AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0289020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0289020 MtrunA17_Chr8g0360761 91.429 35 3 0 10 44 74 108 1.74e-18 74.3
Msa0289020 MtrunA17_Chr4g0002001 61.224 49 19 0 16 64 186 234 2.66e-15 67.8
Msa0289020 MtrunA17_Chr3g0093391 57.143 49 21 0 16 64 203 251 3.60e-15 67.8
Msa0289020 MtrunA17_Chr3g0093571 57.143 49 21 0 16 64 205 253 6.72e-15 67.0
Msa0289020 MtrunA17_Chr6g0486031 60.000 50 19 1 11 59 275 324 8.26e-15 66.6
Msa0289020 MtrunA17_Chr4g0051261 59.184 49 20 0 16 64 169 217 1.57e-14 65.5
Msa0289020 MtrunA17_Chr2g0293491 59.184 49 20 0 16 64 169 217 4.15e-14 64.3
Msa0289020 MtrunA17_Chr3g0130781 58.537 41 17 0 16 56 196 236 6.63e-14 63.9
Msa0289020 MtrunA17_Chr3g0102571 62.500 40 15 0 16 55 247 286 7.20e-14 63.9
Msa0289020 MtrunA17_Chr8g0390341 56.000 50 21 1 11 59 288 337 1.00e-13 63.5
Msa0289020 MtrunA17_Chr1g0193081 64.103 39 14 0 16 54 241 279 1.01e-13 63.5
Msa0289020 MtrunA17_Chr7g0246591 64.103 39 14 0 16 54 307 345 1.34e-13 63.2
Msa0289020 MtrunA17_Chr3g0122781 55.102 49 22 0 16 64 581 629 1.64e-13 63.2
Msa0289020 MtrunA17_Chr4g0030231 54.167 48 22 0 16 63 206 253 1.75e-13 62.8
Msa0289020 MtrunA17_Chr4g0057791 43.478 69 34 1 1 64 365 433 1.76e-13 62.8
Msa0289020 MtrunA17_Chr4g0030151 57.500 40 17 0 16 55 205 244 1.89e-13 62.8
Msa0289020 MtrunA17_Chr4g0030241 54.167 48 22 0 16 63 67 114 2.81e-13 60.8
Msa0289020 MtrunA17_Chr8g0377071 55.102 49 22 0 16 64 550 598 2.89e-13 62.4
Msa0289020 MtrunA17_Chr5g0397261 57.500 40 17 0 16 55 207 246 4.88e-13 61.6
Msa0289020 MtrunA17_Chr2g0277011 61.538 39 15 0 16 54 256 294 4.98e-13 61.6
Msa0289020 MtrunA17_Chr4g0045841 57.500 40 17 0 16 55 221 260 7.30e-13 61.2
Msa0289020 MtrunA17_Chr2g0284091 57.500 40 17 0 16 55 206 245 7.55e-13 61.2
Msa0289020 MtrunA17_Chr2g0320011 57.500 40 17 0 16 55 254 293 7.73e-13 61.2
Msa0289020 MtrunA17_Chr7g0270371 58.974 39 16 0 16 54 241 279 1.27e-12 60.5
Msa0289020 MtrunA17_Chr8g0387401 55.000 40 18 0 16 55 218 257 1.44e-12 60.5
Msa0289020 MtrunA17_Chr7g0218071 51.020 49 24 0 16 64 286 334 2.62e-12 59.7
Msa0289020 MtrunA17_Chr6g0453711 48.980 49 25 0 16 64 276 324 5.88e-12 58.5
Msa0289020 MtrunA17_Chr8g0350311 56.410 39 17 0 16 54 305 343 6.69e-12 58.5
Msa0289020 MtrunA17_Chr1g0187371 53.061 49 23 0 16 64 191 239 7.61e-12 58.2
Msa0289020 MtrunA17_Chr3g0141871 57.500 40 17 0 16 55 199 238 1.12e-11 57.8
