AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1466910


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1466910 MtrunA17_Chr5g0427651 100.000 75 0 0 1 75 810 884 2.57e-48 162
Msa1466910 MtrunA17_Chr3g0132791 82.667 75 13 0 1 75 817 891 2.36e-39 137
Msa1466910 MtrunA17_Chr6g0482711 65.753 73 25 0 2 74 823 895 2.58e-31 114
Msa1466910 MtrunA17_Chr1g0179331 64.000 75 27 0 1 75 719 793 1.52e-30 112
Msa1466910 MtrunA17_Chr1g0191171 64.865 74 26 0 1 74 851 924 1.24e-28 106
Msa1466910 MtrunA17_Chr1g0171451 64.000 75 27 0 1 75 578 652 2.76e-28 105
Msa1466910 MtrunA17_Chr1g0151541 62.162 74 28 0 1 74 825 898 3.11e-28 105
Msa1466910 MtrunA17_Chr4g0068411 63.514 74 27 0 1 74 622 695 3.47e-28 105
Msa1466910 MtrunA17_Chr2g0294351 62.162 74 28 0 1 74 628 701 1.04e-27 103
Msa1466910 MtrunA17_Chr8g0392871 57.534 73 31 0 2 74 902 974 3.66e-26 99.4
Msa1466910 MtrunA17_Chr5g0397931 54.054 74 34 0 1 74 585 658 6.93e-26 98.6
Msa1466910 MtrunA17_Chr7g0244621 47.500 80 34 2 3 74 210 289 3.85e-20 81.6
Msa1466910 MtrunA17_Chr4g0075541 44.595 74 41 0 2 75 252 325 9.68e-19 78.2
Msa1466910 MtrunA17_Chr2g0325851 49.333 75 35 1 1 75 719 790 1.11e-18 78.2
Msa1466910 MtrunA17_Chr4g0059181 47.222 72 38 0 3 74 275 346 1.78e-18 77.4
Msa1466910 MtrunA17_Chr3g0117811 45.833 72 39 0 3 74 246 317 2.42e-18 76.6
Msa1466910 MtrunA17_Chr4g0047191 43.836 73 41 0 3 75 212 284 2.94e-18 76.6
Msa1466910 MtrunA17_Chr4g0047211 43.836 73 41 0 3 75 207 279 3.39e-18 76.3
Msa1466910 MtrunA17_Chr4g0047201 45.205 73 40 0 3 75 368 440 7.43e-18 75.9
Msa1466910 MtrunA17_Chr5g0394681 48.611 72 37 0 3 74 273 344 7.74e-18 75.5
Msa1466910 MtrunA17_Chr6g0450871 47.222 72 38 0 3 74 258 329 1.10e-17 75.1
Msa1466910 MtrunA17_Chr3g0090261 43.836 73 41 0 2 74 247 319 2.16e-17 74.3
Msa1466910 MtrunA17_Chr1g0202101 43.056 72 40 1 3 74 444 514 2.23e-17 74.3
Msa1466910 MtrunA17_Chr1g0205071 45.833 72 39 0 3 74 265 336 4.01e-17 73.6
Msa1466910 MtrunA17_Chr4g0041201 48.000 75 36 1 1 75 709 780 4.24e-17 73.6
Msa1466910 MtrunA17_Chr4g0059121 39.726 73 44 0 3 75 224 296 6.87e-17 72.8
Msa1466910 MtrunA17_Chr4g0065211 42.667 75 41 1 3 75 1294 1368 1.09e-16 72.4
Msa1466910 MtrunA17_Chr2g0310781 40.000 75 43 1 3 75 1018 1092 1.79e-16 72.0
Msa1466910 MtrunA17_Chr5g0406251 41.667 72 42 0 3 74 456 527 1.81e-16 72.0
Msa1466910 MtrunA17_Chr2g0282321 42.466 73 42 0 3 75 329 401 3.40e-16 70.9
Msa1466910 MtrunA17_Chr3g0117731 39.726 73 44 0 3 75 223 295 4.39e-16 70.5
