AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG002977


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002977 MtrunA17_Chr1g0180311 96.970 297 7 2 1 295 1 297 0.0 595
MsaG002977 MtrunA17_Chr1g0197281 36.944 360 145 15 5 295 9 355 5.20e-50 169
MsaG002977 MtrunA17_Chr4g0027991 38.629 321 137 11 3 295 5 293 2.57e-49 165
MsaG002977 MtrunA17_Chr2g0320311 38.486 317 136 15 9 295 10 297 1.87e-47 160
MsaG002977 MtrunA17_Chr7g0263121 37.572 173 67 5 68 240 3 134 3.50e-26 101
MsaG002977 MtrunA17_Chr7g0222831 42.553 141 38 3 80 220 12 109 1.71e-25 100
MsaG002977 MtrunA17_Chr1g0212561 42.553 141 44 4 80 220 16 119 3.65e-25 99.8
MsaG002977 MtrunA17_Chr1g0182161 34.975 203 81 5 68 269 4 156 1.11e-23 95.1
MsaG002977 MtrunA17_Chr1g0182181 38.125 160 52 5 72 230 3 116 1.22e-21 89.4
MsaG002977 MtrunA17_Chr4g0012791 33.906 233 100 8 76 264 158 380 1.63e-21 94.0
MsaG002977 MtrunA17_Chr1g0207451 32.804 189 79 5 76 264 56 196 8.31e-20 86.7
MsaG002977 MtrunA17_Chr1g0152661 37.436 195 88 6 76 269 39 200 8.50e-20 86.3
MsaG002977 MtrunA17_Chr1g0188911 35.152 165 87 4 111 263 37 193 2.11e-19 84.0
MsaG002977 MtrunA17_Chr3g0134711 32.308 195 97 5 76 269 48 208 4.25e-17 79.0
MsaG002977 MtrunA17_Chr4g0061301 35.057 174 83 7 104 264 331 487 1.27e-16 79.7
MsaG002977 MtrunA17_Chr1g0188901 34.568 162 86 3 102 263 44 185 7.36e-16 74.3
MsaG002977 MtrunA17_Chr4g0012691 34.014 147 76 2 118 264 220 345 9.35e-15 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002977 AT5G03510.1 39.871 311 147 15 3 295 4 292 9.12e-55 179
MsaG002977 AT5G04390.1 35.112 356 145 13 19 295 14 362 1.93e-49 168
MsaG002977 AT2G28200.1 38.014 292 161 7 11 295 8 286 4.37e-49 165
MsaG002977 AT3G10470.1 31.043 393 144 14 19 295 17 398 4.18e-37 136
MsaG002977 AT2G37430.1 32.870 216 94 7 68 279 3 171 1.42e-21 89.7
MsaG002977 AT2G28710.1 32.701 211 83 8 68 276 3 156 5.86e-21 87.8
MsaG002977 AT2G45120.1 32.367 207 90 7 77 276 148 311 6.80e-20 88.2
MsaG002977 AT3G19580.1 34.872 195 95 8 76 266 67 233 1.75e-19 86.3
MsaG002977 AT3G19580.2 34.872 195 95 8 76 266 67 233 1.75e-19 86.3
MsaG002977 AT1G02040.1 35.079 191 112 5 76 265 107 286 8.41e-19 85.5
MsaG002977 AT3G53600.1 32.512 203 85 7 68 267 3 156 1.91e-18 81.3
MsaG002977 AT5G67450.1 32.039 206 100 7 76 266 60 240 4.15e-18 82.0
MsaG002977 AT3G60580.1 30.144 209 94 7 77 277 124 288 2.05e-17 80.9
MsaG002977 AT3G46080.1 35.057 174 58 5 70 235 4 130 5.77e-17 77.0
MsaG002977 AT3G49930.1 34.694 147 62 4 76 219 56 171 5.80e-16 75.5
MsaG002977 AT2G17180.1 29.508 183 80 5 75 241 120 269 2.65e-14 72.0
MsaG002977 AT1G27730.1 34.759 187 79 6 76 262 51 194 4.31e-14 70.5
MsaG002977 AT4G35280.1 36.054 147 53 4 75 219 137 244 1.58e-13 69.7
MsaG002977 AT5G56200.1 37.069 116 63 3 120 235 344 449 9.79e-12 65.5

