AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0730710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0730710 MtrunA17_Chr5g0424581 91.589 107 9 0 2 108 291 397 3.33e-59 186
Msa0730710 MtrunA17_Chr5g0424501 90.654 107 10 0 2 108 358 464 9.84e-57 181
Msa0730710 MtrunA17_Chr5g0424651 89.720 107 11 0 2 108 487 593 2.63e-56 183
Msa0730710 MtrunA17_Chr5g0424531 80.189 106 21 0 2 107 182 287 2.92e-49 157
Msa0730710 MtrunA17_Chr3g0115171 73.585 106 25 1 2 107 449 551 3.13e-48 161
Msa0730710 MtrunA17_Chr4g0051191 63.107 103 34 1 2 104 330 428 1.12e-36 128
Msa0730710 MtrunA17_Chr3g0130151 49.412 85 42 1 7 90 417 501 3.49e-24 95.5
Msa0730710 MtrunA17_Chr8g0384301 45.882 85 45 1 7 90 472 556 9.70e-24 94.4
Msa0730710 MtrunA17_Chr1g0202831 53.165 79 36 1 13 90 590 668 4.72e-23 92.4
Msa0730710 MtrunA17_Chr8g0386981 51.807 83 39 1 9 90 583 665 6.44e-23 92.0
Msa0730710 MtrunA17_Chr2g0288841 41.304 92 50 3 2 91 167 256 8.06e-20 82.8
Msa0730710 MtrunA17_Chr5g0402601 43.820 89 48 2 16 104 561 647 1.91e-19 82.0
Msa0730710 MtrunA17_Chr4g0038501 44.706 85 47 0 7 91 192 276 9.17e-19 80.1
Msa0730710 MtrunA17_Chr4g0038091 44.706 85 47 0 7 91 192 276 1.35e-18 79.7
Msa0730710 MtrunA17_Chr1g0205931 46.429 84 40 3 10 89 236 318 1.51e-18 79.3
Msa0730710 MtrunA17_Chr2g0322401 40.000 90 50 3 2 89 169 256 3.15e-18 78.2
Msa0730710 MtrunA17_Chr3g0133541 41.667 96 54 2 1 95 480 574 9.16e-18 77.0
Msa0730710 MtrunA17_Chr4g0052981 42.105 95 49 3 14 103 181 274 1.48e-17 75.9
Msa0730710 MtrunA17_Chr7g0272841 45.783 83 42 2 10 89 249 331 1.94e-17 76.3
Msa0730710 MtrunA17_Chr8g0375141 42.105 95 49 3 14 103 220 313 4.59e-17 74.7
Msa0730710 MtrunA17_Chr4g0025041 42.222 90 48 3 2 89 162 249 1.76e-16 73.2
Msa0730710 MtrunA17_Chr2g0276831 45.122 82 38 2 15 89 207 288 7.84e-16 71.2
Msa0730710 MtrunA17_Chr4g0052961 45.122 82 39 3 14 90 218 298 1.46e-15 70.5
Msa0730710 MtrunA17_Chr5g0402091 42.169 83 44 2 11 89 183 265 2.63e-14 67.0
Msa0730710 MtrunA17_Chr5g0402111 40.741 81 46 2 11 89 182 262 8.26e-14 65.5
Msa0730710 MtrunA17_Chr2g0317001 36.585 82 52 0 9 90 187 268 3.75e-13 63.9
Msa0730710 MtrunA17_Chr5g0430501 41.573 89 48 3 2 89 178 263 2.31e-12 61.6
Msa0730710 MtrunA17_Chr1g0173921 31.579 95 65 0 11 105 180 274 3.01e-11 58.5
Msa0730710 MtrunA17_Chr6g0449691 40.000 85 49 2 9 91 258 342 3.23e-11 58.5
Msa0730710 MtrunA17_Chr4g0047201 37.662 77 47 1 9 84 377 453 6.01e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0730710 AT4G08500.1 67.033 91 30 0 3 93 501 591 1.64e-37 133
