AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0214350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0214350 MtrunA17_Chr2g0315371 85.315 143 21 0 1 143 127 269 7.94e-80 238
Msa0214350 MtrunA17_Chr2g0315361 78.378 148 27 3 1 146 134 278 1.58e-78 234
Msa0214350 MtrunA17_Chr2g0315381 69.863 146 40 2 1 146 130 271 3.29e-68 208
Msa0214350 MtrunA17_Chr8g0350621 53.571 112 43 3 5 111 101 208 1.79e-35 123
Msa0214350 MtrunA17_Chr7g0244981 46.970 132 58 3 5 135 112 232 8.91e-34 119
Msa0214350 MtrunA17_Chr7g0244971 48.624 109 52 2 5 111 113 219 1.19e-31 114
Msa0214350 MtrunA17_Chr8g0334541 48.673 113 44 3 5 111 93 197 1.08e-28 106
Msa0214350 MtrunA17_Chr3g0128671 40.310 129 57 4 10 118 122 250 6.14e-23 91.7
Msa0214350 MtrunA17_Chr5g0428351 38.947 95 57 1 1 95 170 263 3.11e-20 84.3
Msa0214350 MtrunA17_Chr7g0275531 44.086 93 43 1 2 85 96 188 1.13e-19 83.2
Msa0214350 MtrunA17_Chr8g0350631 48.718 78 35 2 36 111 5 79 9.50e-19 77.4
Msa0214350 MtrunA17_Chr8g0347251 41.667 84 41 1 2 77 115 198 3.43e-18 79.3
Msa0214350 MtrunA17_Chr3g0126391 54.098 61 28 0 14 74 132 192 6.29e-18 78.6
Msa0214350 MtrunA17_Chr2g0315401 44.860 107 45 4 45 146 21 118 1.15e-17 74.3
Msa0214350 MtrunA17_Chr8g0387981 43.750 80 37 1 3 74 112 191 3.63e-16 73.9
Msa0214350 MtrunA17_Chr7g0224801 48.052 77 36 2 13 89 91 163 4.61e-15 68.2
Msa0214350 MtrunA17_Chr8g0383351 47.541 61 29 1 13 73 158 215 6.88e-15 68.9
Msa0214350 MtrunA17_Chr2g0315341 42.268 97 43 4 51 143 1 88 2.64e-14 65.1
Msa0214350 MtrunA17_Chr3g0129361 48.333 60 28 1 13 72 142 198 9.28e-14 65.9
Msa0214350 MtrunA17_Chr4g0068541 46.667 60 29 1 14 73 207 263 2.87e-13 65.9
Msa0214350 MtrunA17_Chr5g0418781 49.153 59 27 1 14 72 123 178 3.35e-13 65.1
Msa0214350 MtrunA17_Chr8g0335811 48.333 60 28 1 13 72 152 208 4.62e-13 63.9
Msa0214350 MtrunA17_Chr8g0386241 44.262 61 31 1 13 73 101 158 8.56e-13 62.4
Msa0214350 MtrunA17_Chr7g0270191 47.458 59 28 1 14 72 144 199 9.34e-13 63.9
Msa0214350 MtrunA17_Chr5g0418191 37.255 102 48 3 13 109 318 408 1.05e-12 64.3
Msa0214350 MtrunA17_Chr4g0051881 50.847 59 26 1 14 72 177 232 1.12e-12 63.9
Msa0214350 MtrunA17_Chr5g0443131 49.153 59 27 1 14 72 156 211 1.16e-12 63.5
Msa0214350 MtrunA17_Chr7g0218081 46.667 60 29 1 13 72 408 464 2.16e-12 63.2
Msa0214350 MtrunA17_Chr7g0263531 46.774 62 30 1 11 72 357 415 4.49e-12 62.4
Msa0214350 MtrunA17_Chr2g0294231 41.892 74 40 1 14 87 202 272 5.55e-12 62.0
Msa0214350 MtrunA17_Chr1g0194481 45.763 59 29 1 14 72 157 212 5.71e-12 62.0