Msa1466910 MtrunA17_Chr6g0461841 40.000 75 43 1 3 75 1140 1214 6.08e-16 70.5
Msa1466910 MtrunA17_Chr2g0305141 40.000 75 43 1 3 75 1256 1330 1.05e-15 69.7
Msa1466910 MtrunA17_Chr4g0072741 45.333 75 39 1 3 75 1008 1082 1.21e-15 69.7
Msa1466910 MtrunA17_Chr1g0196631 37.333 75 45 1 3 75 1073 1147 1.42e-15 69.3
Msa1466910 MtrunA17_Chr3g0143531 41.096 73 43 0 2 74 185 257 2.06e-15 68.2
Msa1466910 MtrunA17_Chr8g0357611 40.000 75 43 1 3 75 1543 1617 2.09e-15 68.9
Msa1466910 MtrunA17_Chr2g0310761 40.000 75 43 1 3 75 1112 1186 2.29e-15 68.6
Msa1466910 MtrunA17_Chr1g0211611 41.667 72 42 0 3 74 462 533 7.57e-15 67.4
Msa1466910 MtrunA17_Chr5g0431191 34.211 76 46 1 3 74 491 566 3.06e-13 62.8
Msa1466910 MtrunA17_Chr3g0105891 36.842 76 44 1 3 74 488 563 3.98e-13 62.4
Msa1466910 MtrunA17_Chr6g0449241 41.250 80 38 3 3 74 191 269 1.14e-12 60.8
Msa1466910 MtrunA17_Chr3g0116981 38.750 80 40 3 3 74 191 269 1.46e-11 57.8
Msa1466910 MtrunA17_Chr1g0165941 36.842 57 36 0 17 73 12 68 2.19e-11 53.9
Msa1466910 MtrunA17_Chr1g0157231 52.083 48 22 1 3 49 306 353 3.54e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1466910 AT4G24480.1 89.333 75 8 0 1 75 838 912 3.02e-42 145
Msa1466910 AT4G24480.2 89.333 75 8 0 1 75 833 907 3.39e-42 145
Msa1466910 AT4G24480.3 89.333 75 8 0 1 75 833 907 3.48e-42 145
Msa1466910 AT5G03730.2 66.667 75 25 0 1 75 715 789 1.17e-29 109
Msa1466910 AT5G03730.1 66.667 75 25 0 1 75 715 789 1.17e-29 109
Msa1466910 AT1G08720.2 64.865 74 26 0 1 74 831 904 5.15e-29 107
Msa1466910 AT1G08720.1 64.865 74 26 0 1 74 831 904 5.91e-29 107
Msa1466910 AT5G11850.1 63.514 74 27 0 1 74 771 844 5.01e-28 105
Msa1466910 AT1G73660.1 64.384 73 26 0 2 74 911 983 7.71e-28 104
Msa1466910 AT5G49470.3 64.865 74 26 0 1 74 653 726 1.22e-27 103
Msa1466910 AT5G49470.1 64.865 74 26 0 1 74 366 439 1.29e-27 103
Msa1466910 AT5G49470.7 64.865 74 26 0 1 74 526 599 1.36e-27 103
Msa1466910 AT5G49470.2 64.865 74 26 0 1 74 714 787 1.47e-27 103
Msa1466910 AT5G49470.4 64.865 74 26 0 1 74 627 700 1.66e-27 103
Msa1466910 AT1G18160.2 63.014 73 27 0 2 74 878 950 3.18e-27 102
Msa1466910 AT1G18160.1 63.014 73 27 0 2 74 878 950 3.35e-27 102
Msa1466910 AT1G67890.4 60.811 74 29 0 1 74 520 593 2.64e-26 100
Msa1466910 AT1G67890.3 60.811 74 29 0 1 74 648 721 3.08e-26 100
Msa1466910 AT1G67890.2 60.811 74 29 0 1 74 648 721 3.08e-26 100
Msa1466910 AT1G67890.1 60.811 74 29 0 1 74 648 721 3.08e-26 100