Find 48 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTTCTCTAATTCTTCTT+TGG 0.193682 1:-50028391 MsaT002977.1:CDS
GTAGTAGTAATAGTAGTAAT+AGG 0.197989 1:+50028690 None:intergenic
TTCTTTGCTTCATGAGATTT+AGG 0.214536 1:+50028513 None:intergenic
TAGTAGTAATAGTAGTAATA+GGG 0.291671 1:+50028691 None:intergenic
CATACACAACAAATCATAAA+AGG 0.299770 1:-50029197 MsaT002977.1:CDS
AATAATAGCAACAACAATTC+TGG 0.306288 1:-50029089 MsaT002977.1:CDS
ACATTACAATTTGCCTTGTT+AGG 0.331743 1:+50028813 None:intergenic
TTCTCATCGGGGCAAGCGTT+AGG 0.342012 1:-50028624 MsaT002977.1:CDS
CAAAGAGAGTATGGTATTCA+TGG 0.363698 1:+50028731 None:intergenic
CGCTTGCCCCGATGAGAATT+CGG 0.366069 1:+50028629 None:intergenic
TTCCCTTCATTTCAAGCACT+TGG 0.369504 1:-50028861 MsaT002977.1:CDS
ACAATTTGCCTTGTTAGGTT+TGG 0.388660 1:+50028818 None:intergenic
GTTTCAAATTCTTGCAATGA+AGG 0.402330 1:-50029122 MsaT002977.1:CDS
TCTCATCGGGGCAAGCGTTA+GGG 0.409631 1:-50028623 MsaT002977.1:CDS
GAAGGCTTGCAAAGAGAGTA+TGG 0.416171 1:+50028722 None:intergenic
TCTAGGCTGAAACGAAAACT+TGG 0.422075 1:+50028425 None:intergenic
TTTCTCTAATTCTTCTTTGG+TGG 0.430350 1:-50028388 MsaT002977.1:CDS
CCTTCATTTCAAGCACTTGG+TGG 0.431156 1:-50028858 MsaT002977.1:CDS
CCACCAAGTGCTTGAAATGA+AGG 0.452956 1:+50028858 None:intergenic
TCCACTTAGGTTAACTATGC+CGG 0.455854 1:-50029144 MsaT002977.1:CDS
GATTTGTTGTGTATGATCCT+TGG 0.463931 1:+50029205 None:intergenic
TGTGGTGCCGAATTCTCATC+GGG 0.470426 1:-50028636 MsaT002977.1:CDS
ACTCTCTTTGCAAGCCTTCG+CGG 0.480099 1:-50028718 MsaT002977.1:CDS
TCATTGCAAGAATTTGAAAC+CGG 0.487346 1:+50029125 None:intergenic
TCCAACTTAAAACCATTCCT+AGG 0.495975 1:+50028489 None:intergenic
GGGGACATATGCGGAGACAT+AGG 0.522526 1:-50028602 MsaT002977.1:CDS
CTCATCGGGGCAAGCGTTAG+GGG 0.525637 1:-50028622 MsaT002977.1:CDS
ATGTGGTGCCGAATTCTCAT+CGG 0.538737 1:-50028637 MsaT002977.1:CDS
AGTAATAGGGGTTGCCGCGA+AGG 0.540108 1:+50028704 None:intergenic
AGTAGTAATAGTAGTAATAG+GGG 0.550970 1:+50028692 None:intergenic
TGTCTCATTCTATTAGCTCA+AGG 0.553385 1:-50028993 MsaT002977.1:CDS
GAAAACGAACAAAGCGTCAA+AGG 0.554393 1:-50029175 MsaT002977.1:CDS
GAGAGTATGGTATTCATGGT+TGG 0.560913 1:+50028735 None:intergenic
AAAGGCTACCATCTCCACTT+AGG 0.563673 1:-50029157 MsaT002977.1:CDS
CTTGGAAGATCAACTCGTGA+TGG 0.581786 1:-50029231 MsaT002977.1:CDS
AACTTGAGGAACTTTAGTAA+TGG 0.582855 1:+50028361 None:intergenic
ATAGTTAACCTAAGTGGAGA+TGG 0.586474 1:+50029149 None:intergenic
TCAACTCGTGATGGTTTCCA+AGG 0.587185 1:-50029222 MsaT002977.1:CDS
ACCGGCATAGTTAACCTAAG+TGG 0.587977 1:+50029143 None:intergenic
AAGTCATACCAAACCTAACA+AGG 0.591535 1:-50028826 MsaT002977.1:CDS
CACCAAGTGCTTGAAATGAA+GGG 0.594958 1:+50028859 None:intergenic
TCATCGGGGCAAGCGTTAGG+GGG 0.598586 1:-50028621 MsaT002977.1:CDS
CTCATGAAGCAAAGAAACCT+AGG 0.601432 1:-50028506 MsaT002977.1:CDS
GTTCATGAGTGTTCGATATG+TGG 0.609307 1:-50028654 MsaT002977.1:CDS
GAAGCAAAGAAACCTAGGAA+TGG 0.624910 1:-50028501 MsaT002977.1:CDS
ACTTCTATGAGTTTGAGTAT+CGG 0.635000 1:-50028540 MsaT002977.1:CDS
AATAGCAACAACAATTCTGG+AGG 0.652305 1:-50029086 MsaT002977.1:CDS
GTGGTGCCGAATTCTCATCG+GGG 0.789843 1:-50028635 MsaT002977.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 50028374 50029261 50028374 ID=MsaG002977
Chr1 mRNA 50028374 50029261 50028374 ID=MsaT002977.1;Parent=MsaG002977
Chr1 exon 50028374 50029261 50028374 ID=MsaT002977.1.exon1;Parent=MsaT002977.1
Chr1 CDS 50028374 50029261 50028374 ID=cds.MsaT002977.1;Parent=MsaT002977.1
Gene Sequence

