MsG0280008593.01.T01:CDS
GATGTTGAATGAAACAAACT+GGG 0.726719 2:+34490034 MsG0280008593.01.T01:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2:-34490319 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGCATAAATTATTAAAAT+TGG - Chr2:34489113-34489132 None:intergenic 10.0%
!! AAATAAAATGTTAAGAAAAA+AGG + Chr2:34489538-34489557 MsG0280008593.01.T01:intron 10.0%
!!! AAATCTTATTTATAATAGTT+AGG - Chr2:34489674-34489693 None:intergenic 10.0%
!! AAATCTGTGAAATTAAAATA+GGG - Chr2:34489266-34489285 None:intergenic 15.0%
!! TTATTTATAATAGTTAGGTA+GGG - Chr2:34489669-34489688 None:intergenic 15.0%
!!! TTATGCTTTATTTTCTATTT+TGG + Chr2:34489124-34489143 MsG0280008593.01.T01:intron 15.0%
!! ACAAAACAAGAAAATTGATT+GGG - Chr2:34489868-34489887 None:intergenic 20.0%
!! ACACTTGTCAAAAAATAAAA+GGG + Chr2:34489561-34489580 MsG0280008593.01.T01:intron 20.0%
!! CAAATCTGTGAAATTAAAAT+AGG - Chr2:34489267-34489286 None:intergenic 20.0%
!! CTTATTTATAATAGTTAGGT+AGG - Chr2:34489670-34489689 None:intergenic 20.0%
!! TACAAAACAAGAAAATTGAT+TGG - Chr2:34489869-34489888 None:intergenic 20.0%
!! TTGATTTATGTGAATAATCA+GGG - Chr2:34489933-34489952 None:intergenic 20.0%
! AAGAAAGAAGAAAAACTGAA+CGG + Chr2:34490170-34490189 MsG0280008593.01.T01:CDS 25.0%
! ATTAATAGTCATTCTGACAT+CGG - Chr2:34489029-34489048 None:intergenic 25.0%
! CACTTGTCAAAAAATAAAAG+GGG + Chr2:34489562-34489581 MsG0280008593.01.T01:intron 25.0%
! CTTGATTTATGTGAATAATC+AGG - Chr2:34489934-34489953 None:intergenic 25.0%
! GACACTTGTCAAAAAATAAA+AGG + Chr2:34489560-34489579 MsG0280008593.01.T01:intron 25.0%
! TGAAATTAAAATAGGGTTTC+AGG - Chr2:34489259-34489278 None:intergenic 25.0%
! TTAGTTATCAAAGTCTAATG+TGG - Chr2:34489700-34489719 None:intergenic 25.0%
!! ACTGAAGTGTTTAAATACTA+AGG - Chr2:34489171-34489190 None:intergenic 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG + Chr2:34490562-34490581 MsG0280008593.01.T01:CDS 25.0%
!!! AATTCTTTGGAGAGTTTTAA+GGG + Chr2:34490575-34490594 MsG0280008593.01.T01:CDS 25.0%
!!! CTTGTCTTTTTTTGTAATCT+AGG + Chr2:34489298-34489317 MsG0280008593.01.T01:intron 25.0%
AAAGAAAGAAGGAAAGAACA+AGG - Chr2:34489755-34489774 None:intergenic 30.0%
AAAGCCTAATGAAAACAAGT+TGG - Chr2:34489636-34489655 None:intergenic 30.0%
AAATACTAAGGAAACCCTAA+TGG - Chr2:34489159-34489178 None:intergenic 30.0%
AAGAAAGAAGGAAAGAACAA+GGG - Chr2:34489754-34489773 None:intergenic 30.0%
AAGCCTAATGAAAACAAGTT+GGG - Chr2:34489635-34489654 None:intergenic 30.0%
AATACTAAGGAAACCCTAAT+GGG - Chr2:34489158-34489177 None:intergenic 30.0%