Msa1466910 AT3G06640.2 58.108 74 31 0 1 74 608 681 9.69e-26 98.6
Msa1466910 AT3G06640.3 58.108 74 31 0 1 74 608 681 9.69e-26 98.6
Msa1466910 AT3G06640.1 58.108 74 31 0 1 74 608 681 9.70e-26 98.6
Msa1466910 AT3G06620.1 58.108 74 31 0 1 74 656 729 1.37e-25 98.2
Msa1466910 AT4G23050.1 56.757 74 32 0 1 74 629 702 1.56e-25 98.2
Msa1466910 AT4G23050.2 56.757 74 32 0 1 74 630 703 1.59e-25 98.2
Msa1466910 AT3G06630.2 58.108 74 31 0 1 74 596 669 3.33e-25 97.1
Msa1466910 AT3G06630.1 58.108 74 31 0 1 74 596 669 3.52e-25 97.1
Msa1466910 AT2G42640.1 49.333 75 35 1 1 75 687 758 3.34e-19 80.1
Msa1466910 AT2G42640.4 49.333 75 35 1 1 75 649 720 3.37e-19 80.1
Msa1466910 AT1G62400.1 46.575 73 39 0 3 75 252 324 4.47e-19 79.3
Msa1466910 AT5G50000.1 47.222 72 38 0 3 74 268 339 1.29e-18 78.2
Msa1466910 AT3G01490.1 48.611 72 37 0 3 74 294 365 1.66e-18 77.8
Msa1466910 AT3G58640.1 48.000 75 36 1 1 75 715 786 2.77e-18 77.4
Msa1466910 AT3G58640.2 48.000 75 36 1 1 75 715 786 2.77e-18 77.4
Msa1466910 AT5G01850.1 45.679 81 36 2 2 74 182 262 3.77e-18 76.3
Msa1466910 AT2G31010.1 49.333 75 35 1 1 75 681 752 3.78e-18 77.0
Msa1466910 AT2G31010.2 49.333 75 35 1 1 75 681 752 3.78e-18 77.0
Msa1466910 AT3G22750.1 48.611 72 37 0 3 74 261 332 4.46e-18 76.6
Msa1466910 AT5G01850.2 45.679 81 36 2 2 74 206 286 4.89e-18 76.3
Msa1466910 AT4G14780.1 44.444 72 40 0 3 74 247 318 2.02e-17 74.7
Msa1466910 AT4G31170.7 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.6 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.5 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.1 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.2 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.3 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT4G31170.8 42.466 73 42 0 2 74 296 368 4.10e-17 73.9
Msa1466910 AT2G24360.1 42.466 73 42 0 2 74 295 367 4.89e-17 73.6
Msa1466910 AT3G63260.1 45.833 72 39 0 3 74 274 345 6.10e-17 73.6
Msa1466910 AT3G24715.1 41.333 75 42 1 3 75 1009 1083 1.24e-16 72.8
Msa1466910 AT3G24715.3 41.333 75 42 1 3 75 1009 1083 1.24e-16 72.8
Msa1466910 AT3G24715.2 41.333 75 42 1 3 75 1009 1083 1.24e-16 72.8
Msa1466910 AT5G58950.1 41.096 73 43 0 3 75 375 447 2.10e-16 72.0
Msa1466910 AT4G38470.1 41.667 72 42 0 3 74 451 522 2.97e-16 71.6
Msa1466910 AT4G35780.1 38.889 72 44 0 3 74 453 524 8.11e-16 70.5
Msa1466910 AT4G38470.2 41.667 72 42 0 3 74 451 522 8.75e-16 70.5
Msa1466910 AT2G35050.1 40.000 75 43 1 3 75 1146 1220 9.71e-16 70.1
