AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0437920

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0437920 MtrunA17_Chr1g0213161 73.246 228 25 3 6 198 8 234 2.80e-112 320
Msa0437920 MtrunA17_Chr1g0199671 48.450 258 63 11 8 197 74 329 2.40e-58 186
Msa0437920 MtrunA17_Chr4g0035891 41.117 197 95 5 2 198 115 290 1.94e-38 134
Msa0437920 MtrunA17_Chr2g0326771 46.243 173 63 5 32 188 129 287 3.29e-37 131
Msa0437920 MtrunA17_Chr8g0340401 40.404 198 88 5 2 181 105 290 3.94e-36 129
Msa0437920 MtrunA17_Chr8g0372291 40.415 193 89 5 12 192 113 291 5.81e-36 127
Msa0437920 MtrunA17_Chr1g0146231 41.361 191 88 6 12 181 111 298 7.38e-35 125
Msa0437920 MtrunA17_Chr3g0145121 40.217 184 104 2 2 181 98 279 1.28e-33 121
Msa0437920 MtrunA17_Chr4g0028961 76.923 65 15 0 117 181 232 296 1.45e-33 122
Msa0437920 MtrunA17_Chr5g0404981 37.281 228 99 6 2 192 153 373 1.27e-32 120
Msa0437920 MtrunA17_Chr3g0140331 41.053 190 88 6 7 181 137 317 2.88e-32 119
Msa0437920 MtrunA17_Chr6g0461591 73.134 67 18 0 116 182 191 257 3.61e-32 116
Msa0437920 MtrunA17_Chr1g0169431 70.000 70 21 0 112 181 167 236 3.90e-32 116
Msa0437920 MtrunA17_Chr7g0253101 69.565 69 21 0 114 182 185 253 3.07e-31 114
Msa0437920 MtrunA17_Chr5g0395391 64.865 74 26 0 112 185 265 338 4.89e-31 115
Msa0437920 MtrunA17_Chr5g0395391 63.768 69 25 0 112 180 163 231 7.54e-28 107
Msa0437920 MtrunA17_Chr7g0232671 61.290 62 24 0 117 178 187 248 1.93e-21 88.6
Msa0437920 MtrunA17_Chr7g0232701 56.667 60 26 0 119 178 75 134 8.29e-19 79.0
Msa0437920 MtrunA17_Chr7g0232681 51.515 66 32 0 113 178 128 193 3.72e-18 78.6
Msa0437920 MtrunA17_Chr5g0404131 46.296 54 29 0 96 149 171 224 1.64e-13 67.8
Msa0437920 MtrunA17_Chr7g0271861 56.522 46 19 1 110 154 14 59 5.09e-13 63.2
Msa0437920 MtrunA17_Chr8g0373231 61.111 36 14 0 114 149 122 157 7.58e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0437920 AT4G36240.1 41.209 182 90 3 7 187 69 234 4.02e-38 132
Msa0437920 AT3G54810.1 79.167 72 15 0 116 187 228 299 2.73e-36 129
Msa0437920 AT3G54810.2 79.167 72 15 0 116 187 228 299 2.73e-36 129
Msa0437920 AT3G24050.1 60.825 97 32 1 95 191 178 268 7.03e-36 127
Msa0437920 AT1G08010.2 70.513 78 20 1 111 188 214 288 1.36e-35 127
Msa0437920 AT1G08010.1 70.513 78 20 1 111 188 214 288 1.36e-35 127
Msa0437920 AT1G08010.3 70.513 78 20 1 111 188 214 288 1.36e-35 127
Msa0437920 AT5G66320.2 37.662 231 103 7 2 195 103 329 5.47e-35 126
Msa0437920 AT5G66320.1 37.662 231 103 7 2 195 103 329 5.47e-35 126
Msa0437920 AT4G32890.1 38.342 193 105 4 2 181 70 261 1.16e-33 122