Msa0289020 MtrunA17_Chr1g0194201 55.263 38 17 0 16 53 241 278 1.38e-11 57.4
Msa0289020 MtrunA17_Chr4g0061141 48.980 49 25 0 16 64 271 319 1.60e-11 57.4
Msa0289020 MtrunA17_Chr8g0348481 52.500 40 19 0 16 55 203 242 1.79e-11 57.0
Msa0289020 MtrunA17_Chr5g0396361 48.980 49 25 0 16 64 306 354 2.10e-11 57.0
Msa0289020 MtrunA17_Chr7g0248461 50.000 40 20 0 16 55 204 243 3.01e-11 56.6
Msa0289020 MtrunA17_Chr1g0201571 46.939 49 26 0 16 64 292 340 5.68e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0289020 AT2G38620.3 50.725 69 29 1 1 64 166 234 5.03e-17 72.0
Msa0289020 AT2G38620.1 50.725 69 29 1 1 64 166 234 5.03e-17 72.0
Msa0289020 AT2G38620.4 50.725 69 29 1 1 64 104 172 8.36e-17 71.2
Msa0289020 AT2G38620.2 50.725 69 29 1 1 64 166 234 1.52e-16 71.2
Msa0289020 AT3G54180.1 63.265 49 18 0 16 64 184 232 3.00e-15 67.8
Msa0289020 AT3G48750.1 57.143 49 21 0 16 64 169 217 3.31e-14 65.1
Msa0289020 AT3G59790.1 60.000 40 16 0 16 55 226 265 8.95e-14 63.9
Msa0289020 AT1G76540.1 57.143 49 21 0 16 64 187 235 1.01e-13 63.5
Msa0289020 AT4G11330.1 60.000 40 16 0 16 55 209 248 1.05e-13 63.9
Msa0289020 AT5G63610.1 62.500 40 15 0 16 55 201 240 1.15e-13 63.9
Msa0289020 AT1G20930.1 55.102 49 22 0 16 64 189 237 1.57e-13 63.2
Msa0289020 AT3G05840.2 64.103 39 14 0 16 54 239 277 2.72e-13 62.8
Msa0289020 AT3G05840.1 64.103 39 14 0 16 54 239 277 2.72e-13 62.8
Msa0289020 AT5G26751.1 64.103 39 14 0 16 54 235 273 2.77e-13 62.8
Msa0289020 AT1G07880.1 54.167 48 22 0 16 63 199 246 3.13e-13 62.0
Msa0289020 AT4G18710.2 52.083 48 23 0 16 63 200 247 3.24e-13 62.0
Msa0289020 AT3G45640.1 57.500 40 17 0 16 55 204 243 3.86e-13 62.4
Msa0289020 AT3G01085.1 55.102 49 22 0 16 64 281 329 4.09e-13 62.4
Msa0289020 AT3G01085.2 55.102 49 22 0 16 64 281 329 4.09e-13 62.4
Msa0289020 AT3G01085.3 55.102 49 22 0 16 64 281 329 4.09e-13 62.4
Msa0289020 AT4G28980.3 56.000 50 21 1 11 59 293 342 4.74e-13 62.0
Msa0289020 AT4G28980.1 56.000 50 21 1 11 59 293 342 4.74e-13 62.0
Msa0289020 AT4G28980.2 56.000 50 21 1 11 59 293 342 4.74e-13 62.0
Msa0289020 AT1G07880.2 54.167 48 22 0 16 63 199 246 4.98e-13 62.0
Msa0289020 AT5G63370.5 44.928 69 33 1 1 64 447 515 5.90e-13 61.6
Msa0289020 AT5G63370.10 44.928 69 33 1 1 64 447 515 5.90e-13 61.6
Msa0289020 AT1G57870.1 61.538 39 15 0 16 54 248 286 5.92e-13 61.6
Msa0289020 AT1G57870.4 61.538 39 15 0 16 54 248 286 5.92e-13 61.6
Msa0289020 AT1G57870.2 61.538 39 15 0 16 54 248 286 5.92e-13 61.6