ATTGTGATTTGAGTCTTTGT+TGG + Chr2:34489956-34489975 MsG0280008593.01.T01:intron 30.0%
GATGTTGAATGAAACAAACT+GGG + Chr2:34490034-34490053 MsG0280008593.01.T01:CDS 30.0%
GTCAAAAAATAAAAGGGGAA+GGG + Chr2:34489567-34489586 MsG0280008593.01.T01:intron 30.0%
TAGAATTATTCCACCAATCA+TGG - Chr2:34490517-34490536 None:intergenic 30.0%
TAGTTAGGTAGGGTTTAATT+TGG - Chr2:34489659-34489678 None:intergenic 30.0%
TCAAGAAAAACTTGAAGAAG+AGG + Chr2:34490436-34490455 MsG0280008593.01.T01:CDS 30.0%
TGAATAAAAAACTGTCTCTC+TGG - Chr2:34489199-34489218 None:intergenic 30.0%
TGATGTTGAATGAAACAAAC+TGG + Chr2:34490033-34490052 MsG0280008593.01.T01:CDS 30.0%
TGTCAAAAAATAAAAGGGGA+AGG + Chr2:34489566-34489585 MsG0280008593.01.T01:intron 30.0%
! AGAGTTTTCTCAATTTCTTG+TGG + Chr2:34489231-34489250 MsG0280008593.01.T01:intron 30.0%
! TTCATACATGAGACAACTTT+TGG - Chr2:34489378-34489397 None:intergenic 30.0%
!! GAATTCTTTGGAGAGTTTTA+AGG + Chr2:34490574-34490593 MsG0280008593.01.T01:CDS 30.0%
AACCAAGAAAGTGAGTGATT+GGG + Chr2:34489888-34489907 MsG0280008593.01.T01:intron 35.0%
AAGAACAAGGGAAAGAAAGA+AGG - Chr2:34489742-34489761 None:intergenic 35.0%
AAGAACAAGTTCTATGCATG+TGG + Chr2:34490293-34490312 MsG0280008593.01.T01:CDS 35.0%
AGAAAAACTTGAAGAAGAGG+AGG + Chr2:34490439-34490458 MsG0280008593.01.T01:CDS 35.0%
AGACAAGAACGAAAGAATCT+TGG - Chr2:34489832-34489851 None:intergenic 35.0%
ATGAAATTGCTGAAACCCTA+AGG + Chr2:34490396-34490415 MsG0280008593.01.T01:CDS 35.0%
ATGTCAATTTCCATGATTGG+TGG + Chr2:34490504-34490523 MsG0280008593.01.T01:CDS 35.0%
GAACAAAACTGAACAACACA+CGG + Chr2:34490126-34490145 MsG0280008593.01.T01:CDS 35.0%
GTCTGAAAAGATTACTGCTA+GGG + Chr2:34490082-34490101 MsG0280008593.01.T01:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG + Chr2:34490501-34490520 MsG0280008593.01.T01:CDS 35.0%
GTTTCTGACATAAAGAATGC+TGG + Chr2:34490104-34490123 MsG0280008593.01.T01:CDS 35.0%
TAACCAAGAAAGTGAGTGAT+TGG + Chr2:34489887-34489906 MsG0280008593.01.T01:intron 35.0%
TGCTTCATATTGAAGCCTTA+GGG - Chr2:34490414-34490433 None:intergenic 35.0%
TGTCTGAAAAGATTACTGCT+AGG + Chr2:34490081-34490100 MsG0280008593.01.T01:CDS 35.0%
TTCAGACAGAGAAAGAAAGA+AGG - Chr2:34489766-34489785 None:intergenic 35.0%
TTTGACACAATCGAAAGCAA+AGG - Chr2:34489339-34489358 None:intergenic 35.0%
! AATGAAAACAAGTTGGGTCT+GGG - Chr2:34489629-34489648 None:intergenic 35.0%
! TAATGAAAACAAGTTGGGTC+TGG - Chr2:34489630-34489649 None:intergenic 35.0%
!! AGACCCAACTTGTTTTCATT+AGG + Chr2:34489629-34489648 MsG0280008593.01.T01:intron 35.0%
AACCCAATCACTCACTTTCT+TGG - Chr2:34489893-34489912 None:intergenic 40.0%