Msa0214350 MtrunA17_Chr7g0248721 50.000 60 26 2 13 72 139 194 7.17e-12 60.5
Msa0214350 MtrunA17_Chr7g0238921 49.180 61 28 1 13 73 122 179 8.14e-12 61.2
Msa0214350 MtrunA17_Chr2g0322391 47.541 61 30 1 13 73 347 405 1.20e-11 61.2
Msa0214350 MtrunA17_Chr4g0042831 46.667 60 29 1 13 72 276 332 1.46e-11 60.8
Msa0214350 MtrunA17_Chr3g0101131 45.000 60 30 1 13 72 413 469 1.69e-11 60.8
Msa0214350 MtrunA17_Chr5g0445311 45.000 60 30 1 13 72 362 418 1.87e-11 60.5
Msa0214350 MtrunA17_Chr5g0447701 37.500 88 45 3 11 98 248 325 2.06e-11 60.5
Msa0214350 MtrunA17_Chr1g0150801 44.776 67 32 2 8 72 93 156 2.26e-11 58.5
Msa0214350 MtrunA17_Chr5g0431811 42.857 63 36 0 15 77 672 734 3.43e-11 60.1
Msa0214350 MtrunA17_Chr3g0129321 41.667 60 32 1 13 72 116 172 4.71e-11 58.2
Msa0214350 MtrunA17_Chr1g0147881 46.154 65 32 2 8 72 256 317 7.47e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0214350 AT1G66560.1 47.059 102 46 3 15 108 103 204 4.60e-24 94.0
Msa0214350 AT1G66600.1 50.602 83 34 2 14 89 102 184 1.16e-22 90.1
Msa0214350 AT5G22570.1 52.055 73 31 1 16 88 111 179 2.15e-22 90.1
Msa0214350 AT1G66550.2 55.882 68 29 1 15 81 103 170 2.48e-22 89.4
Msa0214350 AT1G66550.1 55.882 68 29 1 15 81 108 175 3.04e-22 89.4
Msa0214350 AT5G01900.1 60.000 60 24 0 16 75 111 170 4.96e-22 89.0
Msa0214350 AT1G80590.1 54.098 61 28 0 16 76 86 146 8.27e-20 82.4
Msa0214350 AT3G56400.1 51.562 64 31 0 11 74 116 179 1.01e-19 83.2
Msa0214350 AT2G46400.1 52.459 61 29 0 14 74 103 163 4.70e-19 81.3
Msa0214350 AT5G24110.1 48.148 81 34 1 2 74 92 172 5.01e-18 79.0
Msa0214350 AT2G40740.1 53.333 60 28 0 15 74 173 232 8.40e-17 75.5
Msa0214350 AT2G40740.3 52.381 63 30 0 15 77 182 244 1.11e-16 75.1
Msa0214350 AT4G23810.1 51.667 60 29 0 15 74 158 217 1.18e-15 72.4
Msa0214350 AT4G11070.2 51.667 60 29 0 15 74 109 168 1.64e-15 71.6
Msa0214350 AT4G11070.1 51.667 60 29 0 15 74 141 200 2.02e-15 71.6
Msa0214350 AT2G40750.1 45.000 60 33 0 15 74 152 211 3.44e-14 68.6
Msa0214350 AT4G39410.1 44.928 69 35 1 13 81 221 286 1.66e-13 66.2
Msa0214350 AT2G37260.1 49.153 59 27 1 14 72 348 403 2.74e-13 66.2
Msa0214350 AT2G37260.3 49.153 59 27 1 14 72 268 323 3.28e-13 65.9
Msa0214350 AT2G37260.2 49.153 59 27 1 14 72 266 321 3.49e-13 65.9
Msa0214350 AT1G69310.4 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0214350 AT1G69310.2 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0214350 AT1G69310.1 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0214350 AT5G49520.1 49.153 59 27 1 14 72 220 275 4.17e-13 65.5
Msa0214350 AT2G44745.1 48.333 60 28 1 13 72 143 199 4.73e-13 64.3