>MsaT002977.1

ATGCAAGTCTTGGAAGATCAACTCGTGATGGTTTCCAAGGATCATACACAACAAATCATAAAAGGAAAACGAACAAAGCGTCAAAGGCTACCATCTCCACTTAGGTTAACTATGCCGGTTTCAAATTCTTGCAATGAAGGTACAAGTTATAATAATAGCAACAACAATTCTGGAGGAATTGAGTTTGTTAAAATTGATTCGCGCGACCGATCAGAAGAAGAAAAAGAAGAAGAAGATTTGGCGAATTGTCTCATTCTATTAGCTCAAGGTCATAATCATCGTCATGATCAAAACACACATGTATCAAATCATCGCGATCACAATAACAACAAATCTTCAAATTTTTATCTTTACGAATGCAAGACTTGCAATCGTTGCTTCCCTTCATTTCAAGCACTTGGTGGACATAGAGCAAGTCATACCAAACCTAACAAGGCAAATTGTAATGTTACACAACAAAAGCAAGCAGTTACAACATCGTCTTTTGTTGATGATCATTATGATCCAACCATGAATACCATACTCTCTTTGCAAGCCTTCGCGGCAACCCCTATTACTACTATTACTACTACAAAAAAATCAAAAGTTCATGAGTGTTCGATATGTGGTGCCGAATTCTCATCGGGGCAAGCGTTAGGGGGACATATGCGGAGACATAGGAATCTTGTGAACACGTCTACAACGACAACAACGACGACAACTTCTATGAGTTTGAGTATCGGTAGTCCTAAATCTCATGAAGCAAAGAAACCTAGGAATGGTTTTAAGTTGGATTTGAATCTTCCAGCTCCAGAAGTTGATCAAAAAGATCAATCCAAGTTTTCGTTTCAGCCTAGAGAAAATGTTATTGCTTTCTCTAATTCTTCTTTGGTGGATTGCCATTACTAA

Protein sequence

>MsaT002977.1

MQVLEDQLVMVSKDHTQQIIKGKRTKRQRLPSPLRLTMPVSNSCNEGTSYNNSNNNSGGIEFVKIDSRDRSEEEKEEEDLANCLILLAQGHNHRHDQNTHVSNHRDHNNNKSSNFYLYECKTCNRCFPSFQALGGHRASHTKPNKANCNVTQQKQAVTTSSFVDDHYDPTMNTILSLQAFAATPITTITTTKKSKVHECSICGAEFSSGQALGGHMRRHRNLVNTSTTTTTTTTSMSLSIGSPKSHEAKKPRNGFKLDLNLPAPEVDQKDQSKFSFQPRENVIAFSNSSLVDCHY*