AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067574

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067574.t1 MTR_4g083540 95.623 297 9 1 1 297 1 293 0.0 584
MS.gene067574.t1 MTR_2g028830 50.000 324 130 8 1 297 1 319 1.10e-99 295
MS.gene067574.t1 MTR_2g069350 35.422 367 166 9 1 297 1 366 1.90e-60 196
MS.gene067574.t1 MTR_5g013690 32.512 203 129 5 102 297 134 335 3.68e-28 111
MS.gene067574.t1 MTR_5g013690 32.512 203 129 5 102 297 71 272 5.76e-28 109
MS.gene067574.t1 MTR_4g099060 33.654 208 125 4 98 297 84 286 5.52e-26 104
MS.gene067574.t1 MTR_4g099060 34.286 210 121 5 98 297 129 331 1.19e-25 104
MS.gene067574.t1 MTR_1g019250 30.093 216 133 5 85 286 119 330 3.34e-22 95.1
MS.gene067574.t1 MTR_4g036485 32.759 174 109 3 112 285 35 200 4.64e-22 92.0
MS.gene067574.t1 MTR_3g117970 29.082 196 114 4 104 296 22 195 1.72e-17 79.3
MS.gene067574.t1 MTR_4g073070 32.222 180 95 6 109 284 85 241 2.17e-13 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067574.t1 AT5G45100 42.208 308 152 7 1 297 1 293 1.19e-66 210
MS.gene067574.t1 AT4G19700 40.645 310 164 10 1 297 1 303 3.88e-64 204
MS.gene067574.t1 AT5G45100 46.781 233 105 4 76 297 42 266 4.17e-61 195
MS.gene067574.t1 AT3G12920 38.644 295 147 9 25 297 52 334 1.56e-54 180
MS.gene067574.t1 AT1G79110 43.119 218 102 3 102 297 115 332 1.45e-48 165
MS.gene067574.t1 AT1G79110 43.119 218 102 3 102 297 137 354 2.20e-48 165
MS.gene067574.t1 AT1G79110 42.534 221 102 4 102 297 137 357 2.29e-46 160
MS.gene067574.t1 AT1G60610 32.843 204 119 3 107 296 140 339 2.99e-25 103
MS.gene067574.t1 AT1G60610 32.843 204 119 3 107 296 140 339 2.99e-25 103
MS.gene067574.t1 AT1G60610 32.843 204 119 3 107 296 140 339 2.99e-25 103
MS.gene067574.t1 AT1G60610 32.843 204 119 3 107 296 140 339 2.99e-25 103
MS.gene067574.t1 AT1G60610 32.843 204 119 3 107 296 140 339 2.99e-25 103
MS.gene067574.t1 AT1G10650 30.876 217 128 4 97 297 73 283 5.89e-24 99.0
MS.gene067574.t1 AT1G10650 30.876 217 128 4 97 297 129 339 8.11e-24 99.8
MS.gene067574.t1 AT1G45976 27.982 218 128 4 85 286 111 315 1.22e-23 99.0
MS.gene067574.t1 AT4G35070 32.240 183 114 3 108 284 74 252 6.70e-21 90.1
MS.gene067574.t1 AT4G35070 32.240 183 114 3 108 284 19 197 1.46e-20 88.2
MS.gene067574.t1 AT1G32740 30.208 192 128 2 111 296 76 267 1.90e-20 89.0
MS.gene067574.t1 AT1G32740 30.208 192 128 2 111 296 76 267 1.90e-20 89.0
MS.gene067574.t1 AT1G32740 30.208 192 128 2 111 296 109 300 2.37e-20 89.4
