AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0445940

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0445940 MtrunA17_Chr3g0090261 85.714 98 13 1 1 98 234 330 2.55e-56 177
Msa0445940 MtrunA17_Chr8g0388891 67.347 98 10 2 1 98 285 360 1.83e-36 127
Msa0445940 MtrunA17_Chr4g0075541 65.909 88 29 1 11 98 249 335 7.87e-35 122
Msa0445940 MtrunA17_Chr4g0047191 58.621 87 35 1 11 97 208 293 1.08e-34 121
Msa0445940 MtrunA17_Chr4g0047211 58.621 87 35 1 11 97 203 288 1.41e-34 121
Msa0445940 MtrunA17_Chr4g0047201 57.471 87 36 1 11 97 364 449 3.70e-33 119
Msa0445940 MtrunA17_Chr4g0059121 59.551 89 35 1 10 98 219 306 2.55e-32 115
Msa0445940 MtrunA17_Chr3g0117731 57.955 88 36 1 10 97 218 304 1.61e-30 110
Msa0445940 MtrunA17_Chr2g0282321 52.874 87 40 1 11 97 325 410 4.19e-30 110
Msa0445940 MtrunA17_Chr3g0143531 51.613 93 44 1 6 98 177 268 4.98e-29 105
Msa0445940 MtrunA17_Chr5g0406251 50.515 97 47 1 2 98 443 538 5.15e-29 108
Msa0445940 MtrunA17_Chr1g0211611 47.423 97 50 1 2 98 449 544 4.62e-27 103
Msa0445940 MtrunA17_Chr1g0202101 50.538 93 44 2 6 98 435 525 1.38e-26 101
Msa0445940 MtrunA17_Chr7g0244621 47.115 104 46 2 3 98 198 300 1.85e-25 97.1
Msa0445940 MtrunA17_Chr1g0205071 46.667 90 47 1 6 95 256 344 7.22e-22 87.8
Msa0445940 MtrunA17_Chr6g0449241 47.664 107 40 4 3 98 179 280 2.03e-21 86.3
Msa0445940 MtrunA17_Chr3g0117811 42.222 90 51 1 6 95 237 325 7.04e-20 82.0
Msa0445940 MtrunA17_Chr6g0450871 43.333 90 50 1 6 95 249 337 1.62e-19 81.3
Msa0445940 MtrunA17_Chr4g0059181 42.222 90 51 1 6 95 266 354 5.75e-19 79.7
Msa0445940 MtrunA17_Chr3g0116981 43.810 105 47 4 3 98 179 280 1.14e-18 78.6
Msa0445940 MtrunA17_Chr5g0394681 42.222 90 51 1 6 95 264 352 1.31e-18 79.0
Msa0445940 MtrunA17_Chr5g0431191 37.374 99 57 2 4 98 480 577 1.38e-18 79.0
Msa0445940 MtrunA17_Chr3g0105891 37.374 99 57 2 4 98 477 574 1.89e-17 75.9
Msa0445940 MtrunA17_Chr1g0157231 51.562 64 30 1 2 65 293 355 4.60e-17 74.3
Msa0445940 MtrunA17_Chr5g0427651 40.909 88 51 1 11 98 808 894 4.67e-17 74.7
Msa0445940 MtrunA17_Chr1g0151541 39.773 88 52 1 11 98 823 909 1.46e-16 73.2
Msa0445940 MtrunA17_Chr2g0310781 42.391 92 46 3 11 98 1014 1102 2.13e-16 72.8
Msa0445940 MtrunA17_Chr4g0068411 39.362 94 54 2 6 97 613 705 2.16e-16 72.8
Msa0445940 MtrunA17_Chr4g0042731 38.043 92 56 1 6 97 304 394 6.20e-16 71.2
Msa0445940 MtrunA17_Chr2g0310761 41.304 92 47 3 11 98 1108 1196 8.76e-16 71.2
Msa0445940 MtrunA17_Chr6g0482711 38.636 88 53 1 11 98 820 906 9.64e-16 70.9
Msa0445940 MtrunA17_Chr1g0191171 38.636 88 53 1 11 98 849 935 2.55e-15 69.7
Msa0445940 MtrunA17_Chr2g0294351 39.080 87 52 1 11 97 626 711 3.68e-15 69.3
Msa0445940 MtrunA17_Chr2g0305141 39.130 92 49 3 11 98 1252 1340 3.90e-15 69.3