Msa0437920 AT1G08000.2 50.735 136 51 4 61 181 148 282 1.32e-33 122
Msa0437920 AT1G08000.1 50.735 136 51 4 61 181 148 282 1.32e-33 122
Msa0437920 AT3G60530.1 38.500 200 85 5 2 195 67 234 3.07e-33 119
Msa0437920 AT4G34680.1 38.308 201 72 6 4 191 93 254 5.43e-33 119
Msa0437920 AT4G34680.2 38.308 201 72 6 4 191 93 254 5.43e-33 119
Msa0437920 AT5G25830.1 41.262 206 81 7 12 181 82 283 1.81e-32 119
Msa0437920 AT2G45050.1 39.196 199 90 6 2 185 69 251 2.53e-32 117
Msa0437920 AT3G51080.1 66.667 75 23 1 117 191 221 293 6.45e-31 115
Msa0437920 AT2G28340.1 67.606 71 20 1 119 189 193 260 4.60e-29 109
Msa0437920 AT3G45170.1 54.545 77 35 0 109 185 107 183 1.93e-27 103
Msa0437920 AT4G36620.1 58.333 36 15 0 114 149 72 107 1.32e-11 61.6
Msa0437920 AT2G18380.1 60.000 35 14 0 115 149 90 124 6.68e-11 59.7
Msa0437920 AT3G50870.1 58.333 36 15 0 114 149 149 184 7.43e-11 60.5

Find 55 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGGTGAACTTATGCTTTC+AGG 0.155842 3_3:+1929376 None:intergenic
CTAGCAACAGGCCGGTATTC+AGG 0.202243 3_3:+1929055 None:intergenic
ATCAACCTTGTTATTATTAC+AGG 0.242443 3_3:-1929524 None:intergenic
GGGAAATGACATTCTTTCAT+TGG 0.338146 3_3:-1929503 Msa0437920:CDS
AAAAGAATCGTCCACAATAT+CGG 0.373139 3_3:+1929471 None:intergenic
AGACGCAAGGATAATAATTC+TGG 0.376327 3_3:-1928968 Msa0437920:CDS
GTCTCATCACTCTCATTTCA+AGG 0.395161 3_3:+1928987 None:intergenic
GAAAATGTTGGGCTAGCAAC+AGG 0.436477 3_3:+1929043 None:intergenic
TAATTCTGGTATTCTCGCCT+TGG 0.441508 3_3:-1928954 Msa0437920:CDS
TAGCAACAGGCCGGTATTCA+GGG 0.446393 3_3:+1929056 None:intergenic
TCTGCAATGCTTGCGGCGTT+CGG 0.448102 3_3:-1929099 Msa0437920:CDS
GCGCCTCTTCTTGCTGCTCC+AGG 0.448261 3_3:-1929217 Msa0437920:CDS
TGGGTGAACTTATGCTTTCA+GGG 0.452416 3_3:+1929377 None:intergenic
CAATGGAGGTCAGGGCCAGA+GGG 0.460506 3_3:-1929133 Msa0437920:CDS
TGACCTCCATTGTGGTGTCT+TGG 0.470363 3_3:+1929144 None:intergenic
TGCGGCGTTCGGTACAAGTC+AGG 0.475560 3_3:-1929088 Msa0437920:CDS
AAGACACCACAATGGAGGTC+AGG 0.476853 3_3:-1929142 Msa0437920:CDS
ATGACATTCTTTCATTGGAA+TGG 0.478423 3_3:-1929498 Msa0437920:CDS
ACCAAAGTATTATGATCTCC+TGG 0.478922 3_3:+1929199 None:intergenic
GGACTCTAGAGAAGAGGAAG+TGG 0.484892 3_3:+1929261 None:intergenic
GCCGACTTTGCCCTGAATAC+CGG 0.496140 3_3:-1929066 Msa0437920:CDS
GGTTGCAAGACGTGTACGCT+TGG 0.509630 3_3:+1929321 None:intergenic
ACAATGGAGGTCAGGGCCAG+AGG 0.512229 3_3:-1929134 Msa0437920:CDS
GCTCAACTTCTTTCAATGTG+AGG 0.512743 3_3:+1929440 None:intergenic