MS.gene067574.t1 AT1G32740 29.851 201 117 4 111 296 120 311 3.01e-20 89.4
MS.gene067574.t1 AT5G47050 28.713 202 133 2 104 297 102 300 4.01e-20 88.6
MS.gene067574.t1 AT4G17680 26.255 259 153 6 73 296 59 314 5.44e-19 85.9
MS.gene067574.t1 AT4G17680 26.904 197 134 3 107 296 49 242 2.19e-18 82.8
MS.gene067574.t1 AT4G17680 28.108 185 122 4 119 296 10 190 6.14e-14 69.3

Find 60 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATTTCCGATTGTTGATTT+TGG 0.126414 4.1:-24214473 None:intergenic
GTTTCTTTGTTACTGCTTCT+TGG 0.130913 4.1:-24214707 None:intergenic
ATAGAATTGTTGATTGAATT+TGG 0.169802 4.1:-24214205 None:intergenic
GGGAAATTGTGCAGCGGTTG+TGG 0.242036 4.1:+24214999 MS.gene067574:CDS
AAAAGCGAAAACACTGATTA+TGG 0.280960 4.1:+24214788 MS.gene067574:CDS
CTGAAACGCTTCCTTGAATC+AGG 0.292842 4.1:-24214351 None:intergenic
TGAAAAGGAAAGAACGATTC+AGG 0.297477 4.1:-24214276 None:intergenic
GGAAATTGTGCAGCGGTTGT+GGG 0.352965 4.1:+24215000 MS.gene067574:CDS
GTGACAGTACTATCAGCTTT+TGG 0.356081 4.1:-24214318 None:intergenic
TGATTATGGAGAATCAGATT+TGG 0.382990 4.1:+24214802 MS.gene067574:CDS
TAACGAATTAGAACAAGTTC+TGG 0.406835 4.1:+24214869 MS.gene067574:CDS
CAGAAAGACGGTTGATGAAA+AGG 0.417129 4.1:-24214291 None:intergenic
AGAAGAAGAGATTCAGAGAA+TGG 0.421799 4.1:+24214740 MS.gene067574:CDS
CATGGGAATAACACCATTCA+TGG 0.422051 4.1:-24214235 None:intergenic
GAATCAGATTTGGAGAGAAA+TGG 0.423763 4.1:+24214812 MS.gene067574:CDS
TGTGCAGCGGTTGTGGGGTA+AGG 0.425056 4.1:+24215006 MS.gene067574:CDS
AAGCATCGTCGGCGGTGGTT+GGG 0.433268 4.1:+24214979 MS.gene067574:CDS
CCTATCACATCCCTGATTCA+AGG 0.447097 4.1:+24214340 MS.gene067574:CDS
TTCTATAATGCTCCCATGAA+TGG 0.450823 4.1:+24214222 MS.gene067574:CDS
GAAGCATCGTCGGCGGTGGT+TGG 0.467695 4.1:+24214978 MS.gene067574:CDS
CACAAACACAAATGCCTACA+TGG 0.468763 4.1:-24215050 None:intergenic
ACAGACAGAGAGAGTGAGAA+TGG 0.475032 4.1:+24214635 MS.gene067574:intron
GAAGATGCAGCGTCGAGTTG+TGG 0.486897 4.1:+24214918 MS.gene067574:CDS
CCTTGAATCAGGGATGTGAT+AGG 0.487805 4.1:-24214340 None:intergenic
TGTGAAGGAGGAGGTGGTGG+TGG 0.488481 4.1:+24214953 MS.gene067574:CDS
GAAAAGGAAAGAACGATTCA+GGG 0.507955 4.1:-24214275 None:intergenic
TCATCTCCAAAATCAACAAT+CGG 0.509663 4.1:+24214467 MS.gene067574:CDS
CTGTGATTGATTTGTGATTG+TGG 0.510451 4.1:-24214086 None:intergenic
GGAAGAAGCATCGTCGGCGG+TGG 0.519361 4.1:+24214974 MS.gene067574:CDS
TCAGGGATTGTTGAAGACAT+AGG 0.522810 4.1:-24214258 None:intergenic