AATAATCAGGGTTAAGCCCT+AGG - Chr2:34489921-34489940 None:intergenic 40.0%
ATAATCAGGGTTAAGCCCTA+GGG - Chr2:34489920-34489939 None:intergenic 40.0%
CGACAGGAATAATGCTTGTT+TGG + Chr2:34489000-34489019 MsG0280008593.01.T01:intron 40.0%
GTGCTTCATATTGAAGCCTT+AGG - Chr2:34490415-34490434 None:intergenic 40.0%
TCTGAAAAAACACTGCGTGA+TGG + Chr2:34489780-34489799 MsG0280008593.01.T01:intron 40.0%
! AAAAAACACTGCGTGATGGA+CGG + Chr2:34489784-34489803 MsG0280008593.01.T01:intron 40.0%
! GCATAGAACTTGTTCTTGTC+CGG - Chr2:34490290-34490309 None:intergenic 40.0%
! GTCATTCATCGTTTTCTGAC+CGG + Chr2:34490332-34490351 MsG0280008593.01.T01:CDS 40.0%
! TTCGTCCTTTAGAAGAACTC+AGG - Chr2:34489068-34489087 None:intergenic 40.0%
! TTTTCTGACCGGACATATGA+TGG + Chr2:34490343-34490362 MsG0280008593.01.T01:CDS 40.0%
!! TTTGGATTTGCTGCCCATTA+GGG + Chr2:34489142-34489161 MsG0280008593.01.T01:intron 40.0%
!!! TTTTGGATTTGCTGCCCATT+AGG + Chr2:34489141-34489160 MsG0280008593.01.T01:intron 40.0%
AATTTACGTGCAGCAAGCGA+AGG + Chr2:34490599-34490618 MsG0280008593.01.T01:CDS 45.0%
ACGATGAATGACAGCATCAC+AGG - Chr2:34490324-34490343 None:intergenic 45.0%
AGAACTCAGGTGGCTTAAAG+AGG - Chr2:34489055-34489074 None:intergenic 45.0%
AGCCACCTGAGTTCTTCTAA+AGG + Chr2:34489060-34489079 MsG0280008593.01.T01:intron 45.0%
ATCGTCGACCATCATATGTC+CGG - Chr2:34490354-34490373 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG - Chr2:34490323-34490342 None:intergenic 45.0%
GAAAGCTGTCAAAGTCACCA+AGG + Chr2:34490469-34490488 MsG0280008593.01.T01:CDS 45.0%
GACATATGATGGTCGACGAT+GGG + Chr2:34490354-34490373 MsG0280008593.01.T01:CDS 45.0%
GAGTTCTCAAGACGCAAACT+CGG + Chr2:34490197-34490216 MsG0280008593.01.T01:CDS 45.0%
GATGAATGACAGCATCACAG+GGG - Chr2:34490322-34490341 None:intergenic 45.0%
TAAAAGGGGAAGGGATAGTG+TGG + Chr2:34489576-34489595 MsG0280008593.01.T01:intron 45.0%
! AACTCTGGCTCGAGTTCTTT+CGG + Chr2:34488909-34488928 MsG0280008593.01.T01:CDS 45.0%
! AGTGATTGGGTTTTTGCCCT+AGG + Chr2:34489901-34489920 MsG0280008593.01.T01:intron 45.0%
! GACATCACTCTTTTGTGCCT+TGG - Chr2:34490489-34490508 None:intergenic 45.0%
! GTCCTTTAGAAGAACTCAGG+TGG - Chr2:34489065-34489084 None:intergenic 45.0%
! GTGATTGGGTTTTTGCCCTA+GGG + Chr2:34489902-34489921 MsG0280008593.01.T01:intron 45.0%
!! CGAGGAGTGCAGTTTTTGAT+TGG - Chr2:34490259-34490278 None:intergenic 45.0%
GAAGAAGTGACGCATGCGAA+AGG + Chr2:34488975-34488994 MsG0280008593.01.T01:CDS 50.0%
GGACATATGATGGTCGACGA+TGG + Chr2:34490353-34490372 MsG0280008593.01.T01:CDS 50.0%
! AAACAAGTTGGGTCTGGGCT+TGG - Chr2:34489624-34489643 None:intergenic 50.0%