Msa0445940 MtrunA17_Chr3g0132791 37.931 87 53 1 11 97 815 900 6.55e-15 68.6
Msa0445940 MtrunA17_Chr3g0136131 37.374 99 57 2 5 98 251 349 1.51e-14 67.4
Msa0445940 MtrunA17_Chr6g0461841 36.667 90 54 2 11 98 1136 1224 3.87e-14 66.2
Msa0445940 MtrunA17_Chr4g0065211 36.957 92 51 3 11 98 1290 1378 1.17e-13 65.1
Msa0445940 MtrunA17_Chr8g0357611 38.043 92 50 3 11 98 1539 1627 1.66e-13 64.7
Msa0445940 MtrunA17_Chr4g0072741 37.778 90 53 2 11 98 1004 1092 1.69e-13 64.7
Msa0445940 MtrunA17_Chr1g0171571 34.951 103 51 2 11 97 203 305 3.12e-13 63.9
Msa0445940 MtrunA17_Chr1g0196631 33.333 90 57 2 11 98 1069 1157 3.35e-13 63.9
Msa0445940 MtrunA17_Chr5g0397931 32.955 88 56 2 11 97 583 668 5.25e-13 63.2
Msa0445940 MtrunA17_Chr8g0392871 34.091 88 57 1 11 98 899 985 2.02e-12 61.6
Msa0445940 MtrunA17_Chr1g0179331 35.227 88 56 1 11 98 717 803 2.67e-12 61.2
Msa0445940 MtrunA17_Chr8g0347481 38.356 73 45 0 26 98 427 499 7.96e-12 59.7
Msa0445940 MtrunA17_Chr1g0171451 36.364 88 55 1 11 98 576 662 1.04e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0445940 AT4G31170.7 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.6 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.5 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.1 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.2 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.3 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT4G31170.8 78.571 98 20 1 1 98 283 379 1.04e-49 162
Msa0445940 AT2G24360.1 78.351 97 20 1 1 97 282 377 2.46e-49 161
Msa0445940 AT1G62400.1 65.909 88 29 1 11 98 248 334 2.67e-34 121
Msa0445940 AT4G35780.1 49.000 100 48 2 1 98 437 535 2.33e-28 107
Msa0445940 AT4G38470.1 51.546 97 46 1 2 98 438 533 1.64e-27 104
Msa0445940 AT5G58950.1 50.575 87 42 1 11 97 371 456 1.77e-27 104
Msa0445940 AT4G38470.2 51.546 97 46 1 2 98 438 533 2.20e-27 104
Msa0445940 AT2G17700.1 48.913 92 46 1 6 97 438 528 3.83e-26 100
Msa0445940 AT3G46930.1 43.678 87 49 0 11 97 327 413 6.83e-26 99.8
Msa0445940 AT3G46930.2 43.678 87 49 0 11 97 362 448 1.80e-25 99.0
Msa0445940 AT5G01850.1 47.115 104 46 2 3 98 171 273 4.03e-25 96.3
Msa0445940 AT5G01850.2 47.115 104 46 2 3 98 195 297 5.92e-25 96.3
Msa0445940 AT5G50000.1 45.556 90 48 1 6 95 259 347 2.92e-21 86.3
Msa0445940 AT5G50180.1 45.714 105 45 4 3 98 173 274 4.44e-21 85.5
Msa0445940 AT3G27560.1 46.729 107 41 4 3 98 179 280 5.09e-21 85.5
Msa0445940 AT3G63260.1 42.391 92 52 1 4 95 263 353 5.33e-21 85.9
Msa0445940 AT5G40540.3 46.729 107 41 4 3 98 82 183 6.84e-21 84.0
Msa0445940 AT5G40540.2 46.729 107 41 4 3 98 103 204 8.50e-21 84.0
Msa0445940 AT5G40540.1 46.729 107 41 4 3 98 179 280 9.35e-21 84.7
Msa0445940 AT3G01490.1 43.333 90 50 1 6 95 285 373 5.64e-20 83.2
Msa0445940 AT1G14000.1 41.935 93 51 2 6 97 323 413 5.73e-20 83.2