GGAGAGAAGAAATTCATATG+AGG 0.524625 4.1:-24214065 None:intergenic
CCTCTCAATTCTCATGGCAG+TGG 0.525047 4.1:+24214037 None:intergenic
TTGTGTTTGTGTACAATGTG+TGG 0.529559 4.1:+24215062 MS.gene067574:CDS
CCATGTGAAGGAGGAGGTGG+TGG 0.529917 4.1:+24214950 MS.gene067574:CDS
ACGCTGCATCTTCATCGTTA+CGG 0.543093 4.1:-24214908 None:intergenic
CCACCACCTCCTCCTTCACA+TGG 0.554367 4.1:-24214950 None:intergenic
GTGCAGCGGTTGTGGGGTAA+GGG 0.555636 4.1:+24215007 MS.gene067574:CDS
CCACCATGTGAAGGAGGAGG+TGG 0.555830 4.1:+24214947 MS.gene067574:CDS
TGTGTTTGTGTACAATGTGT+GGG 0.556297 4.1:+24215063 MS.gene067574:CDS
CACAATCACAAATCAATCAC+AGG 0.562498 4.1:+24214087 MS.gene067574:CDS
TAGTGCTGTTACTGCCATGT+AGG 0.566923 4.1:+24215036 MS.gene067574:CDS
AAAGAGGGCAATTACGAATG+TGG 0.572431 4.1:-24215088 None:intergenic
AAGAGGGCAATTACGAATGT+GGG 0.595280 4.1:-24215087 None:intergenic
GAGAAGAAATTCATATGAGG+AGG 0.604224 4.1:-24214062 None:intergenic
AGATTCTGATCAACAAAGGA+AGG 0.605193 4.1:-24214438 None:intergenic
ATTGTTGAAGACATAGGCAT+GGG 0.610557 4.1:-24214252 None:intergenic
GGTGGTGGAAGAAGCATCGT+CGG 0.611886 4.1:+24214968 MS.gene067574:CDS
GATTGTTGAAGACATAGGCA+TGG 0.611962 4.1:-24214253 None:intergenic
GTGGTTGGGAAATTGTGCAG+CGG 0.623860 4.1:+24214993 MS.gene067574:CDS
TGAAACGCTTCCTTGAATCA+GGG 0.624896 4.1:-24214350 None:intergenic
ATGGGAATAACACCATTCAT+GGG 0.625023 4.1:-24214234 None:intergenic
GCAATCAAGAATGCTACAAG+CGG 0.626043 4.1:+24214680 MS.gene067574:CDS
GAGGAGATTCTGATCAACAA+AGG 0.626764 4.1:-24214442 None:intergenic
TAACCACCATGTGAAGGAGG+AGG 0.630185 4.1:+24214944 MS.gene067574:CDS
GAAATTGTGCAGCGGTTGTG+GGG 0.636186 4.1:+24215001 MS.gene067574:CDS
TGGAAGTAACCACCATGTGA+AGG 0.636380 4.1:+24214938 MS.gene067574:CDS
AAGTAACCACCATGTGAAGG+AGG 0.656748 4.1:+24214941 MS.gene067574:CDS
GGTGGAAGAAGCATCGTCGG+CGG 0.665786 4.1:+24214971 MS.gene067574:CDS
CCACCTCCTCCTTCACATGG+TGG 0.670919 4.1:-24214947 None:intergenic
AAGAGTGTATGATTCTTCAG+TGG 0.676803 4.1:-24214379 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAATATAAGAAAACTGA+AGG - chr4.1:24214145-24214164 None:intergenic 15.0%
!!! ATAGAATTGTTGATTGAATT+TGG - chr4.1:24214208-24214227 None:intergenic 20.0%
!!! TTACTTAGATTTTGTGATTA+TGG + chr4.1:24214572-24214591 MS.gene067574:intron 20.0%
! ATATAAGAAAACTGAAGGTA+AGG - chr4.1:24214140-24214159 None:intergenic 25.0%
! ATTGAATTTGGTTATATCTC+TGG - chr4.1:24214196-24214215 None:intergenic 25.0%
