AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0905430

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905430 MtrunA17_Chr6g0453341 84.314 102 3 1 4 92 153 254 6.43e-53 165
Msa0905430 MtrunA17_Chr7g0217661 77.451 102 10 1 4 92 141 242 5.75e-48 152
Msa0905430 MtrunA17_Chr5g0417701 70.000 100 17 1 4 90 148 247 5.94e-41 134
Msa0905430 MtrunA17_Chr4g0042521 66.337 101 21 1 4 91 148 248 1.86e-39 130
Msa0905430 MtrunA17_Chr3g0107311 66.000 100 21 1 4 90 155 254 8.43e-39 129
Msa0905430 MtrunA17_Chr3g0107291 66.000 100 21 1 4 90 161 260 9.87e-39 129
Msa0905430 MtrunA17_Chr3g0128801 68.000 100 19 1 4 90 154 253 2.13e-38 128
Msa0905430 MtrunA17_Chr5g0432611 63.000 100 24 1 4 90 152 251 1.04e-37 126
Msa0905430 MtrunA17_Chr3g0128791 67.000 100 20 1 4 90 154 253 2.45e-37 125
Msa0905430 MtrunA17_Chr3g0092071 61.000 100 26 1 4 90 148 247 6.97e-35 119
Msa0905430 MtrunA17_Chr7g0238681 54.000 100 33 1 4 90 157 256 9.83e-29 103
Msa0905430 MtrunA17_Chr5g0435311 52.000 100 35 1 4 90 207 306 1.04e-27 102
Msa0905430 MtrunA17_Chr2g0328261 53.000 100 34 1 4 90 159 258 1.59e-27 100
Msa0905430 MtrunA17_Chr1g0193631 51.515 99 34 1 4 88 156 254 1.94e-27 100
Msa0905430 MtrunA17_Chr4g0031621 53.000 100 34 1 4 90 157 256 2.72e-25 94.7
Msa0905430 MtrunA17_Chr7g0271001 50.000 96 34 1 4 85 153 248 1.33e-24 92.8
Msa0905430 MtrunA17_Chr1g0157061 44.898 98 41 1 4 88 141 238 1.54e-24 92.4
Msa0905430 MtrunA17_Chr4g0021561 45.000 100 42 1 4 90 157 256 2.00e-24 92.4
Msa0905430 MtrunA17_Chr5g0433841 42.157 102 46 1 4 92 165 266 5.98e-24 91.3
Msa0905430 MtrunA17_Chr4g0069711 43.434 99 42 1 4 88 184 282 7.45e-23 89.0
Msa0905430 MtrunA17_Chr2g0324181 42.718 103 46 1 1 90 15 117 1.14e-22 84.3
Msa0905430 MtrunA17_Chr3g0109801 43.000 100 44 1 4 90 185 284 7.01e-22 86.3
Msa0905430 MtrunA17_Chr7g0218741 44.000 100 42 1 4 89 152 251 2.65e-19 79.0
Msa0905430 MtrunA17_Chr4g0022841 40.206 97 45 1 4 87 20 116 7.16e-19 74.7
Msa0905430 MtrunA17_Chr7g0218751 47.423 97 38 1 4 87 151 247 2.38e-18 76.3
Msa0905430 MtrunA17_Chr8g0360041 45.361 97 40 1 4 87 154 250 4.06e-18 75.9
Msa0905430 MtrunA17_Chr7g0218761 41.837 98 44 1 4 88 112 209 1.00e-16 71.6
Msa0905430 MtrunA17_Chr8g0360721 43.158 95 41 1 4 85 121 215 2.04e-16 70.9
Msa0905430 MtrunA17_Chr5g0398271 40.404 99 45 3 4 88 161 259 2.12e-15 68.6
Msa0905430 MtrunA17_Chr8g0359971 41.558 77 31 1 24 86 1 77 9.41e-13 58.2
Msa0905430 MtrunA17_Chr1g0193571 56.522 46 20 0 43 88 12 57 2.41e-12 56.6