Msa1466910 AT2G35050.2 40.000 75 43 1 3 75 1146 1220 9.71e-16 70.1
Msa1466910 AT5G57610.1 44.000 75 40 1 3 75 954 1028 1.12e-15 70.1
Msa1466910 AT1G79570.2 40.000 75 43 1 3 75 1137 1211 1.71e-15 69.3
Msa1466910 AT1G79570.1 40.000 75 43 1 3 75 1137 1211 1.71e-15 69.3
Msa1466910 AT3G46930.1 41.892 74 42 1 3 75 331 404 2.66e-15 68.9
Msa1466910 AT1G04700.1 37.333 75 45 1 3 75 939 1013 3.40e-15 68.6
Msa1466910 AT1G04700.2 37.333 75 45 1 3 75 939 1013 3.40e-15 68.6
Msa1466910 AT1G16270.1 40.000 75 43 1 3 75 1036 1110 4.02e-15 68.6
Msa1466910 AT1G16270.2 40.000 75 43 1 3 75 1036 1110 4.02e-15 68.6
Msa1466910 AT1G16270.3 40.000 75 43 1 3 75 1036 1110 4.02e-15 68.6
Msa1466910 AT5G49470.5 68.889 45 14 0 1 45 653 697 5.32e-15 68.2
Msa1466910 AT3G46930.2 41.892 74 42 1 3 75 366 439 6.01e-15 67.8
Msa1466910 AT2G17700.1 40.278 72 43 0 3 74 447 518 1.15e-14 67.0
Msa1466910 AT3G46920.1 41.333 75 42 1 3 75 979 1053 1.75e-14 66.6
Msa1466910 AT5G49470.6 68.182 44 14 0 1 44 653 696 1.97e-14 66.6
Msa1466910 AT3G46920.2 41.333 75 42 1 3 75 1045 1119 2.05e-14 66.2
Msa1466910 AT3G06630.6 62.222 45 17 0 1 45 512 556 3.50e-14 65.9
Msa1466910 AT3G06630.4 62.222 45 17 0 1 45 596 640 3.96e-14 65.5
Msa1466910 AT3G06630.3 62.222 45 17 0 1 45 596 640 3.96e-14 65.5
Msa1466910 AT3G06630.5 62.222 45 17 0 1 45 596 640 3.96e-14 65.5
Msa1466910 AT5G07140.1 38.158 76 43 1 3 74 485 560 2.20e-13 63.5
Msa1466910 AT5G40540.2 43.750 80 36 4 3 74 115 193 1.74e-12 60.5
Msa1466910 AT5G40540.3 43.750 80 36 4 3 74 94 172 1.97e-12 60.1
Msa1466910 AT5G40540.1 43.750 80 36 4 3 74 191 269 2.74e-12 60.5
Msa1466910 AT5G58520.1 39.474 76 42 1 3 74 506 581 4.19e-12 59.7
Msa1466910 AT5G50180.1 42.500 80 37 4 3 74 185 263 1.11e-11 58.5
Msa1466910 AT3G27560.1 40.000 80 39 3 3 74 191 269 1.19e-11 58.5
Msa1466910 AT3G01490.2 50.000 54 24 1 3 53 294 347 1.80e-11 58.2
Msa1466910 AT5G50000.2 48.000 50 26 0 3 52 268 317 7.55e-11 56.2

Find 27 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCAGTATTGGCCTCCCTTA+TGG 0.244449 tig0049268:+517 Msa1466910:CDS
TCCATAAGGGAGGCCAATAC+TGG 0.287723 tig0049268:-518 Msa1466910:intergenic
CCTCCCTTATGGAATCTTGT+TGG 0.303802 tig0049268:+528 Msa1466910:CDS
AAGTCTGATGTTTATAGTTT+TGG 0.311358 tig0049268:+256 Msa1466910:CDS
CTCCCTTATGGAATCTTGTT+GGG 0.359987 tig0049268:+529 Msa1466910:CDS
ACATCAGACTTCTCGTTTGT+AGG 0.368339 tig0049268:-244 Msa1466910:intergenic
GCCAATACTGGGGAGACATT+TGG 0.386803 tig0049268:-506 Msa1466910:intergenic
GAGACATTTGGAGGGATAGA+AGG 0.399972 tig0049268:-494 Msa1466910:intergenic
GAGCTGTCGCATTTCAGAAT+AGG 0.418005 tig0049268:+468 Msa1466910:CDS
TCCATTCCATGGTTGTTGTA+AGG 0.427541 tig0049268:-302 Msa1466910:intergenic
CAGCCCAACAAGATTCCATA+AGG 0.462865 tig0049268:-532 Msa1466910:intergenic
TCCAAATGTCTCCCCAGTAT+TGG 0.494916 tig0049268:+505 Msa1466910:CDS
CATGTGTATCCTCAGGTGGT+TGG 0.509740 tig0049268:+446 Msa1466910:intron
CCATAAGGGAGGCCAATACT+GGG 0.514867 tig0049268:-517 Msa1466910:intergenic
AATACTGGGGAGACATTTGG+AGG 0.528815 tig0049268:-503 Msa1466910:intergenic
ATGGCTCCAGAGTTTCTTCG+TGG 0.536115 tig0049268:+217 Msa1466910:CDS
GGTTCTCCACGAAGAAACTC+TGG 0.544195 tig0049268:-223 Msa1466910:intergenic
AACTCTGGAGCCATCCACTC+AGG 0.554183 tig0049268:-208 Msa1466910:intergenic
GAATGGACTTAGCCATGCCC+AGG 0.578828 tig0049268:+318 Msa1466910:CDS
AGCCCAACAAGATTCCATAA+GGG 0.583261 tig0049268:-531 Msa1466910:intergenic
ACCTTACAACAACCATGGAA+TGG 0.583688 tig0049268:+301 Msa1466910:CDS
TCAACGAGTTTACCTGGGCA+TGG 0.589325 tig0049268:-330 Msa1466910:intergenic
GCATGGCTAAGTCCATTCCA+TGG 0.604826 tig0049268:-313 Msa1466910:intergenic
TAGTGACCTTACAACAACCA+TGG 0.641251 tig0049268:+296 Msa1466910:CDS
CCAACAAGATTCCATAAGGG+AGG 0.671201 tig0049268:-528 Msa1466900:intergenic
CATAAGGGAGGCCAATACTG+GGG 0.690145 tig0049268:-516 Msa1466900:intergenic
ATACTGGGGAGACATTTGGA+GGG 0.720295 tig0049268:-502 Msa1466900:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTCTGATGTTTATAGTTT+TGG + tig0049268:256-275 Msa1466910:CDS 25.0%
!!! ATAGTTTTGGTGTCATCTTG+TGG + tig0049268:269-288 Msa1466910:CDS 35.0%
!!! TAGTTTTGGTGTCATCTTGT+GGG + tig0049268:270-289 Msa1466910:CDS 35.0%
ATTACTCAACGAGTTTACCT+GGG - tig0049268:338-357 Msa1466910:intergenic 35.0%
AATTACTCAACGAGTTTACC+TGG - tig0049268:339-358 Msa1466910:intergenic 35.0%
! TGCAATGTTTGAAACATGCA+AGG - tig0049268:374-393 Msa1466910:intergenic 35.0%
TAATCTTCATGTGTATCCTC+AGG + tig0049268:439-458 Msa1466910:intron 35.0%
ACATCAGACTTCTCGTTTGT+AGG - tig0049268:247-266 Msa1466910:intergenic 40.0%
TAGTGACCTTACAACAACCA+TGG + tig0049268:296-315 Msa1466910:CDS 40.0%
ACCTTACAACAACCATGGAA+TGG + tig0049268:301-320 Msa1466910:CDS 40.0%
TCCATTCCATGGTTGTTGTA+AGG - tig0049268:305-324 Msa1466910:intergenic 40.0%
CTCCCTTATGGAATCTTGTT+GGG + tig0049268:529-548 Msa1466910:CDS 40.0%
AGCCCAACAAGATTCCATAA+GGG - tig0049268:534-553 Msa1466910:intergenic 40.0%