Msa0214350 AT2G46130.1 48.485 66 29 2 8 72 23 84 5.61e-13 61.6
Msa0214350 AT4G18170.1 49.153 59 27 1 14 72 171 226 1.20e-12 63.9
Msa0214350 AT1G13960.1 48.333 60 28 1 13 72 407 463 1.44e-12 64.3
Msa0214350 AT5G26170.1 45.000 60 30 1 13 72 111 167 1.60e-12 62.0
Msa0214350 AT1G29860.1 49.153 59 27 1 14 72 135 190 1.86e-12 63.2
Msa0214350 AT5G13080.1 48.333 60 28 1 13 72 65 121 2.56e-12 60.8
Msa0214350 AT2G03340.1 48.333 60 28 1 13 72 413 469 3.61e-12 63.2
Msa0214350 AT1G64000.1 48.333 60 28 1 13 72 112 168 3.74e-12 61.2
Msa0214350 AT1G13960.2 48.333 60 28 1 13 72 254 310 4.14e-12 62.8
Msa0214350 AT5G46350.1 46.154 65 32 1 8 72 176 237 4.48e-12 62.4
Msa0214350 AT3G62340.1 47.458 59 28 1 14 72 117 172 9.18e-12 61.2
Msa0214350 AT4G26440.1 47.458 59 27 2 15 73 178 232 1.02e-11 61.6
Msa0214350 AT2G47260.1 45.763 59 29 1 14 72 173 228 3.18e-11 60.1
Msa0214350 AT5G41570.1 46.667 60 29 1 13 72 96 152 3.30e-11 58.5
Msa0214350 AT2G04880.2 40.000 60 32 2 13 72 109 164 3.33e-11 60.1
Msa0214350 AT5G45260.1 40.580 69 38 2 7 72 1197 1265 3.34e-11 60.5
Msa0214350 AT2G04880.1 40.000 60 32 2 13 72 109 164 3.34e-11 60.5
Msa0214350 AT3G01970.1 45.000 60 30 1 13 72 63 119 5.40e-11 57.4
Msa0214350 AT4G26640.7 35.714 98 56 3 13 106 339 433 8.95e-11 58.9

Find 30 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACCATTCAGACTTAAATT+TGG 0.184409 2_1:+58900015 Msa0214350:CDS
AATTAAGTACCTGAAATATT+TGG 0.227860 2_1:-58899599 None:intergenic
TAACAAATGCCAAATATTTC+AGG 0.288144 2_1:+58899590 Msa0214350:CDS
TTGTACAGGACTACATATTA+TGG 0.292618 2_1:+58899971 Msa0214350:CDS
ATTGTTATCAGAGGACAAAA+TGG 0.379017 2_1:-58900041 None:intergenic
ATCATTGTGGATCACTTCCT+TGG 0.416994 2_1:-58900173 None:intergenic
ATTCCAAATTTAAGTCTGAA+TGG 0.467467 2_1:-58900018 None:intergenic
TAAGGTCAAGTGCACCAACT+TGG 0.477818 2_1:+58899503 None:intergenic
ATGTATGCAGGAATTACTAT+AGG 0.486763 2_1:+58899879 Msa0214350:intron
GATGGTGGTCGCGGTCGAAA+TGG 0.511390 2_1:-58900112 None:intergenic
AAGGTCAAGTGCACCAACTT+GGG 0.523767 2_1:+58899504 None:intergenic
ACTTCTTGCATCTACAAAAG+AGG 0.541554 2_1:+58900147 Msa0214350:CDS
GCCTCAATATTGCTTGATGA+TGG 0.544274 2_1:+58899535 Msa0214350:CDS
AAGAGAACCCTCCTTTGTAC+AGG 0.557218 2_1:+58899957 Msa0214350:CDS
AGTGGTGGCGATGGTGGTCG+CGG 0.559099 2_1:-58900121 None:intergenic
ATCTACAAAAGAGGAATCCA+AGG 0.562435 2_1:+58900156 Msa0214350:CDS
CGTTCTCCTATGCGAACGAT+TGG 0.564300 2_1:-58900210 None:intergenic
GGTCATACATGGAGAAAGTA+CGG 0.571382 2_1:+58899556 Msa0214350:CDS