Msa0905430 MtrunA17_Chr4g0057091 37.113 97 47 3 4 86 160 256 1.80e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905430 AT3G29030.1 72.549 102 15 1 4 92 154 255 2.28e-44 144
Msa0905430 AT1G26770.1 67.000 100 20 1 4 90 149 248 5.07e-40 132
Msa0905430 AT1G26770.2 67.000 100 20 1 4 90 159 258 5.98e-40 132
Msa0905430 AT2G03090.1 67.000 100 20 1 4 90 153 252 4.34e-39 130
Msa0905430 AT1G69530.2 66.000 100 21 1 4 90 150 249 2.75e-36 123
Msa0905430 AT1G69530.1 66.000 100 21 1 4 90 150 249 2.75e-36 123
Msa0905430 AT2G40610.1 62.376 101 24 1 4 90 153 253 4.91e-36 122
Msa0905430 AT5G56320.1 61.000 100 26 1 4 90 152 251 1.25e-35 121
Msa0905430 AT5G56320.2 61.000 100 26 1 4 90 152 251 1.25e-35 121
Msa0905430 AT5G56320.3 61.000 100 26 1 4 90 152 251 2.68e-35 122
Msa0905430 AT1G69530.3 66.667 96 19 1 4 86 150 245 1.07e-34 119
Msa0905430 AT5G05290.1 54.455 101 32 1 4 90 155 255 2.74e-31 110
Msa0905430 AT5G02260.1 57.000 100 30 1 4 90 157 256 1.49e-30 108
Msa0905430 AT2G37640.2 55.000 100 32 1 4 90 136 235 4.33e-29 104
Msa0905430 AT3G55500.1 53.000 100 34 1 4 90 159 258 7.20e-29 104
Msa0905430 AT2G37640.1 55.000 100 32 1 4 90 161 260 8.35e-29 104
Msa0905430 AT2G39700.1 52.000 100 35 1 4 90 156 255 5.75e-28 102
Msa0905430 AT1G20190.2 52.083 96 33 1 4 86 93 188 1.03e-26 97.1
Msa0905430 AT1G20190.1 52.083 96 33 1 4 86 152 247 4.20e-26 97.1
Msa0905430 AT2G28950.1 55.000 100 32 1 4 90 156 255 7.79e-26 96.7
Msa0905430 AT4G01630.1 46.875 96 37 1 4 85 154 249 2.30e-22 87.4
Msa0905430 AT4G38210.1 46.000 100 41 1 4 90 155 254 4.56e-22 86.7
Msa0905430 AT3G15370.1 44.231 104 42 2 4 91 149 252 2.60e-21 84.7
Msa0905430 AT3G03220.1 41.000 100 46 1 4 90 164 263 3.68e-21 84.3
Msa0905430 AT3G15370.2 44.231 104 42 2 4 91 179 282 4.59e-21 84.3
Msa0905430 AT1G69530.4 52.809 89 21 2 4 90 150 219 7.67e-20 80.1
Msa0905430 AT5G39270.1 42.857 98 43 1 4 88 179 276 3.68e-19 79.3
Msa0905430 AT5G39290.1 41.837 98 44 1 4 88 179 276 3.92e-19 79.3
Msa0905430 AT1G69530.5 52.941 85 19 2 4 86 150 215 2.66e-18 76.6
Msa0905430 AT1G12560.1 46.875 96 37 3 4 85 160 255 1.12e-17 75.1
Msa0905430 AT1G62980.1 43.434 99 42 3 4 88 155 253 4.30e-16 70.9
Msa0905430 AT5G39280.1 37.755 98 48 1 4 88 175 272 1.74e-15 69.3
Msa0905430 AT5G39300.1 37.755 98 48 1 4 88 176 273 1.93e-15 69.3
Msa0905430 AT5G39260.1 39.796 98 46 1 4 88 162 259 3.21e-15 68.6
Msa0905430 AT5G39310.1 37.374 99 48 2 4 88 211 309 1.94e-12 61.2