Msa0289020 AT1G57870.3 61.538 39 15 0 16 54 248 286 6.57e-13 61.6
Msa0289020 AT5G63370.7 44.928 69 33 1 1 64 447 515 7.13e-13 61.6
Msa0289020 AT5G63370.8 44.928 69 33 1 1 64 447 515 7.13e-13 61.6
Msa0289020 AT5G63370.4 44.928 69 33 1 1 64 447 515 7.13e-13 61.6
Msa0289020 AT5G63370.6 44.928 69 33 1 1 64 447 515 7.13e-13 61.6
Msa0289020 AT5G63370.1 44.928 69 33 1 1 64 447 515 7.13e-13 61.6
Msa0289020 AT4G18710.1 52.083 48 23 0 16 63 206 253 8.07e-13 61.2
Msa0289020 AT1G09840.3 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.7 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.10 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.6 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.4 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.1 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.9 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.5 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.8 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G09840.2 58.974 39 16 0 16 54 249 287 1.11e-12 60.8
Msa0289020 AT1G67580.1 55.102 49 22 0 16 64 571 619 1.21e-12 60.8
Msa0289020 AT1G67580.2 55.102 49 22 0 16 64 571 619 1.21e-12 60.8
Msa0289020 AT5G14640.1 58.974 39 16 0 16 54 240 278 1.73e-12 60.5
Msa0289020 AT5G14640.2 58.974 39 16 0 16 54 240 278 1.73e-12 60.5
Msa0289020 AT2G43790.1 57.500 40 17 0 16 55 229 268 1.86e-12 60.5
Msa0289020 AT5G63370.2 44.928 69 33 1 1 64 313 381 2.57e-12 60.1
Msa0289020 AT5G63370.3 44.928 69 33 1 1 64 313 381 2.57e-12 60.1
Msa0289020 AT5G39420.1 51.020 49 24 0 16 64 271 319 3.72e-12 59.7
Msa0289020 AT4G00720.1 53.061 49 22 1 16 63 304 352 4.70e-12 59.3
Msa0289020 AT5G63370.9 55.102 49 22 0 16 64 333 381 4.71e-12 59.3
Msa0289020 AT2G30980.1 55.000 40 18 0 16 55 238 277 4.99e-12 59.3
Msa0289020 AT1G09840.11 58.974 39 16 0 16 54 122 160 5.67e-12 58.9
Msa0289020 AT1G06390.2 55.000 40 18 0 16 55 236 275 5.82e-12 58.9
Msa0289020 AT1G06390.1 55.000 40 18 0 16 55 236 275 5.82e-12 58.9
Msa0289020 AT5G10270.1 48.980 49 25 0 16 64 206 254 6.26e-12 58.9
Msa0289020 AT1G01560.4 47.917 48 25 0 16 63 206 253 9.82e-12 58.2
Msa0289020 AT1G01560.1 47.917 48 25 0 16 63 206 253 9.82e-12 58.2
Msa0289020 AT1G01560.3 47.917 48 25 0 16 63 206 253 1.20e-11 58.2
Msa0289020 AT1G01560.2 47.917 48 25 0 16 63 206 253 1.23e-11 58.2
Msa0289020 AT1G10210.2 57.500 40 17 0 16 55 199 238 1.48e-11 57.8
Msa0289020 AT1G10210.3 57.500 40 17 0 16 55 199 238 1.48e-11 57.8
Msa0289020 AT1G10210.1 57.500 40 17 0 16 55 199 238 1.48e-11 57.8
Msa0289020 AT2G46070.2 52.500 40 19 0 16 55 207 246 1.64e-11 57.8
Msa0289020 AT3G61160.3 53.846 39 18 0 16 54 268 306 1.67e-11 57.8
Msa0289020 AT3G61160.6 53.846 39 18 0 16 54 275 313 1.68e-11 57.8
Msa0289020 AT3G61160.5 53.846 39 18 0 16 54 268 306 1.71e-11 57.8
Msa0289020 AT3G61160.4 53.846 39 18 0 16 54 268 306 1.73e-11 57.8
Msa0289020 AT3G61160.1 53.846 39 18 0 16 54 268 306 1.73e-11 57.8
Msa0289020 AT2G46070.1 52.500 40 19 0 16 55 207 246 1.73e-11 57.8
Msa0289020 AT3G61160.2 53.846 39 18 0 16 54 275 313 1.74e-11 57.8
Msa0289020 AT1G59580.2 57.500 40 17 0 16 55 199 238 1.76e-11 57.8
Msa0289020 AT1G59580.1 57.500 40 17 0 16 55 199 238 1.76e-11 57.8
Msa0289020 AT2G46070.3 52.500 40 19 0 16 55 241 280 1.76e-11 57.8
Msa0289020 AT4G36450.1 57.500 40 17 0 16 55 196 235 1.77e-11 57.4
Msa0289020 AT2G18170.1 57.500 40 17 0 16 55 199 238 1.82e-11 57.4
Msa0289020 AT1G74330.3 46.939 49 26 0 16 64 289 337 3.97e-11 56.6
Msa0289020 AT1G74330.2 46.939 49 26 0 16 64 289 337 3.97e-11 56.6
Msa0289020 AT1G74330.1 46.939 49 26 0 16 64 289 337 3.97e-11 56.6
Msa0289020 AT1G33770.1 46.939 49 26 0 16 64 307 355 5.74e-11 56.2

Find 16 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATATTGGCTGCGATATTT+TGG 0.233067 2_3:+35241279 Msa0289020:CDS
TGCAGTTGATGTCTGGTCTA+TGG 0.282898 2_3:+35241196 Msa0289020:CDS
ATCAACTGCAGTTGAGTAAT+TGG 0.293246 2_3:-35241183 None:intergenic
AGCAATAACCTTCAATGGTT+TGG 0.308387 2_3:-35241088 None:intergenic
TGAAGATATACCGCAGATAT+TGG 0.373622 2_3:+35241265 Msa0289020:CDS
AGGCTCCAACCTCTGTTCAT+TGG 0.396329 2_3:+35241242 Msa0289020:CDS
ACAGAAGCAATAACCTTCAA+TGG 0.414424 2_3:-35241093 None:intergenic
GCATATTTGCTGAGATGCTT+AGG 0.419785 2_3:+35241222 Msa0289020:CDS
ATGTTACTCCAAACCATTGA+AGG 0.442393 2_3:+35241080 Msa0289020:CDS
GTAGAACCCATCAAAAGTTC+AGG 0.451436 2_3:-35241161 None:intergenic
ACTCAACTGCAGTTGATGTC+TGG 0.472124 2_3:+35241189 Msa0289020:CDS
GCAGTTGATGTCTGGTCTAT+GGG 0.486060 2_3:+35241197 Msa0289020:CDS
AGTTCAGGTGCTTTATAGCA+AGG 0.509440 2_3:-35241146 None:intergenic
CTTCACCAATGAACAGAGGT+TGG 0.529289 2_3:-35241247 None:intergenic
AATATCGCAGCCAATATCTG+CGG 0.719781 2_3:-35241275 None:intergenic
ATATCTTCACCAATGAACAG+AGG 0.733276 2_3:-35241251 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTTCAACTTTCAGA+TGG + chr2_3:35241118-35241137 Msa0289020:intron 20.0%