TCCAGGAGATCATAATACTT+TGG 0.514433 3_3:-1929200 Msa0437920:CDS
GAAGATCCGGAGAAAATGTT+GGG 0.515937 3_3:+1929032 None:intergenic
TGAGTTGCATGGTTGAATGA+TGG 0.525185 3_3:+1929290 None:intergenic
TGTGAGTTAGAGTGAAGATC+CGG 0.525870 3_3:+1929019 None:intergenic
TGAAGATCCGGAGAAAATGT+TGG 0.538158 3_3:+1929031 None:intergenic
GAGTTGCATGGTTGAATGAT+GGG 0.547753 3_3:+1929291 None:intergenic
TCCTTGTTCACTGACGATGA+TGG 0.555427 3_3:+1929412 None:intergenic
CTCCCTTCACACGTATTCCA+AGG 0.557994 3_3:+1928937 None:intergenic
ACCATCATCGTCAGTGAACA+AGG 0.562264 3_3:-1929413 Msa0437920:CDS
CTTCTTGGACTCTAGAGAAG+AGG 0.565275 3_3:+1929255 None:intergenic
GGAATGGCAGTCCGATATTG+TGG 0.569142 3_3:-1929482 Msa0437920:CDS
GACTCTAGAGAAGAGGAAGT+GGG 0.570792 3_3:+1929262 None:intergenic
TCGCCTTGGAATACGTGTGA+AGG 0.571882 3_3:-1928940 None:intergenic
TCTGGCCCTGACCTCCATTG+TGG 0.574213 3_3:+1929136 None:intergenic
GCCGGTATTCAGGGCAAAGT+CGG 0.582975 3_3:+1929065 None:intergenic
TCAACCTTGTTATTATTACA+GGG 0.602548 3_3:-1929523 None:intergenic
ATTTCCCTGTAATAATAACA+AGG 0.619005 3_3:+1929519 None:intergenic
AGACACCACAATGGAGGTCA+GGG 0.625833 3_3:-1929141 Msa0437920:CDS
ATGTTGGGCTAGCAACAGGC+CGG 0.635385 3_3:+1929047 None:intergenic
TCTCCTGGAGCAGCAAGAAG+AGG 0.648108 3_3:+1929214 None:intergenic
AAAACACTCTGCAATGCTTG+CGG 0.650171 3_3:-1929106 Msa0437920:CDS
AGTTGCATGGTTGAATGATG+GGG 0.654848 3_3:+1929292 None:intergenic
AATGGAGGTCAGGGCCAGAG+GGG 0.656879 3_3:-1929132 Msa0437920:CDS
CGACCAAGACACCACAATGG+AGG 0.657049 3_3:-1929147 Msa0437920:CDS
AATGAGAGTGATGAGACGCA+AGG 0.663400 3_3:-1928981 Msa0437920:CDS
AGTGGGAGAAATGAGTTGCA+TGG 0.665035 3_3:+1929279 None:intergenic
AGGCGACCAAGACACCACAA+TGG 0.710774 3_3:-1929150 Msa0437920:CDS
GAAGAAATGCATGCATTGTG+AGG 0.712899 3_3:-1929170 Msa0437920:CDS
GTTGCATGGTTGAATGATGG+GGG 0.728694 3_3:+1929293 None:intergenic
GGAGCGTGTACGTCTCACTG+TGG 0.764287 3_3:+1929342 None:intergenic
ATCATCGTCAGTGAACAAGG+AGG 0.776115 3_3:-1929410 Msa0437920:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGTTTTCTTTTTCTTCT+TGG + chr3_3:1929223-1929242 None:intergenic 25.0%
! CAAGAAGAAAAAGAAAACAA+AGG - chr3_3:1929221-1929240 Msa0437920:CDS 25.0%
ATGACATTCTTTCATTGGAA+TGG - chr3_3:1928962-1928981 Msa0437920:CDS 30.0%
AAAAGAATCGTCCACAATAT+CGG + chr3_3:1928992-1929011 None:intergenic 30.0%
GGGAAATGACATTCTTTCAT+TGG - chr3_3:1928957-1928976 Msa0437920:CDS 35.0%
! ACTGTGGTATTTTCACAAGT+GGG + chr3_3:1929105-1929124 None:intergenic 35.0%
TCCAGGAGATCATAATACTT+TGG - chr3_3:1929260-1929279 Msa0437920:CDS 35.0%