! AACAAGTTGGGTCTGGGCTT+GGG - Chr2:34489623-34489642 None:intergenic 50.0%
! ACTCTGGCTCGAGTTCTTTC+GGG + Chr2:34488910-34488929 MsG0280008593.01.T01:CDS 50.0%
! GTGGTGGAGACTAATGTAGG+AGG + Chr2:34488933-34488952 MsG0280008593.01.T01:CDS 50.0%
ACGCATGCGAAAGGTTCGAC+AGG + Chr2:34488984-34489003 MsG0280008593.01.T01:intron 55.0%
TCTTGTCCGGCGATTTGACG+AGG - Chr2:34490277-34490296 None:intergenic 55.0%
TGCACTCCTCGTCAAATCGC+CGG + Chr2:34490268-34490287 MsG0280008593.01.T01:CDS 55.0%
! CTCTGGCTCGAGTTCTTTCG+GGG + Chr2:34488911-34488930 MsG0280008593.01.T01:CDS 55.0%
!! ACACTGCGTGATGGACGGTA+CGG + Chr2:34489789-34489808 MsG0280008593.01.T01:intron 55.0%
!! GGGGTGGTGGAGACTAATGT+AGG + Chr2:34488930-34488949 MsG0280008593.01.T01:CDS 55.0%
CTCGAGTTCTTTCGGGGTGG+TGG + Chr2:34488917-34488936 MsG0280008593.01.T01:CDS 60.0%
TGGCTCGAGTTCTTTCGGGG+TGG + Chr2:34488914-34488933 MsG0280008593.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 34488900 34490628 34488900 ID=MsG0280008593.01;Name=MsG0280008593.01
Chr2 mRNA 34488900 34490628 34488900 ID=MsG0280008593.01.T01;Parent=MsG0280008593.01;Name=MsG0280008593.01.T01;_AED=0.57;_eAED=0.57;_QI=0|0|0|0.5|1|0.5|2|0|235
Chr2 exon 34488900 34488996 34488900 ID=MsG0280008593.01.T01:exon:20376;Parent=MsG0280008593.01.T01
Chr2 exon 34490018 34490628 34490018 ID=MsG0280008593.01.T01:exon:20377;Parent=MsG0280008593.01.T01
Chr2 CDS 34488900 34488996 34488900 ID=MsG0280008593.01.T01:cds;Parent=MsG0280008593.01.T01
Chr2 CDS 34490018 34490628 34490018 ID=MsG0280008593.01.T01:cds;Parent=MsG0280008593.01.T01
Gene Sequence

>MsG0280008593.01.T01

ATGAATGAGAACTCTGGCTCGAGTTCTTTCGGGGTGGTGGAGACTAATGTAGGAGGTCTGACAGCACGTATCGAAGAAGAAGTGACGCATGCGAAAGATAATTCATCATCAGTGATGTTGAATGAAACAAACTGGGACAACATGAATAAGAATTGTGAATTGTCTGAAAAGATTACTGCTAGGGTTTCTGACATAAAGAATGCTGGAACAAAACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGTTCTGAGTTCTCAAGACGCAAACTCGGAATATTCAACAAAGCAATAGAACTGTCTATTCTATGCCAATCAAAAACTGCACTCCTCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTGACCGGACATATGATGGTCGACGATGGGAAAAAGAAGAAACAAGATGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGAGGATAATTTGAAAGCTGTCAAAGTCACCAAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTTAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>MsG0280008593.01.T01

MNENSGSSSFGVVETNVGGLTARIEEEVTHAKDNSSSVMLNETNWDNMNKNCELSEKITARVSDIKNAGTKLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTALLVKSPDKNKFYACGYPCDAVIHRFLTGHMMVDDGKKKKQDDEIAETLRLQYEALQEKLEEEEDNLKAVKVTKAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK*