AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene95990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene95990.t1 MTR_2g072500 97.802 91 2 0 3 93 1 91 1.12e-64 190
MS.gene95990.t1 MTR_8g089400 43.678 87 47 1 9 93 36 122 4.67e-21 81.6
MS.gene95990.t1 MTR_8g089400 43.678 87 47 1 9 93 56 142 9.85e-21 81.3
MS.gene95990.t1 MTR_8g085440 44.565 92 50 1 2 92 24 115 1.95e-20 79.0
MS.gene95990.t1 MTR_7g026340 48.193 83 42 1 9 90 364 446 1.36e-19 81.6
MS.gene95990.t1 MTR_8g085420 44.318 88 48 1 2 88 24 111 9.81e-19 75.1
MS.gene95990.t1 MTR_1g084820 46.512 86 43 3 4 88 415 498 6.83e-18 77.0
MS.gene95990.t1 MTR_1g084820 46.512 86 43 3 4 88 415 498 9.68e-18 76.6
MS.gene95990.t1 MTR_8g085400 45.455 88 42 3 1 86 24 107 1.01e-17 72.0
MS.gene95990.t1 MTR_6g088885 41.758 91 49 2 5 92 365 454 2.29e-17 75.5
MS.gene95990.t1 MTR_1g022160 40.449 89 52 1 5 92 386 474 2.49e-17 75.5
MS.gene95990.t1 MTR_3g116510 41.176 85 49 1 10 93 237 321 4.98e-17 73.9
MS.gene95990.t1 MTR_4g083500 39.535 86 51 1 8 92 400 485 7.36e-17 74.3
MS.gene95990.t1 MTR_3g116510 41.176 85 49 1 10 93 371 455 7.92e-17 73.9
MS.gene95990.t1 MTR_7g111600 45.882 85 43 2 10 92 160 243 1.02e-16 72.4
MS.gene95990.t1 MTR_7g111600 45.882 85 43 2 10 92 160 243 2.02e-16 72.4
MS.gene95990.t1 MTR_1g031900 39.773 88 51 1 8 93 359 446 2.61e-16 72.4
MS.gene95990.t1 MTR_4g069940 40.000 85 49 1 10 92 375 459 2.95e-16 72.4
MS.gene95990.t1 MTR_1g031900 39.773 88 51 1 8 93 359 446 3.01e-16 72.4
MS.gene95990.t1 MTR_7g111600 45.882 85 43 2 10 92 160 243 3.61e-16 71.6
MS.gene95990.t1 MTR_1g053320 43.529 85 46 2 7 90 371 454 3.88e-16 72.0
MS.gene95990.t1 MTR_5g078200 37.931 87 52 1 8 92 358 444 4.81e-16 72.0
MS.gene95990.t1 MTR_8g085390 39.583 96 54 2 1 92 18 113 5.17e-16 69.3
MS.gene95990.t1 MTR_5g078200 37.931 87 52 1 8 92 325 411 5.28e-16 71.6
MS.gene95990.t1 MTR_8g102340 38.636 88 52 1 7 92 331 418 1.24e-15 70.5
MS.gene95990.t1 MTR_5g085580 38.095 84 50 1 9 90 381 464 1.56e-15 70.5
MS.gene95990.t1 MTR_4g132280 39.080 87 51 1 8 92 380 466 1.69e-15 70.1
MS.gene95990.t1 MTR_1g056640 38.462 91 54 1 2 90 398 488 1.73e-15 70.1
MS.gene95990.t1 MTR_3g083580 37.234 94 57 1 2 93 354 447 1.95e-15 70.1
MS.gene95990.t1 MTR_3g065460 37.931 87 52 1 8 92 359 445 1.16e-14 67.8
MS.gene95990.t1 MTR_4g079530 37.500 88 53 1 7 92 34 121 1.66e-14 64.3
MS.gene95990.t1 MTR_5g091650 38.462 91 53 2 4 92 102 191 1.86e-14 65.5
MS.gene95990.t1 MTR_1g022160 37.079 89 55 1 5 92 386 474 2.38e-14 67.0
MS.gene95990.t1 MTR_5g091650 38.462 91 53 2 4 92 102 191 3.47e-14 65.9
MS.gene95990.t1 MTR_4g109490 41.667 84 47 2 10 92 24 106 3.49e-14 65.1
MS.gene95990.t1 MTR_4g079530 37.500 88 53 1 7 92 34 121 4.73e-14 63.9
MS.gene95990.t1 MTR_8g012400 36.264 91 48 3 8 92 372 458 9.43e-14 65.5
MS.gene95990.t1 MTR_5g015720 39.326 89 51 1 7 92 326 414 1.02e-13 65.1
MS.gene95990.t1 MTR_8g012400 36.264 91 48 3 8 92 292 378 1.46e-13 64.7
MS.gene95990.t1 MTR_3g048280 36.264 91 55 2 4 92 106 195 1.56e-13 63.2
MS.gene95990.t1 MTR_4g112025 37.931 87 52 2 7 92 371 456 1.95e-13 64.3
MS.gene95990.t1 MTR_1g022160 37.805 82 50 1 5 85 386 467 2.03e-13 64.3
MS.gene95990.t1 MTR_5g097420 35.632 87 54 1 8 92 28 114 3.40e-13 60.5
MS.gene95990.t1 MTR_1g116870 38.095 84 51 1 10 92 276 359 3.94e-13 63.5
MS.gene95990.t1 MTR_2g049670 42.353 85 47 2 10 93 158 241 7.38e-13 62.4
MS.gene95990.t1 MTR_8g085720 37.778 90 54 1 5 92 359 448 5.43e-12 60.5