Msa0730710 AT4G12020.3 66.667 87 29 0 7 93 1779 1865 1.18e-35 128
Msa0730710 AT4G12020.10 66.667 87 29 0 7 93 1771 1857 1.24e-35 128
Msa0730710 AT4G12020.2 66.667 87 29 0 7 93 1795 1881 1.30e-35 128
Msa0730710 AT4G12020.4 66.667 87 29 0 7 93 1787 1873 1.36e-35 128
Msa0730710 AT4G12020.5 66.667 87 29 0 7 93 1720 1806 1.44e-35 128
Msa0730710 AT4G08480.1 63.333 90 33 0 3 92 669 758 8.56e-35 126
Msa0730710 AT4G08470.3 66.667 87 29 0 3 89 389 475 2.08e-34 123
Msa0730710 AT4G08470.1 66.667 87 29 0 3 89 471 557 3.01e-34 124
Msa0730710 AT1G63700.1 54.762 84 37 1 9 91 575 658 1.25e-24 97.1
Msa0730710 AT1G63700.2 54.762 84 37 1 9 91 575 658 1.25e-24 97.1
Msa0730710 AT1G53570.6 46.535 101 53 1 9 108 389 489 1.04e-23 94.4
Msa0730710 AT1G53570.7 46.535 101 53 1 9 108 389 489 1.09e-23 94.4
Msa0730710 AT1G53570.1 46.535 101 53 1 9 108 389 489 1.36e-23 94.0
Msa0730710 AT1G53570.2 46.535 101 53 1 9 108 389 489 1.37e-23 94.0
Msa0730710 AT1G53570.3 46.535 101 53 1 9 108 389 489 1.37e-23 94.0
Msa0730710 AT1G53570.4 46.535 101 53 1 9 108 389 489 1.41e-23 94.0
Msa0730710 AT1G53570.5 46.535 101 53 1 9 108 363 463 1.64e-23 94.0
Msa0730710 AT1G09000.1 45.652 92 48 2 10 99 250 341 2.39e-21 87.8
Msa0730710 AT1G09000.2 45.652 92 48 2 10 99 250 341 2.46e-21 87.8
Msa0730710 AT1G54960.1 50.000 82 39 2 10 89 249 330 3.28e-21 87.4
Msa0730710 AT1G54960.2 50.000 82 39 2 10 89 249 330 3.28e-21 87.4
Msa0730710 AT5G66850.1 43.023 86 48 1 16 101 535 619 2.02e-19 82.4
Msa0730710 AT5G66850.2 43.023 86 48 1 16 101 535 619 2.07e-19 82.4
Msa0730710 AT5G55090.1 42.222 90 48 3 2 89 169 256 3.23e-19 81.6
Msa0730710 AT5G55090.2 42.222 90 48 3 2 89 231 318 3.53e-19 81.6
Msa0730710 AT4G26890.1 42.222 90 48 3 2 89 166 253 2.38e-18 79.0
Msa0730710 AT1G05100.1 43.478 92 46 3 2 89 174 263 2.85e-18 78.2
Msa0730710 AT3G13530.1 43.529 85 48 0 7 91 192 276 4.74e-18 78.6
Msa0730710 AT3G07980.3 40.000 85 51 0 7 91 7 91 9.41e-17 74.7
Msa0730710 AT1G07150.2 40.196 102 57 3 2 102 180 278 9.49e-17 74.7
Msa0730710 AT1G07150.1 40.196 102 57 3 2 102 194 292 1.18e-16 74.3
Msa0730710 AT3G07980.2 40.000 85 51 0 7 91 192 276 1.21e-16 74.3
Msa0730710 AT3G07980.1 40.000 85 51 0 7 91 192 276 1.28e-16 74.3
Msa0730710 AT5G67080.1 42.169 83 44 2 11 89 187 269 3.20e-16 72.8
Msa0730710 AT3G06030.1 41.111 90 47 3 10 93 249 338 3.33e-16 73.2
Msa0730710 AT3G50310.1 43.373 83 43 2 11 89 186 268 3.76e-16 72.4
Msa0730710 AT2G32510.1 39.785 93 49 3 2 89 169 259 6.25e-16 72.0
Msa0730710 AT2G42550.1 44.000 75 42 0 16 90 201 275 2.64e-15 70.1
Msa0730710 AT2G30040.1 43.820 89 46 3 2 89 185 270 7.13e-15 69.3
Msa0730710 AT3G15220.1 37.805 82 51 0 9 90 187 268 1.28e-14 68.6
Msa0730710 AT1G53165.3 37.805 82 51 0 9 90 187 268 7.15e-14 66.6
Msa0730710 AT1G53165.2 37.805 82 51 0 9 90 187 268 7.72e-14 66.2
Msa0730710 AT1G53165.1 37.805 82 51 0 9 90 187 268 7.80e-14 66.2
Msa0730710 AT5G27510.1 40.000 80 48 0 16 95 196 275 2.27e-13 64.7
Msa0730710 AT3G46160.1 37.634 93 52 3 2 90 243 333 9.78e-13 63.2
Msa0730710 AT5G12090.1 37.838 74 46 0 16 89 220 293 1.01e-11 60.1
Msa0730710 AT5G40440.4 42.169 83 46 2 11 91 259 341 1.23e-11 60.1
Msa0730710 AT5G40440.1 42.169 83 46 2 11 91 259 341 1.23e-11 60.1
Msa0730710 AT5G40440.5 42.169 83 46 2 11 91 177 259 1.34e-11 60.1
Msa0730710 AT5G40440.6 42.169 83 46 2 11 91 241 323 1.70e-11 59.7
Msa0730710 AT5G40440.3 42.169 83 46 2 11 91 241 323 1.70e-11 59.7
Msa0730710 AT5G40440.2 42.169 83 46 2 11 91 241 323 1.70e-11 59.7
Msa0730710 AT1G69220.2 34.694 98 61 2 11 106 396 492 2.02e-11 59.3
Msa0730710 AT1G69220.1 34.694 98 61 2 11 106 423 519 2.21e-11 59.3
Msa0730710 AT3G20860.1 36.559 93 56 3 11 102 179 269 2.23e-11 59.3
Msa0730710 AT3G46140.1 36.559 93 53 3 2 90 280 370 2.64e-11 58.9

Find 31 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGGAGAAGTTAAAGGTTA+TGG 0.328156 5_1:-40524616 Msa0730710:CDS
ATGGACTTCCGGCTGATATA+TGG 0.328532 5_1:-40524597 Msa0730710:CDS
ACACATTCTATAGGAAAGTA+TGG 0.342574 5_1:+40524532 None:intergenic
GTTGTAAGAGGAGAAGTTAA+AGG 0.346623 5_1:-40524622 Msa0730710:CDS
ATCAGCGCAATGTTTAGAAT+TGG 0.352345 5_1:-40524308 Msa0730710:CDS
GCCGCAGTGGGACGATAATC+TGG 0.379542 5_1:+40524206 None:intergenic
TGACAAGTTTAACTTCTTCT+CGG 0.384408 5_1:+40524113 None:intergenic
AGTTAAAGGTTATGGACTTC+CGG 0.401887 5_1:-40524608 Msa0730710:CDS
AGGCCATTCTCCCAGTCCTC+TGG 0.409860 5_1:-40524155 Msa0730710:CDS
GAGCCAGAGGACTGGGAGAA+TGG 0.426184 5_1:+40524152 None:intergenic
GAGACGCTGAGCCAGAGGAC+TGG 0.427580 5_1:+40524144 None:intergenic
GCATCTCTTGAAAGAGAATC+AGG 0.428783 5_1:+40524263 None:intergenic
ATGATACATACACATTCTAT+AGG 0.429660 5_1:+40524523 None:intergenic
ACTGTGTTGGAGATGTTAAC+TGG 0.438819 5_1:-40524562 Msa0730710:CDS
AGACGCTGAGCCAGAGGACT+GGG 0.451496 5_1:+40524145 None:intergenic
TAACTTCTTCTCGGAATATG+TGG 0.489251 5_1:+40524122 None:intergenic