Msa0445940 AT3G22750.1 42.222 90 51 1 6 95 252 340 2.70e-19 80.9
Msa0445940 AT4G14780.1 42.105 95 54 1 1 95 233 326 5.19e-19 80.1
Msa0445940 AT4G38470.3 59.375 64 25 1 2 65 438 500 1.87e-18 79.0
Msa0445940 AT5G66710.1 43.519 108 43 6 2 97 222 323 4.65e-17 74.7
Msa0445940 AT1G08720.1 40.909 88 51 1 11 98 829 915 1.43e-16 73.6
Msa0445940 AT5G58520.1 37.374 99 57 2 4 98 495 592 2.33e-16 73.2
Msa0445940 AT4G24480.3 42.529 87 49 1 11 97 831 916 5.71e-16 72.0
Msa0445940 AT4G24480.1 42.529 87 49 1 11 97 836 921 6.42e-16 72.0
Msa0445940 AT4G24480.2 42.529 87 49 1 11 97 831 916 6.48e-16 72.0
Msa0445940 AT1G67890.1 40.230 87 51 1 11 97 646 731 8.24e-16 71.6
Msa0445940 AT2G35050.1 42.857 91 45 3 11 97 1142 1229 1.04e-15 71.2
Msa0445940 AT2G35050.2 42.857 91 45 3 11 97 1142 1229 1.04e-15 71.2
Msa0445940 AT5G07140.1 36.364 99 58 2 4 98 474 571 3.01e-15 70.1
Msa0445940 AT3G24715.1 36.667 90 54 2 11 98 1005 1093 3.62e-15 69.7
Msa0445940 AT3G24715.3 36.667 90 54 2 11 98 1005 1093 3.62e-15 69.7
Msa0445940 AT3G24715.2 36.667 90 54 2 11 98 1005 1093 3.62e-15 69.7
Msa0445940 AT5G11850.1 37.500 88 54 1 11 98 769 855 5.54e-15 69.3
Msa0445940 AT1G79570.2 40.217 92 48 3 11 98 1133 1221 6.98e-15 68.9
Msa0445940 AT1G79570.1 40.217 92 48 3 11 98 1133 1221 6.98e-15 68.9
Msa0445940 AT1G16270.1 40.217 92 48 3 11 98 1032 1120 1.82e-14 67.8
Msa0445940 AT1G16270.2 40.217 92 48 3 11 98 1032 1120 1.82e-14 67.8
Msa0445940 AT1G16270.3 40.217 92 48 3 11 98 1032 1120 1.82e-14 67.8
Msa0445940 AT5G49470.7 37.234 94 56 2 6 97 517 609 2.73e-14 67.0
Msa0445940 AT1G04700.1 37.778 90 53 2 11 98 935 1023 3.62e-14 67.0
Msa0445940 AT1G04700.2 37.778 90 53 2 11 98 935 1023 3.62e-14 67.0
Msa0445940 AT5G49470.3 37.234 94 56 2 6 97 644 736 4.09e-14 66.6
Msa0445940 AT5G49470.2 37.234 94 56 2 6 97 705 797 4.48e-14 66.6
Msa0445940 AT5G49470.4 37.234 94 56 2 6 97 618 710 4.72e-14 66.6
Msa0445940 AT4G23050.1 36.364 88 53 2 11 97 627 712 5.10e-14 66.6
Msa0445940 AT4G23050.2 36.364 88 53 2 11 97 628 713 5.10e-14 66.6
Msa0445940 AT5G49470.1 37.234 94 56 2 6 97 357 449 6.26e-14 66.2
Msa0445940 AT5G57610.1 37.778 90 53 2 11 98 950 1038 9.32e-14 65.9
Msa0445940 AT1G18160.1 36.782 87 54 1 11 97 875 960 9.76e-14 65.5
Msa0445940 AT1G73660.1 34.091 88 57 1 11 98 908 994 1.97e-13 64.7
Msa0445940 AT3G50720.1 34.615 104 51 4 5 97 203 300 3.65e-13 63.9
Msa0445940 AT3G46930.6 45.455 55 30 0 11 65 266 320 4.80e-13 63.5
Msa0445940 AT3G46930.5 45.455 55 30 0 11 65 327 381 5.34e-13 63.5
Msa0445940 AT3G46930.4 45.455 55 30 0 11 65 362 416 5.68e-13 63.5
Msa0445940 AT3G46930.3 45.455 55 30 0 11 65 362 416 5.95e-13 63.2
Msa0445940 AT5G40540.4 49.296 71 27 2 3 65 179 248 6.89e-13 62.8
