AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0294010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0294010 MtrunA17_Chr2g0315371 85.315 143 21 0 1 143 127 269 7.94e-80 238
Msa0294010 MtrunA17_Chr2g0315361 78.378 148 27 3 1 146 134 278 1.58e-78 234
Msa0294010 MtrunA17_Chr2g0315381 69.863 146 40 2 1 146 130 271 3.29e-68 208
Msa0294010 MtrunA17_Chr8g0350621 53.571 112 43 3 5 111 101 208 1.79e-35 123
Msa0294010 MtrunA17_Chr7g0244981 46.970 132 58 3 5 135 112 232 8.91e-34 119
Msa0294010 MtrunA17_Chr7g0244971 48.624 109 52 2 5 111 113 219 1.19e-31 114
Msa0294010 MtrunA17_Chr8g0334541 48.673 113 44 3 5 111 93 197 1.08e-28 106
Msa0294010 MtrunA17_Chr3g0128671 40.310 129 57 4 10 118 122 250 6.14e-23 91.7
Msa0294010 MtrunA17_Chr5g0428351 38.947 95 57 1 1 95 170 263 3.11e-20 84.3
Msa0294010 MtrunA17_Chr7g0275531 44.086 93 43 1 2 85 96 188 1.13e-19 83.2
Msa0294010 MtrunA17_Chr8g0350631 48.718 78 35 2 36 111 5 79 9.50e-19 77.4
Msa0294010 MtrunA17_Chr8g0347251 41.667 84 41 1 2 77 115 198 3.43e-18 79.3
Msa0294010 MtrunA17_Chr3g0126391 54.098 61 28 0 14 74 132 192 6.29e-18 78.6
Msa0294010 MtrunA17_Chr2g0315401 44.860 107 45 4 45 146 21 118 1.15e-17 74.3
Msa0294010 MtrunA17_Chr8g0387981 43.750 80 37 1 3 74 112 191 3.63e-16 73.9
Msa0294010 MtrunA17_Chr7g0224801 48.052 77 36 2 13 89 91 163 4.61e-15 68.2
Msa0294010 MtrunA17_Chr8g0383351 47.541 61 29 1 13 73 158 215 6.88e-15 68.9
Msa0294010 MtrunA17_Chr2g0315341 42.268 97 43 4 51 143 1 88 2.64e-14 65.1
Msa0294010 MtrunA17_Chr3g0129361 48.333 60 28 1 13 72 142 198 9.28e-14 65.9
Msa0294010 MtrunA17_Chr4g0068541 46.667 60 29 1 14 73 207 263 2.87e-13 65.9
Msa0294010 MtrunA17_Chr5g0418781 49.153 59 27 1 14 72 123 178 3.35e-13 65.1
Msa0294010 MtrunA17_Chr8g0335811 48.333 60 28 1 13 72 152 208 4.62e-13 63.9
Msa0294010 MtrunA17_Chr8g0386241 44.262 61 31 1 13 73 101 158 8.56e-13 62.4
Msa0294010 MtrunA17_Chr7g0270191 47.458 59 28 1 14 72 144 199 9.34e-13 63.9
Msa0294010 MtrunA17_Chr5g0418191 37.255 102 48 3 13 109 318 408 1.05e-12 64.3
Msa0294010 MtrunA17_Chr4g0051881 50.847 59 26 1 14 72 177 232 1.12e-12 63.9
Msa0294010 MtrunA17_Chr5g0443131 49.153 59 27 1 14 72 156 211 1.16e-12 63.5
Msa0294010 MtrunA17_Chr7g0218081 46.667 60 29 1 13 72 408 464 2.16e-12 63.2
Msa0294010 MtrunA17_Chr7g0263531 46.774 62 30 1 11 72 357 415 4.49e-12 62.4
Msa0294010 MtrunA17_Chr2g0294231 41.892 74 40 1 14 87 202 272 5.55e-12 62.0
Msa0294010 MtrunA17_Chr1g0194481 45.763 59 29 1 14 72 157 212 5.71e-12 62.0
Msa0294010 MtrunA17_Chr7g0248721 50.000 60 26 2 13 72 139 194 7.17e-12 60.5
Msa0294010 MtrunA17_Chr7g0238921 49.180 61 28 1 13 73 122 179 8.14e-12 61.2
Msa0294010 MtrunA17_Chr2g0322391 47.541 61 30 1 13 73 347 405 1.20e-11 61.2
Msa0294010 MtrunA17_Chr4g0042831 46.667 60 29 1 13 72 276 332 1.46e-11 60.8
Msa0294010 MtrunA17_Chr3g0101131 45.000 60 30 1 13 72 413 469 1.69e-11 60.8
Msa0294010 MtrunA17_Chr5g0445311 45.000 60 30 1 13 72 362 418 1.87e-11 60.5
Msa0294010 MtrunA17_Chr5g0447701 37.500 88 45 3 11 98 248 325 2.06e-11 60.5
Msa0294010 MtrunA17_Chr1g0150801 44.776 67 32 2 8 72 93 156 2.26e-11 58.5
Msa0294010 MtrunA17_Chr5g0431811 42.857 63 36 0 15 77 672 734 3.43e-11 60.1
Msa0294010 MtrunA17_Chr3g0129321 41.667 60 32 1 13 72 116 172 4.71e-11 58.2
Msa0294010 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
Msa0294010 AT1G66560.1 47.059 102 46 3 15 108 103 204 4.60e-24 94.0
Msa0294010 AT1G66600.1 50.602 83 34 2 14 89 102 184 1.16e-22 90.1
Msa0294010 AT5G22570.1 52.055 73 31 1 16 88 111 179 2.15e-22 90.1
Msa0294010 AT1G66550.2 55.882 68 29 1 15 81 103 170 2.48e-22 89.4
Msa0294010 AT1G66550.1 55.882 68 29 1 15 81 108 175 3.04e-22 89.4
Msa0294010 AT5G01900.1 60.000 60 24 0 16 75 111 170 4.96e-22 89.0
Msa0294010 AT1G80590.1 54.098 61 28 0 16 76 86 146 8.27e-20 82.4
Msa0294010 AT3G56400.1 51.562 64 31 0 11 74 116 179 1.01e-19 83.2
Msa0294010 AT2G46400.1 52.459 61 29 0 14 74 103 163 4.70e-19 81.3
Msa0294010 AT5G24110.1 48.148 81 34 1 2 74 92 172 5.01e-18 79.0
Msa0294010 AT2G40740.1 53.333 60 28 0 15 74 173 232 8.40e-17 75.5
Msa0294010 AT2G40740.3 52.381 63 30 0 15 77 182 244 1.11e-16 75.1
Msa0294010 AT4G23810.1 51.667 60 29 0 15 74 158 217 1.18e-15 72.4
Msa0294010 AT4G11070.2 51.667 60 29 0 15 74 109 168 1.64e-15 71.6
Msa0294010 AT4G11070.1 51.667 60 29 0 15 74 141 200 2.02e-15 71.6
Msa0294010 AT2G40750.1 45.000 60 33 0 15 74 152 211 3.44e-14 68.6
Msa0294010 AT4G39410.1 44.928 69 35 1 13 81 221 286 1.66e-13 66.2
Msa0294010 AT2G37260.1 49.153 59 27 1 14 72 348 403 2.74e-13 66.2
Msa0294010 AT2G37260.3 49.153 59 27 1 14 72 268 323 3.28e-13 65.9
Msa0294010 AT2G37260.2 49.153 59 27 1 14 72 266 321 3.49e-13 65.9
Msa0294010 AT1G69310.4 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0294010 AT1G69310.2 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0294010 AT1G69310.1 47.458 59 28 1 14 72 146 201 3.73e-13 65.5
Msa0294010 AT5G49520.1 49.153 59 27 1 14 72 220 275 4.17e-13 65.5
Msa0294010 AT2G44745.1 48.333 60 28 1 13 72 143 199 4.73e-13 64.3
Msa0294010 AT2G46130.1 48.485 66 29 2 8 72 23 84 5.61e-13 61.6
Msa0294010 AT4G18170.1 49.153 59 27 1 14 72 171 226 1.20e-12 63.9
Msa0294010 AT1G13960.1 48.333 60 28 1 13 72 407 463 1.44e-12 64.3
Msa0294010 AT5G26170.1 45.000 60 30 1 13 72 111 167 1.60e-12 62.0
Msa0294010 AT1G29860.1 49.153 59 27 1 14 72 135 190 1.86e-12 63.2
Msa0294010 AT5G13080.1 48.333 60 28 1 13 72 65 121 2.56e-12 60.8
Msa0294010 AT2G03340.1 48.333 60 28 1 13 72 413 469 3.61e-12 63.2
Msa0294010 AT1G64000.1 48.333 60 28 1 13 72 112 168 3.74e-12 61.2
Msa0294010 AT1G13960.2 48.333 60 28 1 13 72 254 310 4.14e-12 62.8
Msa0294010 AT5G46350.1 46.154 65 32 1 8 72 176 237 4.48e-12 62.4
Msa0294010 AT3G62340.1 47.458 59 28 1 14 72 117 172 9.18e-12 61.2
Msa0294010 AT4G26440.1 47.458 59 27 2 15 73 178 232 1.02e-11 61.6
Msa0294010 AT2G47260.1 45.763 59 29 1 14 72 173 228 3.18e-11 60.1
Msa0294010 AT5G41570.1 46.667 60 29 1 13 72 96 152 3.30e-11 58.5
Msa0294010 AT2G04880.2 40.000 60 32 2 13 72 109 164 3.33e-11 60.1
Msa0294010 AT5G45260.1 40.580 69 38 2 7 72 1197 1265 3.34e-11 60.5
Msa0294010 AT2G04880.1 40.000 60 32 2 13 72 109 164 3.34e-11 60.5
Msa0294010 AT3G01970.1 45.000 60 30 1 13 72 63 119 5.40e-11 57.4
Msa0294010 AT4G26640.7 35.714 98 56 3 13 106 339 433 8.95e-11 58.9

Find 30 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACCATTCAGACTTAAATT+TGG 0.184409 2_3:+45585191 Msa0294010:CDS
AATTAAGTACCTGAAATATT+TGG 0.227860 2_3:-45584775 None:intergenic
TAACAAATGCCAAATATTTC+AGG 0.288144 2_3:+45584766 Msa0294010:CDS
TTGTACAGGACTACATATTA+TGG 0.292618 2_3:+45585147 Msa0294010:CDS
ATTGTTATCAGAGGACAAAA+TGG 0.379017 2_3:-45585217 None:intergenic
ATCATTGTGGATCACTTCCT+TGG 0.416994 2_3:-45585349 None:intergenic
ATTCCAAATTTAAGTCTGAA+TGG 0.467467 2_3:-45585194 None:intergenic
TAAGGTCAAGTGCACCAACT+TGG 0.477818 2_3:+45584679 None:intergenic
ATGTATGCAGGAATTACTAT+AGG 0.486763 2_3:+45585055 Msa0294010:intron
GATGGTGGTCGCGGTCGAAA+TGG 0.511390 2_3:-45585288 None:intergenic
AAGGTCAAGTGCACCAACTT+GGG 0.523767 2_3:+45584680 None:intergenic
ACTTCTTGCATCTACAAAAG+AGG 0.541554 2_3:+45585323 Msa0294010:CDS
GCCTCAATATTGCTTGATGA+TGG 0.544274 2_3:+45584711 Msa0294010:CDS
AAGAGAACCCTCCTTTGTAC+AGG 0.557218 2_3:+45585133 Msa0294010:CDS
AGTGGTGGCGATGGTGGTCG+CGG 0.559099 2_3:-45585297 None:intergenic
ATCTACAAAAGAGGAATCCA+AGG 0.562435 2_3:+45585332 Msa0294010:CDS
CGTTCTCCTATGCGAACGAT+TGG 0.564300 2_3:-45585386 None:intergenic
GGTCATACATGGAGAAAGTA+CGG 0.571382 2_3:+45584732 Msa0294010:CDS
TGCACCAACTTGGGAAAAGA+CGG 0.575025 2_3:+45584689 Msa0294010:CDS
AGTGGCAGTGGTGGCGATGG+TGG 0.575810 2_3:-45585303 None:intergenic
ACCATCATCAAGCAATATTG+AGG 0.577098 2_3:-45584712 None:intergenic
ATGTAGTCCTGTACAAAGGA+GGG 0.583465 2_3:-45585140 None:intergenic
AGAAGTGGCAGTGGTGGCGA+TGG 0.586410 2_3:-45585306 None:intergenic
TGCTTGATGATGGTCATACA+TGG 0.592377 2_3:+45584721 Msa0294010:CDS
TATGTAGTCCTGTACAAAGG+AGG 0.603277 2_3:-45585141 None:intergenic
GCGAGACCAATCGTTCGCAT+AGG 0.611909 2_3:+45585380 Msa0294010:CDS
TAATATAGAATTGTTATCAG+AGG 0.636655 2_3:-45585226 None:intergenic
GTAGATGCAAGAAGTGGCAG+TGG 0.639668 2_3:-45585315 None:intergenic
TAATATGTAGTCCTGTACAA+AGG 0.665931 2_3:-45585144 None:intergenic
GATGCAAGAAGTGGCAGTGG+TGG 0.676252 2_3:-45585312 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATAATTCAAAACTTAAT+TGG + chr2_3:45585028-45585047 Msa0294010:intron 10.0%
!!! AATTATTTTTCTTGTAGATT+AGG + chr2_3:45584888-45584907 Msa0294010:intron 15.0%
!! AATTAAGTACCTGAAATATT+TGG - chr2_3:45584778-45584797 None:intergenic 20.0%
!! TAATATAGAATTGTTATCAG+AGG - chr2_3:45585229-45585248 None:intergenic 20.0%
! TAACAAATGCCAAATATTTC+AGG + chr2_3:45584766-45584785 Msa0294010:CDS 25.0%
! TTGGAACAATAGTCAAAATT+AGG + chr2_3:45584862-45584881 Msa0294010:intron 25.0%
!! TTAATTGGTAATATGTATGC+AGG + chr2_3:45585043-45585062 Msa0294010:intron 25.0%
!! AGTTCTTTGAACATGTTTTA+TGG - chr2_3:45585112-45585131 None:intergenic 25.0%
! TTACCATTCAGACTTAAATT+TGG + chr2_3:45585191-45585210 Msa0294010:CDS 25.0%
! ATTCCAAATTTAAGTCTGAA+TGG - chr2_3:45585197-45585216 None:intergenic 25.0%
! ATCATGTACTTGTTAGTTGT+TGG + chr2_3:45584843-45584862 Msa0294010:intron 30.0%
ATGTATGCAGGAATTACTAT+AGG + chr2_3:45585055-45585074 Msa0294010:intron 30.0%
TAATATGTAGTCCTGTACAA+AGG - chr2_3:45585147-45585166 None:intergenic 30.0%
TTGTACAGGACTACATATTA+TGG + chr2_3:45585147-45585166 Msa0294010:CDS 30.0%
ATTGTTATCAGAGGACAAAA+TGG - chr2_3:45585220-45585239 None:intergenic 30.0%
ACCATCATCAAGCAATATTG+AGG - chr2_3:45584715-45584734 None:intergenic 35.0%
GACTAATCTTGATTCTCAAG+TGG - chr2_3:45584820-45584839 None:intergenic 35.0%
! AAGAGCTTTTGCAAATGTGA+TGG - chr2_3:45585173-45585192 None:intergenic 35.0%
! TCTTTTGTAGATGCAAGAAG+TGG - chr2_3:45585324-45585343 None:intergenic 35.0%
ACTTCTTGCATCTACAAAAG+AGG + chr2_3:45585323-45585342 Msa0294010:CDS 35.0%
ATCTACAAAAGAGGAATCCA+AGG + chr2_3:45585332-45585351 Msa0294010:CDS 35.0%
CTCGCGAAAAATTATCATTG+TGG - chr2_3:45585365-45585384 None:intergenic 35.0%
GCCTCAATATTGCTTGATGA+TGG + chr2_3:45584711-45584730 Msa0294010:CDS 40.0%
!! TGCTTGATGATGGTCATACA+TGG + chr2_3:45584721-45584740 Msa0294010:CDS 40.0%
GGTCATACATGGAGAAAGTA+CGG + chr2_3:45584732-45584751 Msa0294010:CDS 40.0%
GATTCTCAAGTGGATGTAGA+TGG - chr2_3:45584810-45584829 None:intergenic 40.0%
ATGTAGTCCTGTACAAAGGA+GGG - chr2_3:45585143-45585162 None:intergenic 40.0%
TATGTAGTCCTGTACAAAGG+AGG - chr2_3:45585144-45585163 None:intergenic 40.0%
ATCATTGTGGATCACTTCCT+TGG - chr2_3:45585352-45585371 None:intergenic 40.0%
TGCACCAACTTGGGAAAAGA+CGG + chr2_3:45584689-45584708 Msa0294010:CDS 45.0%
AAGAGAACCCTCCTTTGTAC+AGG + chr2_3:45585133-45585152 Msa0294010:CDS 45.0%
GTAGATGCAAGAAGTGGCAG+TGG - chr2_3:45585318-45585337 None:intergenic 50.0%
! GAGGCCGTCTTTTCCCAAGT+TGG - chr2_3:45584696-45584715 None:intergenic 55.0%
GATGCAAGAAGTGGCAGTGG+TGG - chr2_3:45585315-45585334 None:intergenic 55.0%
! GATGGTGGTCGCGGTCGAAA+TGG - chr2_3:45585291-45585310 None:intergenic 60.0%
! AGAAGTGGCAGTGGTGGCGA+TGG - chr2_3:45585309-45585328 None:intergenic 60.0%
! AGTGGTGGCGATGGTGGTCG+CGG - chr2_3:45585300-45585319 None:intergenic 65.0%
! AGTGGCAGTGGTGGCGATGG+TGG - chr2_3:45585306-45585325 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 45584684 45585401 45584684 ID=Msa0294010;Name=Msa0294010
chr2_3 mRNA 45584684 45585401 45584684 ID=Msa0294010-mRNA-1;Parent=Msa0294010;Name=Msa0294010-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|0|0|1|1|1|2|0|146
chr2_3 exon 45584684 45584787 45584684 ID=Msa0294010-mRNA-1:exon:14201;Parent=Msa0294010-mRNA-1
chr2_3 exon 45585065 45585401 45585065 ID=Msa0294010-mRNA-1:exon:14202;Parent=Msa0294010-mRNA-1
chr2_3 CDS 45584684 45584787 45584684 ID=Msa0294010-mRNA-1:cds;Parent=Msa0294010-mRNA-1
chr2_3 CDS 45585065 45585401 45585065 ID=Msa0294010-mRNA-1:cds;Parent=Msa0294010-mRNA-1
Gene Sequence

>Msa0294010

TCAAGTGCACCAACTTGGGAAAAGACGGCCTCAATATTGCTTGATGATGGTCATACATGGAGAAAGTACGGACAAAAGATGATAACAAATGCCAAATATTTCAGGAATTACTATAGGTGCACTCACAGTTATGATCAACATTGTGAAGCCATAAAACATGTTCAAAGAACTCAAGAGAACCCTCCTTTGTACAGGACTACATATTATGGCCATCACATTTGCAAAAGCTCTTACCATTCAGACTTAAATTTGGAATCCATTTTGTCCTCTGATAACAATTCTATATTACTTACTTTCGATAACAACATTTCAAGTGAACATGAATATCCATTTCGACCGCGACCACCATCGCCACCACTGCCACTTCTTGCATCTACAAAAGAGGAATCCAAGGAAGTGATCCACAATGATAATTTTTCGCGAGACCAATCGTTCGCATAG
Protein sequence

>Msa0294010

SSAPTWEKTASILLDDGHTWRKYGQKMITNAKYFRNYYRCTHSYDQHCEAIKHVQRTQENPPLYRTTYYGHHICKSSYHSDLNLESILSSDNNSILLTFDNNISSEHEYPFRPRPPSPPLPLLASTKEESKEVIHNDNFSRDQSFA*