TGGTTAATGCAGGTTGTAAG+AGG 0.499527 5_1:-40524634 None:intergenic
AGGACTGGGAGAATGGCCTC+TGG 0.523339 5_1:+40524159 None:intergenic
GCAATGTTTAGAATTGGAAA+AGG 0.534493 5_1:-40524302 Msa0730710:CDS
ATGGCCTCTGGACAAATTTG+TGG 0.547546 5_1:+40524171 None:intergenic
CCGGCTGATATATGGAGTCT+AGG 0.550239 5_1:-40524589 Msa0730710:CDS
GAAAGAGAATCAGGCACTAG+AGG 0.561342 5_1:+40524272 None:intergenic
GATTAACTTTAAGACACTGC+AGG 0.562865 5_1:+40524228 None:intergenic
CCTAGACTCCATATATCAGC+CGG 0.562948 5_1:+40524589 None:intergenic
ATGTGGAGACGCTGAGCCAG+AGG 0.603856 5_1:+40524139 None:intergenic
TGTAAGAGTTGAGCCGCAGT+GGG 0.627742 5_1:+40524194 None:intergenic
GAGTCTAGGATGCACTGTGT+TGG 0.638667 5_1:-40524575 Msa0730710:CDS
CTGTGTTGGAGATGTTAACT+GGG 0.645031 5_1:-40524561 Msa0730710:CDS
TACACCACAAATTTGTCCAG+AGG 0.645222 5_1:-40524175 Msa0730710:CDS
GTGTAAGAGTTGAGCCGCAG+TGG 0.655520 5_1:+40524193 None:intergenic
TCCAGATTATCGTCCCACTG+CGG 0.754456 5_1:-40524207 Msa0730710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATTTTATATAGAGATA+GGG + chr5_1:40524358-40524377 None:intergenic 10.0%
!!! TATAAATTTTATATAGAGAT+AGG + chr5_1:40524359-40524378 None:intergenic 10.0%
!! AGTTTAATCTTCTGTTAATA+GGG + chr5_1:40524290-40524309 None:intergenic 20.0%
!! AAGTTTAATCTTCTGTTAAT+AGG + chr5_1:40524291-40524310 None:intergenic 20.0%
! ATGATACATACACATTCTAT+AGG + chr5_1:40524229-40524248 None:intergenic 25.0%
ACACATTCTATAGGAAAGTA+TGG + chr5_1:40524220-40524239 None:intergenic 30.0%
! AAGAATGAGTTGGATTGAAA+TGG + chr5_1:40524257-40524276 None:intergenic 30.0%
TGGTAAAAAGAAGAATGAGT+TGG + chr5_1:40524267-40524286 None:intergenic 30.0%
TTAATCTTCTGTTAATAGGG+TGG + chr5_1:40524287-40524306 None:intergenic 30.0%
! GCAATGTTTAGAATTGGAAA+AGG - chr5_1:40524447-40524466 Msa0730710:intron 30.0%
GTTGTAAGAGGAGAAGTTAA+AGG - chr5_1:40524127-40524146 Msa0730710:CDS 35.0%
AGAGGAGAAGTTAAAGGTTA+TGG - chr5_1:40524133-40524152 Msa0730710:CDS 35.0%
AGTTAAAGGTTATGGACTTC+CGG - chr5_1:40524141-40524160 Msa0730710:CDS 35.0%
AGAAGAGATTCATCAAAGCT+TGG + chr5_1:40524413-40524432 None:intergenic 35.0%
! ATCAGCGCAATGTTTAGAAT+TGG - chr5_1:40524441-40524460 Msa0730710:intron 35.0%
!! GATTAACTTTAAGACACTGC+AGG + chr5_1:40524524-40524543 None:intergenic 35.0%
TAACTTCTTCTCGGAATATG+TGG + chr5_1:40524630-40524649 None:intergenic 35.0%
ACTGTGTTGGAGATGTTAAC+TGG - chr5_1:40524187-40524206 Msa0730710:CDS 40.0%
CTGTGTTGGAGATGTTAACT+GGG - chr5_1:40524188-40524207 Msa0730710:CDS 40.0%