TCTTCATGTGTATCCTCAGG+TGG + tig0049268:442-461 Msa1466910:intron 45.0%
GAGCTGTCGCATTTCAGAAT+AGG + tig0049268:468-487 Msa1466910:CDS 45.0%
GAGACATTTGGAGGGATAGA+AGG - tig0049268:497-516 Msa1466910:intergenic 45.0%
ATACTGGGGAGACATTTGGA+GGG - tig0049268:505-524 Msa1466910:intergenic 45.0%
AATACTGGGGAGACATTTGG+AGG - tig0049268:506-525 Msa1466910:intergenic 45.0%
TCCAAATGTCTCCCCAGTAT+TGG + tig0049268:505-524 Msa1466910:CDS 45.0%
CCAACAAGATTCCATAAGGG+AGG - tig0049268:531-550 Msa1466910:intergenic 45.0%
CCTCCCTTATGGAATCTTGT+TGG + tig0049268:528-547 Msa1466910:CDS 45.0%
ATGGCTCCAGAGTTTCTTCG+TGG + tig0049268:217-236 Msa1466910:CDS 50.0%
GGTTCTCCACGAAGAAACTC+TGG - tig0049268:226-245 Msa1466910:intergenic 50.0%
GCATGGCTAAGTCCATTCCA+TGG - tig0049268:316-335 Msa1466910:intergenic 50.0%
TCAACGAGTTTACCTGGGCA+TGG - tig0049268:333-352 Msa1466910:intergenic 50.0%
CATGTGTATCCTCAGGTGGT+TGG + tig0049268:446-465 Msa1466910:intron 50.0%
GCCAATACTGGGGAGACATT+TGG - tig0049268:509-528 Msa1466910:intergenic 50.0%
CATAAGGGAGGCCAATACTG+GGG - tig0049268:519-538 Msa1466910:intergenic 50.0%
CCATAAGGGAGGCCAATACT+GGG - tig0049268:520-539 Msa1466910:intergenic 50.0%
TCCATAAGGGAGGCCAATAC+TGG - tig0049268:521-540 Msa1466910:intergenic 50.0%
!! AACTCTGGAGCCATCCACTC+AGG - tig0049268:211-230 None:intergenic 55.0%
! GAATGGACTTAGCCATGCCC+AGG + tig0049268:318-337 Msa1466910:CDS 55.0%
!! CCCAGTATTGGCCTCCCTTA+TGG + tig0049268:517-536 Msa1466910:CDS 55.0%
GCGACAGCTCCAACCACCTG+AGG - tig0049268:458-477 Msa1466910:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0049268 gene 208 553 208 ID=Msa1466910;Name=Msa1466910
tig0049268 mRNA 208 553 208 ID=Msa1466910-mRNA-1;Parent=Msa1466910;Name=Msa1466910-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|1|0|1|1|1|2|0|75
tig0049268 exon 208 339 208 ID=Msa1466910-mRNA-1:exon:25166;Parent=Msa1466910-mRNA-1
tig0049268 exon 461 553 461 ID=Msa1466910-mRNA-1:exon:25167;Parent=Msa1466910-mRNA-1
tig0049268 CDS 208 339 208 ID=Msa1466910-mRNA-1:cds;Parent=Msa1466910-mRNA-1
tig0049268 CDS 461 553 461 ID=Msa1466910-mRNA-1:cds;Parent=Msa1466910-mRNA-1
Gene Sequence

>Msa1466910

CCTGAGTGGATGGCTCCAGAGTTTCTTCGTGGAGAACCTACAAACGAGAAGTCTGATGTTTATAGTTTTGGTGTCATCTTGTGGGAACTAGTGACCTTACAACAACCATGGAATGGACTTAGCCATGCCCAGGTGGTTGGAGCTGTCGCATTTCAGAATAGGAGACCTTCTATCCCTCCAAATGTCTCCCCAGTATTGGCCTCCCTTATGGAATCTTGTTGGGCT

Protein sequence

>Msa1466910

PEWMAPEFLRGEPTNEKSDVYSFGVILWELVTLQQPWNGLSHAQVVGAVAFQNRRPSIPPNVSPVLASLMESCWA