TGCACCAACTTGGGAAAAGA+CGG 0.575025 2_1:+58899513 Msa0214350:CDS
AGTGGCAGTGGTGGCGATGG+TGG 0.575810 2_1:-58900127 None:intergenic
ACCATCATCAAGCAATATTG+AGG 0.577098 2_1:-58899536 None:intergenic
ATGTAGTCCTGTACAAAGGA+GGG 0.583465 2_1:-58899964 None:intergenic
AGAAGTGGCAGTGGTGGCGA+TGG 0.586410 2_1:-58900130 None:intergenic
TGCTTGATGATGGTCATACA+TGG 0.592377 2_1:+58899545 Msa0214350:CDS
TATGTAGTCCTGTACAAAGG+AGG 0.603277 2_1:-58899965 None:intergenic
GCGAGACCAATCGTTCGCAT+AGG 0.611909 2_1:+58900204 Msa0214350:CDS
TAATATAGAATTGTTATCAG+AGG 0.636655 2_1:-58900050 None:intergenic
GTAGATGCAAGAAGTGGCAG+TGG 0.639668 2_1:-58900139 None:intergenic
TAATATGTAGTCCTGTACAA+AGG 0.665931 2_1:-58899968 None:intergenic
GATGCAAGAAGTGGCAGTGG+TGG 0.676252 2_1:-58900136 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATAATTCAAAACTTAAT+TGG + chr2_1:58899852-58899871 Msa0214350:intron 10.0%
!!! AATTATTTTTCTTGTAGATT+AGG + chr2_1:58899712-58899731 Msa0214350:intron 15.0%
!! AATTAAGTACCTGAAATATT+TGG - chr2_1:58899602-58899621 None:intergenic 20.0%
!! ATTACAATTATATCTAAGAG+TGG - chr2_1:58899774-58899793 None:intergenic 20.0%
!! TAATATAGAATTGTTATCAG+AGG - chr2_1:58900053-58900072 None:intergenic 20.0%
! TAACAAATGCCAAATATTTC+AGG + chr2_1:58899590-58899609 Msa0214350:CDS 25.0%
! TTGGAACAATAGTCAAAATT+AGG + chr2_1:58899686-58899705 Msa0214350:intron 25.0%
!! TTAATTGGTAATATGTATGC+AGG + chr2_1:58899867-58899886 Msa0214350:intron 25.0%
!! AGTTCTTTGAACATGTTTTA+TGG - chr2_1:58899936-58899955 None:intergenic 25.0%
! TTACCATTCAGACTTAAATT+TGG + chr2_1:58900015-58900034 Msa0214350:CDS 25.0%
! ATTCCAAATTTAAGTCTGAA+TGG - chr2_1:58900021-58900040 None:intergenic 25.0%
! ATCATGTACTTGTTAGTTGT+TGG + chr2_1:58899667-58899686 Msa0214350:intron 30.0%
ATGTATGCAGGAATTACTAT+AGG + chr2_1:58899879-58899898 Msa0214350:intron 30.0%
TAATATGTAGTCCTGTACAA+AGG - chr2_1:58899971-58899990 None:intergenic 30.0%
TTGTACAGGACTACATATTA+TGG + chr2_1:58899971-58899990 Msa0214350:CDS 30.0%
ATTGTTATCAGAGGACAAAA+TGG - chr2_1:58900044-58900063 None:intergenic 30.0%
ACCATCATCAAGCAATATTG+AGG - chr2_1:58899539-58899558 None:intergenic 35.0%
GACTAATCTTGATTCTCAAG+TGG - chr2_1:58899644-58899663 None:intergenic 35.0%
! AAGAGCTTTTGCAAATGTGA+TGG - chr2_1:58899997-58900016 None:intergenic 35.0%
! TCTTTTGTAGATGCAAGAAG+TGG - chr2_1:58900148-58900167 None:intergenic 35.0%
ACTTCTTGCATCTACAAAAG+AGG + chr2_1:58900147-58900166 Msa0214350:CDS 35.0%
ATCTACAAAAGAGGAATCCA+AGG + chr2_1:58900156-58900175 Msa0214350:CDS 35.0%
CTCGCGAAAAATTATCATTG+TGG - chr2_1:58900189-58900208 None:intergenic 35.0%