! TAATTCCAGAAAAACAAAGA+GGG - chr4.1:24215106-24215125 None:intergenic 25.0%
! TTAATTCCAGAAAAACAAAG+AGG - chr4.1:24215107-24215126 None:intergenic 25.0%
TAACGAATTAGAACAAGTTC+TGG + chr4.1:24214869-24214888 MS.gene067574:CDS 30.0%
TCATCTCCAAAATCAACAAT+CGG + chr4.1:24214467-24214486 MS.gene067574:CDS 30.0%
TGATTATGGAGAATCAGATT+TGG + chr4.1:24214802-24214821 MS.gene067574:CDS 30.0%
! AAAAGCGAAAACACTGATTA+TGG + chr4.1:24214788-24214807 MS.gene067574:CDS 30.0%
! TTATATCTCTGGAAAAACAG+AGG - chr4.1:24214185-24214204 None:intergenic 30.0%
!! GAGAGTTTGATATTTTTGTG+AGG - chr4.1:24214411-24214430 None:intergenic 30.0%
!! TTGATATTTTTGTGAGGAAG+TGG - chr4.1:24214405-24214424 None:intergenic 30.0%
AGAAGAAGAGATTCAGAGAA+TGG + chr4.1:24214740-24214759 MS.gene067574:CDS 35.0%
AGATTCTGATCAACAAAGGA+AGG - chr4.1:24214441-24214460 None:intergenic 35.0%
ATGGGAATAACACCATTCAT+GGG - chr4.1:24214237-24214256 None:intergenic 35.0%
ATTGTTGAAGACATAGGCAT+GGG - chr4.1:24214255-24214274 None:intergenic 35.0%
CACAATCACAAATCAATCAC+AGG + chr4.1:24214087-24214106 MS.gene067574:CDS 35.0%
GAAAAGGAAAGAACGATTCA+GGG - chr4.1:24214278-24214297 None:intergenic 35.0%
GAATCAGATTTGGAGAGAAA+TGG + chr4.1:24214812-24214831 MS.gene067574:CDS 35.0%
GAGAAGAAATTCATATGAGG+AGG - chr4.1:24214065-24214084 None:intergenic 35.0%
GGAGAGAAGAAATTCATATG+AGG - chr4.1:24214068-24214087 None:intergenic 35.0%
GTTTCTTTGTTACTGCTTCT+TGG - chr4.1:24214710-24214729 None:intergenic 35.0%
TGAAAAGGAAAGAACGATTC+AGG - chr4.1:24214279-24214298 None:intergenic 35.0%
TGTGTTTGTGTACAATGTGT+GGG + chr4.1:24215063-24215082 MS.gene067574:CDS 35.0%
TTCTATAATGCTCCCATGAA+TGG + chr4.1:24214222-24214241 MS.gene067574:CDS 35.0%
TTGTGTTTGTGTACAATGTG+TGG + chr4.1:24215062-24215081 MS.gene067574:CDS 35.0%
! AAGAGTGTATGATTCTTCAG+TGG - chr4.1:24214382-24214401 None:intergenic 35.0%
!! CTGTGATTGATTTGTGATTG+TGG - chr4.1:24214089-24214108 None:intergenic 35.0%
!! GTTGATTTTGGAGATGATAG+AGG - chr4.1:24214464-24214483 None:intergenic 35.0%
!!! AATTGCCCTCTTTGTTTTTC+TGG + chr4.1:24215098-24215117 MS.gene067574:CDS 35.0%
!!! CGATTTCCGATTGTTGATTT+TGG - chr4.1:24214476-24214495 None:intergenic 35.0%
AAAGAGGGCAATTACGAATG+TGG - chr4.1:24215091-24215110 None:intergenic 40.0%
AAGAGGGCAATTACGAATGT+GGG - chr4.1:24215090-24215109 None:intergenic 40.0%
CACAAACACAAATGCCTACA+TGG - chr4.1:24215053-24215072 None:intergenic 40.0%
CATGGGAATAACACCATTCA+TGG - chr4.1:24214238-24214257 None:intergenic 40.0%