Msa0445940 AT3G50730.1 35.238 105 51 4 5 97 190 289 7.63e-13 62.8
Msa0445940 AT3G06630.2 35.632 87 55 1 11 97 594 679 1.14e-12 62.8
Msa0445940 AT1G08720.2 40.506 79 46 1 11 89 829 906 1.75e-12 62.0
Msa0445940 AT1G67890.4 40.260 77 45 1 11 87 518 593 3.15e-12 61.2
Msa0445940 AT1G67890.3 40.260 77 45 1 11 87 646 721 3.19e-12 61.2
Msa0445940 AT1G67890.2 40.260 77 45 1 11 87 646 721 3.19e-12 61.2
Msa0445940 AT3G06620.1 34.483 87 56 1 11 97 654 739 3.24e-12 61.2
Msa0445940 AT5G03730.2 38.636 88 53 1 11 98 713 799 5.77e-12 60.5
Msa0445940 AT5G03730.1 38.636 88 53 1 11 98 713 799 5.77e-12 60.5
Msa0445940 AT3G46920.2 36.957 92 51 3 11 98 1041 1129 6.47e-12 60.5
Msa0445940 AT3G46920.1 36.957 92 51 3 11 98 975 1063 7.84e-12 60.1
Msa0445940 AT3G06640.2 34.483 87 56 1 11 97 606 691 1.13e-11 59.7
Msa0445940 AT3G06640.3 34.483 87 56 1 11 97 606 691 1.13e-11 59.7
Msa0445940 AT3G06640.1 34.483 87 56 1 11 97 606 691 1.29e-11 59.7
Msa0445940 AT1G64300.2 38.356 73 45 0 26 98 431 503 4.60e-11 58.2
Msa0445940 AT1G64300.1 38.356 73 45 0 26 98 431 503 4.60e-11 58.2

Find 25 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGCTATAATTTAAGAAAA+TGG 0.226287 3_3:+20843620 None:intergenic
ATAGCTTTATGATTGTTCTC+TGG 0.359801 3_3:-20843808 Msa0445940:CDS
GTCATTATTTCACGGAGAAC+AGG 0.380682 3_3:+20843677 None:intergenic
GAAAATGGTGGCCTAACATC+AGG 0.402307 3_3:+20843635 None:intergenic
TAGCTTTATGATTGTTCTCT+GGG 0.411950 3_3:-20843807 Msa0445940:CDS
GAGAACAGGCAAACAATCAT+TGG 0.416206 3_3:+20843691 None:intergenic
GTTCTCTGGGAGCTCATAAC+TGG 0.417397 3_3:-20843794 Msa0445940:CDS
GGGATACAAACCCTGATGTT+AGG 0.435314 3_3:-20843646 Msa0445940:CDS
AAACAATCATTGGGTAAGAT+TGG 0.447812 3_3:+20843701 None:intergenic
GTGAAATAATGACAAGGTGC+TGG 0.454947 3_3:-20843667 Msa0445940:CDS
ACATCTACTTTAAGTGTGTA+AGG 0.463881 3_3:+20843833 None:intergenic
AGCACCTTGTCATTATTTCA+CGG 0.488236 3_3:+20843669 None:intergenic
TAAGTGTGTAAGGCCTATGT+TGG 0.512303 3_3:+20843843 None:intergenic
GAAGGAATGACTCTCAAGAC+TGG 0.526345 3_3:-20843896 Msa0445940:CDS
TGAAATAATGACAAGGTGCT+GGG 0.534114 3_3:-20843666 Msa0445940:CDS
AGAACAGGCAAACAATCATT+GGG 0.539053 3_3:+20843692 None:intergenic
TCATCTGCGGAGCCATCCTA+CGG 0.600750 3_3:+20843867 None:intergenic
CGGATTGAGATGCAAACTGA+AGG 0.601662 3_3:-20843914 None:intergenic
GCTATAATTTAAGAAAATGG+TGG 0.604618 3_3:+20843623 None:intergenic
AAAATGGTGGCCTAACATCA+GGG 0.606028 3_3:+20843636 None:intergenic
GACTGGAACATACCGTAGGA+TGG 0.620272 3_3:-20843879 Msa0445940:CDS
CTCCGCAGATGATCCAACAT+AGG 0.638723 3_3:-20843856 Msa0445940:CDS
GGCCTATGTTGGATCATCTG+CGG 0.649608 3_3:+20843854 None:intergenic
TCAAGACTGGAACATACCGT+AGG 0.675999 3_3:-20843883 Msa0445940:CDS