!!! TTTATTTTCAACTTTCAGAT+GGG + chr2_3:35241119-35241138 Msa0289020:intron 20.0%
ATGTTACTCCAAACCATTGA+AGG + chr2_3:35241080-35241099 Msa0289020:CDS 35.0%
AGCAATAACCTTCAATGGTT+TGG - chr2_3:35241091-35241110 None:intergenic 35.0%
ACAGAAGCAATAACCTTCAA+TGG - chr2_3:35241096-35241115 None:intergenic 35.0%
!! TAAAGCACCTGAACTTTTGA+TGG + chr2_3:35241154-35241173 Msa0289020:CDS 35.0%
!! AAAGCACCTGAACTTTTGAT+GGG + chr2_3:35241155-35241174 Msa0289020:CDS 35.0%
ATCAACTGCAGTTGAGTAAT+TGG - chr2_3:35241186-35241205 None:intergenic 35.0%
ATATCTTCACCAATGAACAG+AGG - chr2_3:35241254-35241273 None:intergenic 35.0%
TGAAGATATACCGCAGATAT+TGG + chr2_3:35241265-35241284 Msa0289020:CDS 35.0%
!! AGATATTGGCTGCGATATTT+TGG + chr2_3:35241279-35241298 Msa0289020:CDS 35.0%
AGTTCAGGTGCTTTATAGCA+AGG - chr2_3:35241149-35241168 None:intergenic 40.0%
GTAGAACCCATCAAAAGTTC+AGG - chr2_3:35241164-35241183 None:intergenic 40.0%
! GCATATTTGCTGAGATGCTT+AGG + chr2_3:35241222-35241241 Msa0289020:CDS 40.0%
AATATCGCAGCCAATATCTG+CGG - chr2_3:35241278-35241297 None:intergenic 40.0%
! ACTCAACTGCAGTTGATGTC+TGG + chr2_3:35241189-35241208 Msa0289020:CDS 45.0%
! TGCAGTTGATGTCTGGTCTA+TGG + chr2_3:35241196-35241215 Msa0289020:CDS 45.0%
! GCAGTTGATGTCTGGTCTAT+GGG + chr2_3:35241197-35241216 Msa0289020:CDS 45.0%
CTTCACCAATGAACAGAGGT+TGG - chr2_3:35241250-35241269 None:intergenic 45.0%
AGGCTCCAACCTCTGTTCAT+TGG + chr2_3:35241242-35241261 Msa0289020:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 35241072 35241304 35241072 ID=Msa0289020;Name=Msa0289020
chr2_3 mRNA 35241072 35241304 35241072 ID=Msa0289020-mRNA-1;Parent=Msa0289020;Name=Msa0289020-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|0.5|0|0.5|2|0|65
chr2_3 exon 35241072 35241101 35241072 ID=Msa0289020-mRNA-1:exon:11388;Parent=Msa0289020-mRNA-1
chr2_3 exon 35241137 35241304 35241137 ID=Msa0289020-mRNA-1:exon:11389;Parent=Msa0289020-mRNA-1
chr2_3 CDS 35241072 35241101 35241072 ID=Msa0289020-mRNA-1:cds;Parent=Msa0289020-mRNA-1
chr2_3 CDS 35241137 35241304 35241137 ID=Msa0289020-mRNA-1:cds;Parent=Msa0289020-mRNA-1
Gene Sequence

>Msa0289020

ATGAATAAATGTTACTCCAAACCATTGAAGATGGGTAATCCTTGCTATAAAGCACCTGAACTTTTGATGGGTTCTACCAATTACTCAACTGCAGTTGATGTCTGGTCTATGGGATGCATATTTGCTGAGATGCTTAGGCTCCAACCTCTGTTCATTGGTGAAGATATACCGCAGATATTGGCTGCGATATTTTGGTAA
Protein sequence

>Msa0289020

MNKCYSKPLKMGNPCYKAPELLMGSTNYSTAVDVWSMGCIFAEMLRLQPLFIGEDIPQILAAIFW*