GAGGAGATTCTGATCAACAA+AGG - chr4.1:24214445-24214464 None:intergenic 40.0%
GATTGTTGAAGACATAGGCA+TGG - chr4.1:24214256-24214275 None:intergenic 40.0%
GCAATCAAGAATGCTACAAG+CGG + chr4.1:24214680-24214699 MS.gene067574:CDS 40.0%
TCAGGGATTGTTGAAGACAT+AGG - chr4.1:24214261-24214280 None:intergenic 40.0%
TGAAACGCTTCCTTGAATCA+GGG - chr4.1:24214353-24214372 None:intergenic 40.0%
! GTGACAGTACTATCAGCTTT+TGG - chr4.1:24214321-24214340 None:intergenic 40.0%
!! CAGAAAGACGGTTGATGAAA+AGG - chr4.1:24214294-24214313 None:intergenic 40.0%
!!! GCTTTTGGTTCACAGAAAGA+CGG - chr4.1:24214306-24214325 None:intergenic 40.0%
AAGTAACCACCATGTGAAGG+AGG + chr4.1:24214941-24214960 MS.gene067574:CDS 45.0%
ACAGACAGAGAGAGTGAGAA+TGG + chr4.1:24214635-24214654 MS.gene067574:intron 45.0%
ACGCTGCATCTTCATCGTTA+CGG - chr4.1:24214911-24214930 None:intergenic 45.0%
CCTATCACATCCCTGATTCA+AGG + chr4.1:24214340-24214359 MS.gene067574:CDS 45.0%
CCTTGAATCAGGGATGTGAT+AGG - chr4.1:24214343-24214362 None:intergenic 45.0%
CTGAAACGCTTCCTTGAATC+AGG - chr4.1:24214354-24214373 None:intergenic 45.0%
TGGAAGTAACCACCATGTGA+AGG + chr4.1:24214938-24214957 MS.gene067574:CDS 45.0%
! TAGTGCTGTTACTGCCATGT+AGG + chr4.1:24215036-24215055 MS.gene067574:CDS 45.0%
GAAATTGTGCAGCGGTTGTG+GGG + chr4.1:24215001-24215020 MS.gene067574:CDS 50.0%
GGAAATTGTGCAGCGGTTGT+GGG + chr4.1:24215000-24215019 MS.gene067574:CDS 50.0%
GTGGTTGGGAAATTGTGCAG+CGG + chr4.1:24214993-24215012 MS.gene067574:CDS 50.0%
TAACCACCATGTGAAGGAGG+AGG + chr4.1:24214944-24214963 MS.gene067574:CDS 50.0%
GGGAAATTGTGCAGCGGTTG+TGG + chr4.1:24214999-24215018 MS.gene067574:CDS 55.0%
! GAAGATGCAGCGTCGAGTTG+TGG + chr4.1:24214918-24214937 MS.gene067574:CDS 55.0%
!! GGTGGTGGAAGAAGCATCGT+CGG + chr4.1:24214968-24214987 MS.gene067574:CDS 55.0%
CCACCACCTCCTCCTTCACA+TGG - chr4.1:24214953-24214972 None:intergenic 60.0%
CCACCATGTGAAGGAGGAGG+TGG + chr4.1:24214947-24214966 MS.gene067574:CDS 60.0%
CCACCTCCTCCTTCACATGG+TGG - chr4.1:24214950-24214969 None:intergenic 60.0%
CCATGTGAAGGAGGAGGTGG+TGG + chr4.1:24214950-24214969 MS.gene067574:CDS 60.0%
GTGCAGCGGTTGTGGGGTAA+GGG + chr4.1:24215007-24215026 MS.gene067574:CDS 60.0%
TGTGCAGCGGTTGTGGGGTA+AGG + chr4.1:24215006-24215025 MS.gene067574:CDS 60.0%
! AAGCATCGTCGGCGGTGGTT+GGG + chr4.1:24214979-24214998 MS.gene067574:CDS 60.0%
! TGTGAAGGAGGAGGTGGTGG+TGG + chr4.1:24214953-24214972 MS.gene067574:CDS 60.0%