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAGTCCTTGAACCTTTGA+TGG 0.288910 6_2:+3565083 None:intergenic
CAAAGGTTCAAGGACTAAAT+TGG 0.294728 6_2:-3565079 Msa0905430:intron
GCCCCACCCAGTTGGTCCTT+TGG 0.320692 6_2:-3564972 Msa0905430:CDS
CAGAGTAACTCTTATTTGAA+TGG 0.388733 6_2:-3565056 Msa0905430:CDS
TTAGTTCTTGTGACTAATGT+TGG 0.397492 6_2:-3565132 Msa0905430:CDS
GGTTTGTCCAAAGGACCAAC+TGG 0.413288 6_2:+3564965 None:intergenic
TTTGTAGTCACCACTGGTAA+TGG 0.425157 6_2:-3565020 Msa0905430:CDS
GTGACTAATGTTGGAGGTGC+AGG 0.476012 6_2:-3565123 Msa0905430:CDS
GGAATAACGTTCACAATCAA+TGG 0.478951 6_2:-3565171 Msa0905430:CDS
CTTTCATTTGTAGTCACCAC+TGG 0.482315 6_2:-3565026 Msa0905430:CDS
TCCAAAGGACCAACTGGGTG+GGG 0.487484 6_2:+3564971 None:intergenic
GTTCTTGTGACTAATGTTGG+AGG 0.514997 6_2:-3565129 Msa0905430:CDS
TTAATGTTGCCCCACCCAGT+TGG 0.531923 6_2:-3564980 Msa0905430:CDS
TTTAAAGGGTTGGTTAGTAG+AGG 0.543847 6_2:+3564925 None:intergenic
TCCTTTGGACAAACCTACAC+TGG 0.547722 6_2:-3564957 Msa0905430:CDS
GAGGAACTGCCTTCCAGTGT+AGG 0.551003 6_2:+3564944 None:intergenic
GTCCAAAGGACCAACTGGGT+GGG 0.563335 6_2:+3564970 None:intergenic
TCCAGTGTAGGTTTGTCCAA+AGG 0.584012 6_2:+3564956 None:intergenic
GTGCATTCTGTAGCCATCAA+AGG 0.587053 6_2:-3565096 Msa0905430:intron
TGTCCAAAGGACCAACTGGG+TGG 0.615300 6_2:+3564969 None:intergenic
TTGGACAAACCTACACTGGA+AGG 0.627049 6_2:-3564953 Msa0905430:CDS
GTTTGTCCAAAGGACCAACT+GGG 0.667033 6_2:+3564966 None:intergenic
AATACTATGACCATTACCAG+TGG 0.725625 6_2:+3565010 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATCTTTTACTACTTGTT+TGG - chr6_2:3564973-3564992 Msa0905430:CDS 20.0%
!! AAGAAAAAAAGTTAGCTTCA+TGG + chr6_2:3564999-3565018 None:intergenic 25.0%
!! ATGCATGCTTTTTGATTGAA+GGG - chr6_2:3565020-3565039 Msa0905430:CDS 30.0%
! TTAGTTCTTGTGACTAATGT+TGG - chr6_2:3565102-3565121 Msa0905430:CDS 30.0%
! CAGAGTAACTCTTATTTGAA+TGG - chr6_2:3565178-3565197 Msa0905430:CDS 30.0%
!! CATGCATGCTTTTTGATTGA+AGG - chr6_2:3565019-3565038 Msa0905430:CDS 35.0%
!! TGCTTTTTGATTGAAGGGTA+AGG - chr6_2:3565025-3565044 Msa0905430:CDS 35.0%
GGAATAACGTTCACAATCAA+TGG - chr6_2:3565063-3565082 Msa0905430:CDS 35.0%
TTTAGTCCTTGAACCTTTGA+TGG + chr6_2:3565154-3565173 None:intergenic 35.0%
CAAAGGTTCAAGGACTAAAT+TGG - chr6_2:3565155-3565174 Msa0905430:CDS 35.0%
AATACTATGACCATTACCAG+TGG + chr6_2:3565227-3565246 None:intergenic 35.0%
AGGGTAAGGTGTAGAAAAAG+AGG - chr6_2:3565039-3565058 Msa0905430:CDS 40.0%
GTAAGGTGTAGAAAAAGAGG+TGG - chr6_2:3565042-3565061 Msa0905430:CDS 40.0%