! ACCAAAGTATTATGATCTCC+TGG + chr3_3:1929264-1929283 None:intergenic 35.0%
AGACGCAAGGATAATAATTC+TGG - chr3_3:1929492-1929511 Msa0437920:CDS 35.0%
GCTCAACTTCTTTCAATGTG+AGG + chr3_3:1929023-1929042 None:intergenic 40.0%
TGGGTGAACTTATGCTTTCA+GGG + chr3_3:1929086-1929105 None:intergenic 40.0%
! CACTGTGGTATTTTCACAAG+TGG + chr3_3:1929106-1929125 None:intergenic 40.0%
AGTTGCATGGTTGAATGATG+GGG + chr3_3:1929171-1929190 None:intergenic 40.0%
GAGTTGCATGGTTGAATGAT+GGG + chr3_3:1929172-1929191 None:intergenic 40.0%
TGAGTTGCATGGTTGAATGA+TGG + chr3_3:1929173-1929192 None:intergenic 40.0%
GAAGAAATGCATGCATTGTG+AGG - chr3_3:1929290-1929309 Msa0437920:CDS 40.0%
!! CAAGCATTGCAGAGTGTTTT+CGG + chr3_3:1929354-1929373 None:intergenic 40.0%
AAAACACTCTGCAATGCTTG+CGG - chr3_3:1929354-1929373 Msa0437920:CDS 40.0%
GAAGATCCGGAGAAAATGTT+GGG + chr3_3:1929431-1929450 None:intergenic 40.0%
TGAAGATCCGGAGAAAATGT+TGG + chr3_3:1929432-1929451 None:intergenic 40.0%
TGTGAGTTAGAGTGAAGATC+CGG + chr3_3:1929444-1929463 None:intergenic 40.0%
GTCTCATCACTCTCATTTCA+AGG + chr3_3:1929476-1929495 None:intergenic 40.0%
TAATTCTGGTATTCTCGCCT+TGG - chr3_3:1929506-1929525 Msa0437920:CDS 40.0%
ACCATCATCGTCAGTGAACA+AGG - chr3_3:1929047-1929066 Msa0437920:CDS 45.0%
TCCTTGTTCACTGACGATGA+TGG + chr3_3:1929051-1929070 None:intergenic 45.0%
ATCATCGTCAGTGAACAAGG+AGG - chr3_3:1929050-1929069 Msa0437920:CDS 45.0%
GTGGGTGAACTTATGCTTTC+AGG + chr3_3:1929087-1929106 None:intergenic 45.0%
GTTGCATGGTTGAATGATGG+GGG + chr3_3:1929170-1929189 None:intergenic 45.0%
AGTGGGAGAAATGAGTTGCA+TGG + chr3_3:1929184-1929203 None:intergenic 45.0%
! GACTCTAGAGAAGAGGAAGT+GGG + chr3_3:1929201-1929220 None:intergenic 45.0%
! CTTCTTGGACTCTAGAGAAG+AGG + chr3_3:1929208-1929227 None:intergenic 45.0%
!! GAAAATGTTGGGCTAGCAAC+AGG + chr3_3:1929420-1929439 None:intergenic 45.0%
! TGCTAGCCCAACATTTTCTC+CGG - chr3_3:1929422-1929441 Msa0437920:CDS 45.0%
AATGAGAGTGATGAGACGCA+AGG - chr3_3:1929479-1929498 Msa0437920:CDS 45.0%
GGAATGGCAGTCCGATATTG+TGG - chr3_3:1928978-1928997 Msa0437920:CDS 50.0%
! GGACTCTAGAGAAGAGGAAG+TGG + chr3_3:1929202-1929221 None:intergenic 50.0%
TGACCTCCATTGTGGTGTCT+TGG + chr3_3:1929319-1929338 None:intergenic 50.0%
AAGACACCACAATGGAGGTC+AGG - chr3_3:1929318-1929337 Msa0437920:CDS 50.0%
AGACACCACAATGGAGGTCA+GGG - chr3_3:1929319-1929338 Msa0437920:CDS 50.0%
TAGCAACAGGCCGGTATTCA+GGG + chr3_3:1929407-1929426 None:intergenic 50.0%
GGTTGCAAGACGTGTACGCT+TGG + chr3_3:1929142-1929161 None:intergenic 55.0%