!! GGTGGAAGAAGCATCGTCGG+CGG + chr4.1:24214971-24214990 MS.gene067574:CDS 60.0%
!! GAAGCATCGTCGGCGGTGGT+TGG + chr4.1:24214978-24214997 MS.gene067574:CDS 65.0%
!! GGAAGAAGCATCGTCGGCGG+TGG + chr4.1:24214974-24214993 MS.gene067574:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 24214050 24215154 24214050 ID=MS.gene067574
chr4.1 mRNA 24214050 24215154 24214050 ID=MS.gene067574.t1;Parent=MS.gene067574
chr4.1 exon 24214050 24214108 24214050 ID=MS.gene067574.t1.exon1;Parent=MS.gene067574.t1
chr4.1 CDS 24214050 24214108 24214050 ID=cds.MS.gene067574.t1;Parent=MS.gene067574.t1
chr4.1 exon 24214197 24214515 24214197 ID=MS.gene067574.t1.exon2;Parent=MS.gene067574.t1
chr4.1 CDS 24214197 24214515 24214197 ID=cds.MS.gene067574.t1;Parent=MS.gene067574.t1
chr4.1 exon 24214639 24215154 24214639 ID=MS.gene067574.t1.exon3;Parent=MS.gene067574.t1
chr4.1 CDS 24214639 24215154 24214639 ID=cds.MS.gene067574.t1;Parent=MS.gene067574.t1
Gene Sequence

>MS.gene067574

ATGGCAGTGGAACCTCCTCATATGAATTTCTTCTCTCCACAATCACAAATCAATCACAGGTAATATATATAACACATTCATTCTTTTCCTTACCTTCAGTTTTCTTATATTATATATAGTTTTAACACTTTTCCTCTGTTTTTCCAGAGATATAACCAAATTCAATCAACAATTCTATAATGCTCCCATGAATGGTGTTATTCCCATGCCTATGTCTTCAACAATCCCTGAATCGTTCTTTCCTTTTCATCAACCGTCTTTCTGTGAACCAAAAGCTGATAGTACTGTCACCTATCACATCCCTGATTCAAGGAAGCGTTTCAGAGACTCCACTGAAGAATCATACACTCTTCCACTTCCTCACAAAAATATCAAACTCTCATCTCAACCTTCCTTTGTTGATCAGAATCTCCTCTATCATCTCCAAAATCAACAATCGGAAATCGATCTCTTCATTGCTCAACATGTAAGTCATTCATTCAAGAAAAAAAAAGAAACTGTTAAAAAGAAGTTACAGATTTATTACTTAGATTTTGTGATTATGGTTAATTATTAGTAATTAATATTGTTAATTTTTGTTGATTAACAGACAGAGAGAGTGAGAATGGAGATAGAAGAGCAAAGCATGAAGCAATCAAGAATGCTACAAGCGGCAATCCAAGAAGCAGTAACAAAGAAACTGAAACAAAAAGAAGAAGAGATTCAGAGAATGGAGAAACAAAATCTAATGCTTCAAGAAAAAGCGAAAACACTGATTATGGAGAATCAGATTTGGAGAGAAATGGCTTTGACAAACGAATCTGCTGTAAACACGTTACGTAACGAATTAGAACAAGTTCTGGCACATGTTGAGAATCACCGTAACGATGAAGATGCAGCGTCGAGTTGTGGAAGTAACCACCATGTGAAGGAGGAGGTGGTGGTGGAAGAAGCATCGTCGGCGGTGGTTGGGAAATTGTGCAGCGGTTGTGGGGTAAGGGAGTCAGTAGTGCTGTTACTGCCATGTAGGCATTTGTGTTTGTGTACAATGTGTGGGACCCACATTCGTAATTGCCCTCTTTGTTTTTCTGGAATTAATGCTAGTGTTCATGTAAATTTTTCTTAG
Protein sequence

>MS.gene067574.t1

MAVEPPHMNFFSPQSQINHRDITKFNQQFYNAPMNGVIPMPMSSTIPESFFPFHQPSFCEPKADSTVTYHIPDSRKRFRDSTEESYTLPLPHKNIKLSSQPSFVDQNLLYHLQNQQSEIDLFIAQHTERVRMEIEEQSMKQSRMLQAAIQEAVTKKLKQKEEEIQRMEKQNLMLQEKAKTLIMENQIWREMALTNESAVNTLRNELEQVLAHVENHRNDEDAASSCGSNHHVKEEVVVEEASSAVVGKLCSGCGVRESVVLLLPCRHLCLCTMCGTHIRNCPLCFSGINASVHVNFS