GCATCTCTTGAAAGAGAATC+AGG + chr5_1:40524489-40524508 None:intergenic 40.0%
TACACCACAAATTTGTCCAG+AGG - chr5_1:40524574-40524593 Msa0730710:CDS 40.0%
ATGGACTTCCGGCTGATATA+TGG - chr5_1:40524152-40524171 Msa0730710:CDS 45.0%
CCTAGACTCCATATATCAGC+CGG + chr5_1:40524163-40524182 None:intergenic 45.0%
GAAAGAGAATCAGGCACTAG+AGG + chr5_1:40524480-40524499 None:intergenic 45.0%
ATGGCCTCTGGACAAATTTG+TGG + chr5_1:40524581-40524600 None:intergenic 45.0%
CCGGCTGATATATGGAGTCT+AGG - chr5_1:40524160-40524179 Msa0730710:CDS 50.0%
! GAGTCTAGGATGCACTGTGT+TGG - chr5_1:40524174-40524193 Msa0730710:CDS 50.0%
TCCAGATTATCGTCCCACTG+CGG - chr5_1:40524542-40524561 Msa0730710:CDS 50.0%
TGTAAGAGTTGAGCCGCAGT+GGG + chr5_1:40524558-40524577 None:intergenic 50.0%
GTGTAAGAGTTGAGCCGCAG+TGG + chr5_1:40524559-40524578 None:intergenic 55.0%
GCCGCAGTGGGACGATAATC+TGG + chr5_1:40524546-40524565 None:intergenic 60.0%
AGGACTGGGAGAATGGCCTC+TGG + chr5_1:40524593-40524612 None:intergenic 60.0%
AGGCCATTCTCCCAGTCCTC+TGG - chr5_1:40524594-40524613 Msa0730710:CDS 60.0%
GAGCCAGAGGACTGGGAGAA+TGG + chr5_1:40524600-40524619 None:intergenic 60.0%
AGACGCTGAGCCAGAGGACT+GGG + chr5_1:40524607-40524626 None:intergenic 60.0%
ATGTGGAGACGCTGAGCCAG+AGG + chr5_1:40524613-40524632 None:intergenic 60.0%
GAGACGCTGAGCCAGAGGAC+TGG + chr5_1:40524608-40524627 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 40524121 40524650 40524121 ID=Msa0730710;Name=Msa0730710
chr5_1 mRNA 40524121 40524650 40524121 ID=Msa0730710-mRNA-1;Parent=Msa0730710;Name=Msa0730710-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|1|0|1|1|1|2|0|108
chr5_1 exon 40524534 40524650 40524534 ID=Msa0730710-mRNA-1:exon:11810;Parent=Msa0730710-mRNA-1
chr5_1 exon 40524121 40524330 40524121 ID=Msa0730710-mRNA-1:exon:11809;Parent=Msa0730710-mRNA-1
chr5_1 CDS 40524534 40524650 40524534 ID=Msa0730710-mRNA-1:cds;Parent=Msa0730710-mRNA-1
chr5_1 CDS 40524121 40524330 40524121 ID=Msa0730710-mRNA-1:cds;Parent=Msa0730710-mRNA-1
Gene Sequence

>Msa0730710

ATGCAGGTTGTAAGAGGAGAAGTTAAAGGTTATGGACTTCCGGCTGATATATGGAGTCTAGGATGCACTGTGTTGGAGATGTTAACTGGGCAAGTTCCATACTTTCCTATAGAATGTATCAGCGCAATGTTTAGAATTGGAAAAGGTGAACTACCTCTAGTGCCTGATTCTCTTTCAAGAGATGCACGTGATTTCATCCTGCAGTGTCTTAAAGTTAATCCAGATTATCGTCCCACTGCGGCTCAACTCTTACACCACAAATTTGTCCAGAGGCCATTCTCCCAGTCCTCTGGCTCAGCGTCTCCACATATTCCGAGAAGAAGTTAA
Protein sequence

>Msa0730710

MQVVRGEVKGYGLPADIWSLGCTVLEMLTGQVPYFPIECISAMFRIGKGELPLVPDSLSRDARDFILQCLKVNPDYRPTAAQLLHHKFVQRPFSQSSGSASPHIPRRS*