GCCTCAATATTGCTTGATGA+TGG + chr2_1:58899535-58899554 Msa0214350:CDS 40.0%
!! TGCTTGATGATGGTCATACA+TGG + chr2_1:58899545-58899564 Msa0214350:CDS 40.0%
GGTCATACATGGAGAAAGTA+CGG + chr2_1:58899556-58899575 Msa0214350:CDS 40.0%
GATTCTCAAGTGGATGTAGA+TGG - chr2_1:58899634-58899653 None:intergenic 40.0%
ATGTAGTCCTGTACAAAGGA+GGG - chr2_1:58899967-58899986 None:intergenic 40.0%
TATGTAGTCCTGTACAAAGG+AGG - chr2_1:58899968-58899987 None:intergenic 40.0%
ATCATTGTGGATCACTTCCT+TGG - chr2_1:58900176-58900195 None:intergenic 40.0%
TGCACCAACTTGGGAAAAGA+CGG + chr2_1:58899513-58899532 Msa0214350:CDS 45.0%
AAGAGAACCCTCCTTTGTAC+AGG + chr2_1:58899957-58899976 Msa0214350:CDS 45.0%
GTAGATGCAAGAAGTGGCAG+TGG - chr2_1:58900142-58900161 None:intergenic 50.0%
! GAGGCCGTCTTTTCCCAAGT+TGG - chr2_1:58899520-58899539 None:intergenic 55.0%
GATGCAAGAAGTGGCAGTGG+TGG - chr2_1:58900139-58900158 None:intergenic 55.0%
! GATGGTGGTCGCGGTCGAAA+TGG - chr2_1:58900115-58900134 None:intergenic 60.0%
! AGAAGTGGCAGTGGTGGCGA+TGG - chr2_1:58900133-58900152 None:intergenic 60.0%
! AGTGGTGGCGATGGTGGTCG+CGG - chr2_1:58900124-58900143 None:intergenic 65.0%
! AGTGGCAGTGGTGGCGATGG+TGG - chr2_1:58900130-58900149 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 58899508 58900225 58899508 ID=Msa0214350;Name=Msa0214350
chr2_1 mRNA 58899508 58900225 58899508 ID=Msa0214350-mRNA-1;Parent=Msa0214350;Name=Msa0214350-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|0|0|1|1|1|2|0|146
chr2_1 exon 58899508 58899611 58899508 ID=Msa0214350-mRNA-1:exon:16159;Parent=Msa0214350-mRNA-1
chr2_1 exon 58899889 58900225 58899889 ID=Msa0214350-mRNA-1:exon:16160;Parent=Msa0214350-mRNA-1
chr2_1 CDS 58899508 58899611 58899508 ID=Msa0214350-mRNA-1:cds;Parent=Msa0214350-mRNA-1
chr2_1 CDS 58899889 58900225 58899889 ID=Msa0214350-mRNA-1:cds;Parent=Msa0214350-mRNA-1
Gene Sequence

>Msa0214350

TCAAGTGCACCAACTTGGGAAAAGACGGCCTCAATATTGCTTGATGATGGTCATACATGGAGAAAGTACGGACAAAAGATGATAACAAATGCCAAATATTTCAGGAATTACTATAGGTGCACTCACAGTTATGATCAACATTGTGAAGCCATAAAACATGTTCAAAGAACTCAAGAGAACCCTCCTTTGTACAGGACTACATATTATGGCCATCACATTTGCAAAAGCTCTTACCATTCAGACTTAAATTTGGAATCCATTTTGTCCTCTGATAACAATTCTATATTACTTACTTTCGATAACAACATTTCAAGTGAACATGAATATCCATTTCGACCGCGACCACCATCGCCACCACTGCCACTTCTTGCATCTACAAAAGAGGAATCCAAGGAAGTGATCCACAATGATAATTTTTCGCGAGACCAATCGTTCGCATAG
Protein sequence

>Msa0214350

SSAPTWEKTASILLDDGHTWRKYGQKMITNAKYFRNYYRCTHSYDQHCEAIKHVQRTQENPPLYRTTYYGHHICKSSYHSDLNLESILSSDNNSILLTFDNNISSEHEYPFRPRPPSPPLPLLASTKEESKEVIHNDNFSRDQSFA*