! GGTTGAATGATGGGGGCTGA+AGG + chr3_3:1929163-1929182 None:intergenic 55.0%
TCTCCTGGAGCAGCAAGAAG+AGG + chr3_3:1929249-1929268 None:intergenic 55.0%
AGGCGACCAAGACACCACAA+TGG - chr3_3:1929310-1929329 Msa0437920:CDS 55.0%
CGACCAAGACACCACAATGG+AGG - chr3_3:1929313-1929332 Msa0437920:CDS 55.0%
TCTGCAATGCTTGCGGCGTT+CGG - chr3_3:1929361-1929380 Msa0437920:CDS 55.0%
! GCCGACTTTGCCCTGAATAC+CGG - chr3_3:1929394-1929413 Msa0437920:CDS 55.0%
GCCGGTATTCAGGGCAAAGT+CGG + chr3_3:1929398-1929417 None:intergenic 55.0%
CTAGCAACAGGCCGGTATTC+AGG + chr3_3:1929408-1929427 None:intergenic 55.0%
!! ATGTTGGGCTAGCAACAGGC+CGG + chr3_3:1929416-1929435 None:intergenic 55.0%
GGAGCGTGTACGTCTCACTG+TGG + chr3_3:1929121-1929140 None:intergenic 60.0%
TCTGGCCCTGACCTCCATTG+TGG + chr3_3:1929327-1929346 None:intergenic 60.0%
ACAATGGAGGTCAGGGCCAG+AGG - chr3_3:1929326-1929345 Msa0437920:CDS 60.0%
CAATGGAGGTCAGGGCCAGA+GGG - chr3_3:1929327-1929346 Msa0437920:CDS 60.0%
AATGGAGGTCAGGGCCAGAG+GGG - chr3_3:1929328-1929347 Msa0437920:CDS 60.0%
!! CAGAGTGTTTTCGGCCCCTC+TGG + chr3_3:1929345-1929364 None:intergenic 60.0%
TGCGGCGTTCGGTACAAGTC+AGG - chr3_3:1929372-1929391 Msa0437920:CDS 60.0%
GCGCCTCTTCTTGCTGCTCC+AGG - chr3_3:1929243-1929262 Msa0437920:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 1928943 1929539 1928943 ID=Msa0437920;Name=Msa0437920
chr3_3 mRNA 1928943 1929539 1928943 ID=Msa0437920-mRNA-1;Parent=Msa0437920;Name=Msa0437920-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|198
chr3_3 exon 1928943 1929539 1928943 ID=Msa0437920-mRNA-1:exon:402;Parent=Msa0437920-mRNA-1
chr3_3 CDS 1928943 1929539 1928943 ID=Msa0437920-mRNA-1:cds;Parent=Msa0437920-mRNA-1
Gene Sequence

>Msa0437920

TTGTTATTATTACAGGGAAATGACATTCTTTCATTGGAATGGCAGTCCGATATTGTGGACGATTCTTTTGATGAGAGCCTCACATTGAAAGAAGTTGAGCAACAACCATCATCGTCAGTGAACAAGGAGGATTTTGTACTCCCTGAAAGCATAAGTTCACCCACTTGTGAAAATACCACAGTGAGACGTACACGCTCCAAGCGTACACGTCTTGCAACCTTCAGCCCCCATCATTCAACCATGCAACTCATTTCTCCCACTTCCTCTTCTCTAGAGTCCAAGAAGAAAAAGAAAACAAAGGCGCCTCTTCTTGCTGCTCCAGGAGATCATAATACTTTGGTACTTGTGAAGAAATGCATGCATTGTGAGGCGACCAAGACACCACAATGGAGGTCAGGGCCAGAGGGGCCGAAAACACTCTGCAATGCTTGCGGCGTTCGGTACAAGTCAGGCCGACTTTGCCCTGAATACCGGCCTGTTGCTAGCCCAACATTTTCTCCGGATCTTCACTCTAACTCACATAAGAAGATCCTTGAAATGAGAGTGATGAGACGCAAGGATAATAATTCTGGTATTCTCGCCTTGGAATACGTGTGA
Protein sequence

>Msa0437920

LLLLQGNDILSLEWQSDIVDDSFDESLTLKEVEQQPSSSVNKEDFVLPESISSPTCENTTVRRTRSKRTRLATFSPHHSTMQLISPTSSSLESKKKKKTKAPLLAAPGDHNTLVLVKKCMHCEATKTPQWRSGPEGPKTLCNACGVRYKSGRLCPEYRPVASPTFSPDLHSNSHKKILEMRVMRRKDNNSGILALEYV*