GTTCTTGTGACTAATGTTGG+AGG - chr6_2:3565105-3565124 Msa0905430:CDS 40.0%
CTTTCATTTGTAGTCACCAC+TGG - chr6_2:3565208-3565227 Msa0905430:intron 40.0%
TTTGTAGTCACCACTGGTAA+TGG - chr6_2:3565214-3565233 Msa0905430:intron 40.0%
GTGCATTCTGTAGCCATCAA+AGG - chr6_2:3565138-3565157 Msa0905430:CDS 45.0%
CTGTAGCCATCAAAGGTTCA+AGG - chr6_2:3565145-3565164 Msa0905430:CDS 45.0%
GTTTGTCCAAAGGACCAACT+GGG + chr6_2:3565271-3565290 None:intergenic 45.0%
TCCTTTGGACAAACCTACAC+TGG - chr6_2:3565277-3565296 Msa0905430:intron 45.0%
TCCAGTGTAGGTTTGTCCAA+AGG + chr6_2:3565281-3565300 None:intergenic 45.0%
TTGGACAAACCTACACTGGA+AGG - chr6_2:3565281-3565300 Msa0905430:intron 45.0%
! GTGACTAATGTTGGAGGTGC+AGG - chr6_2:3565111-3565130 Msa0905430:CDS 50.0%
TTAATGTTGCCCCACCCAGT+TGG - chr6_2:3565254-3565273 Msa0905430:intron 50.0%
GGTTTGTCCAAAGGACCAAC+TGG + chr6_2:3565272-3565291 None:intergenic 50.0%
TCCAAAGGACCAACTGGGTG+GGG + chr6_2:3565266-3565285 None:intergenic 55.0%
GTCCAAAGGACCAACTGGGT+GGG + chr6_2:3565267-3565286 None:intergenic 55.0%
TGTCCAAAGGACCAACTGGG+TGG + chr6_2:3565268-3565287 None:intergenic 55.0%
GAGGAACTGCCTTCCAGTGT+AGG + chr6_2:3565293-3565312 None:intergenic 55.0%
GCCCCACCCAGTTGGTCCTT+TGG - chr6_2:3565262-3565281 Msa0905430:intron 65.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 3564938 3565318 3564938 ID=Msa0905430;Name=Msa0905430
chr6_2 mRNA 3564938 3565318 3564938 ID=Msa0905430-mRNA-1;Parent=Msa0905430;Name=Msa0905430-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|3|0|92
chr6_2 exon 3565311 3565318 3565311 ID=Msa0905430-mRNA-1:exon:1079;Parent=Msa0905430-mRNA-1
chr6_2 exon 3565097 3565215 3565097 ID=Msa0905430-mRNA-1:exon:1078;Parent=Msa0905430-mRNA-1
chr6_2 exon 3564938 3565089 3564938 ID=Msa0905430-mRNA-1:exon:1077;Parent=Msa0905430-mRNA-1
chr6_2 CDS 3565311 3565318 3565311 ID=Msa0905430-mRNA-1:cds;Parent=Msa0905430-mRNA-1
chr6_2 CDS 3565097 3565215 3565097 ID=Msa0905430-mRNA-1:cds;Parent=Msa0905430-mRNA-1
chr6_2 CDS 3564938 3565089 3564938 ID=Msa0905430-mRNA-1:cds;Parent=Msa0905430-mRNA-1
Gene Sequence

>Msa0905430

ATGACTATGGTAAGGTGTAGAAAAAGAGGTGGAATAACGTTCACAATCAATGGTCATTCTTACTTCAATTTAGTTCTTGTGACTAATGTTGGAGGTGCAGGTGATGTGCATTCTGTAGCCATCAAAGGACTAAATTGGCAGAGTAACTCTTATTTGAATGGACAAAGTCTTTCATTTGTAGTCACCACTGGTAATGGTCATAGTATTGTGTCATTTAATGTTGCCCCACCCAGTTGGTCCTTTGGACAAACCTACACTGGAAGGCAGTTCCTCTACTAA
Protein sequence

>Msa0905430

MTMVRCRKRGGITFTINGHSYFNLVLVTNVGGAGDVHSVAIKGLNWQSNSYLNGQSLSFVVTTGNGHSIVSFNVAPPSWSFGQTYTGRQFLY*