TTCTCCGTGAAATAATGACA+AGG 0.688796 3_3:-20843673 Msa0445940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CAGTTGTCAATAAAAATGAA+CGG - chr3_3:20843812-20843831 Msa0445940:CDS 25.0%
ACATCTACTTTAAGTGTGTA+AGG + chr3_3:20843706-20843725 None:intergenic 30.0%
!! ATAGCTTTATGATTGTTCTC+TGG - chr3_3:20843728-20843747 Msa0445940:CDS 30.0%
!! TAGCTTTATGATTGTTCTCT+GGG - chr3_3:20843729-20843748 Msa0445940:CDS 30.0%
AAACAATCATTGGGTAAGAT+TGG + chr3_3:20843838-20843857 None:intergenic 30.0%
!!! ACTGCTGTCATGTTTTGAAA+TGG + chr3_3:20843775-20843794 None:intergenic 35.0%
AGAACAGGCAAACAATCATT+GGG + chr3_3:20843847-20843866 None:intergenic 35.0%
TTCTCCGTGAAATAATGACA+AGG - chr3_3:20843863-20843882 Msa0445940:CDS 35.0%
AGCACCTTGTCATTATTTCA+CGG + chr3_3:20843870-20843889 None:intergenic 35.0%
! TGAAATAATGACAAGGTGCT+GGG - chr3_3:20843870-20843889 Msa0445940:CDS 35.0%
TAAGTGTGTAAGGCCTATGT+TGG + chr3_3:20843696-20843715 None:intergenic 40.0%
GAGAACAGGCAAACAATCAT+TGG + chr3_3:20843848-20843867 None:intergenic 40.0%
GTCATTATTTCACGGAGAAC+AGG + chr3_3:20843862-20843881 None:intergenic 40.0%
GTGAAATAATGACAAGGTGC+TGG - chr3_3:20843869-20843888 Msa0445940:CDS 40.0%
AAAATGGTGGCCTAACATCA+GGG + chr3_3:20843903-20843922 None:intergenic 40.0%
GAAGGAATGACTCTCAAGAC+TGG - chr3_3:20843640-20843659 Msa0445940:CDS 45.0%
TCAAGACTGGAACATACCGT+AGG - chr3_3:20843653-20843672 Msa0445940:CDS 45.0%
GGGATACAAACCCTGATGTT+AGG - chr3_3:20843890-20843909 Msa0445940:CDS 45.0%
GAAAATGGTGGCCTAACATC+AGG + chr3_3:20843904-20843923 None:intergenic 45.0%
GACTGGAACATACCGTAGGA+TGG - chr3_3:20843657-20843676 Msa0445940:CDS 50.0%
CTCCGCAGATGATCCAACAT+AGG - chr3_3:20843680-20843699 Msa0445940:CDS 50.0%
GGCCTATGTTGGATCATCTG+CGG + chr3_3:20843685-20843704 None:intergenic 50.0%
! GTTCTCTGGGAGCTCATAAC+TGG - chr3_3:20843742-20843761 Msa0445940:CDS 50.0%
TCATCTGCGGAGCCATCCTA+CGG + chr3_3:20843672-20843691 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 20843631 20843927 20843631 ID=Msa0445940;Name=Msa0445940
chr3_3 mRNA 20843631 20843927 20843631 ID=Msa0445940-mRNA-1;Parent=Msa0445940;Name=Msa0445940-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|98
chr3_3 exon 20843631 20843927 20843631 ID=Msa0445940-mRNA-1:exon:4399;Parent=Msa0445940-mRNA-1
chr3_3 CDS 20843631 20843927 20843631 ID=Msa0445940-mRNA-1:cds;Parent=Msa0445940-mRNA-1
Gene Sequence

>Msa0445940

ATGCAAACTGAAGGAATGACTCTCAAGACTGGAACATACCGTAGGATGGCTCCGCAGATGATCCAACATAGGCCTTACACACTTAAAGTAGATGTATATAGCTTTATGATTGTTCTCTGGGAGCTCATAACTGGTATGCTTCCATTTCAAAACATGACAGCAGTACAGCATGCAGCATTTGCAGTTGTCAATAAAAATGAACGGCCAATCTTACCCAATGATTGTTTGCCTGTTCTCCGTGAAATAATGACAAGGTGCTGGGATACAAACCCTGATGTTAGGCCACCATTTTCTTAA
Protein sequence

>Msa0445940

MQTEGMTLKTGTYRRMAPQMIQHRPYTLKVDVYSFMIVLWELITGMLPFQNMTAVQHAAFAVVNKNERPILPNDCLPVLREIMTRCWDTNPDVRPPFS*