MS.gene95990.t1 MTR_3g095050 34.483 87 55 2 7 92 370 455 1.06e-11 59.3
MS.gene95990.t1 MTR_3g082080 37.179 78 48 1 10 86 157 234 1.16e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene95990.t1 AT1G78520 65.591 93 31 1 1 92 22 114 2.88e-42 134
MS.gene95990.t1 AT2G43670 55.422 83 37 0 10 92 35 117 2.36e-33 112
MS.gene95990.t1 AT3G28250 51.948 77 37 0 10 86 3 79 3.62e-26 93.6
MS.gene95990.t1 AT2G43660 50.562 89 42 1 6 92 31 119 2.22e-25 91.7
MS.gene95990.t1 AT2G43660 50.562 89 42 1 6 92 30 118 2.40e-25 91.7
MS.gene95990.t1 AT4G09462 44.792 96 49 2 2 93 18 113 7.99e-24 87.4
MS.gene95990.t1 AT5G53600 43.333 90 51 0 3 92 22 111 1.08e-23 87.0
MS.gene95990.t1 AT4G09467 44.086 93 51 1 2 93 23 115 3.45e-23 85.9
MS.gene95990.t1 AT4G09464 44.086 93 51 1 2 93 23 115 3.45e-23 85.9
MS.gene95990.t1 AT4G09465 44.086 93 51 1 2 93 23 115 4.94e-23 85.5
MS.gene95990.t1 AT4G09466 41.935 93 53 1 2 93 23 115 4.50e-21 80.5
MS.gene95990.t1 AT1G66852 42.529 87 47 2 8 92 24 109 1.04e-20 79.7
MS.gene95990.t1 AT1G66870 41.379 87 49 1 8 92 24 110 2.00e-20 79.0
MS.gene95990.t1 AT1G66870 41.379 87 49 1 8 92 51 137 3.13e-20 79.3
MS.gene95990.t1 AT1G09460 49.438 89 43 2 4 92 132 218 4.48e-20 82.4
MS.gene95990.t1 AT4G09090 41.304 92 53 1 2 92 23 114 1.40e-19 77.0
MS.gene95990.t1 AT4G16165 40.909 88 50 1 8 93 24 111 1.95e-19 76.3
MS.gene95990.t1 AT5G63225 42.391 92 52 1 2 92 17 108 9.02e-19 74.7
MS.gene95990.t1 AT5G53610 40.964 83 49 0 8 90 26 108 2.77e-18 73.6
MS.gene95990.t1 AT4G05430 39.535 86 50 1 9 92 22 107 5.49e-18 73.6
MS.gene95990.t1 AT4G05430 39.535 86 50 1 9 92 47 132 1.01e-17 73.6
MS.gene95990.t1 AT5G24318 37.079 89 55 1 5 92 367 455 3.86e-17 75.1
MS.gene95990.t1 AT5G63240 36.667 90 53 1 7 92 37 126 4.23e-17 70.9
MS.gene95990.t1 AT5G24318 37.079 89 55 1 5 92 228 316 5.48e-17 73.9
MS.gene95990.t1 AT2G05790 42.857 84 46 1 9 90 383 466 6.89e-17 74.3
MS.gene95990.t1 AT4G29360 39.080 87 51 1 8 92 389 475 1.05e-16 73.9
MS.gene95990.t1 AT4G29360 39.080 87 51 1 8 92 399 485 1.09e-16 73.6
MS.gene95990.t1 AT1G11820 40.230 87 50 1 8 92 379 465 1.88e-16 73.2
MS.gene95990.t1 AT1G66855 39.773 88 51 1 8 93 24 111 2.27e-16 68.6
MS.gene95990.t1 AT4G34480 36.905 84 52 1 10 92 253 336 4.11e-16 72.0
MS.gene95990.t1 AT4G34480 36.905 84 52 1 10 92 364 447 5.43e-16 71.6
MS.gene95990.t1 AT5G63230 39.535 86 51 1 8 92 24 109 8.35e-16 67.0
MS.gene95990.t1 AT5G55180 40.000 85 49 1 8 90 370 454 9.11e-16 71.2
MS.gene95990.t1 AT2G01630 36.782 87 53 1 8 92 358 444 1.33e-15 70.5
MS.gene95990.t1 AT2G39640 37.349 83 51 1 10 91 460 542 1.78e-15 70.1
MS.gene95990.t1 AT2G39640 37.500 88 54 1 4 90 353 440 2.99e-15 69.7
MS.gene95990.t1 AT3G13560 38.889 90 53 1 5 92 357 446 2.96e-15 69.7
MS.gene95990.t1 AT3G13560 38.889 90 53 1 5 92 357 446 2.96e-15 69.7
MS.gene95990.t1 AT3G13560 38.889 90 53 1 5 92 357 446 2.96e-15 69.7
MS.gene95990.t1 AT3G13560 38.889 90 53 1 5 92 357 446 2.96e-15 69.7
MS.gene95990.t1 AT3G13560 38.889 90 53 1 5 92 357 446 2.96e-15 69.7
MS.gene95990.t1 AT4G05430 37.500 80 48 1 9 86 47 126 1.58e-14 64.3
MS.gene95990.t1 AT1G66250 35.227 88 55 1 8 93 366 453 2.12e-14 67.4
MS.gene95990.t1 AT3G55430 38.095 84 51 1 10 92 366 449 3.17e-14 66.6
MS.gene95990.t1 AT1G18650 36.471 85 53 1 9 92 20 104 3.76e-14 63.5
MS.gene95990.t1 AT1G18650 36.471 85 53 1 9 92 20 104 7.32e-14 63.9
MS.gene95990.t1 AT5G67460 36.364 88 54 1 5 90 288 375 7.98e-14 65.5
MS.gene95990.t1 AT4G26830 39.286 84 49 1 9 90 366 449 1.51e-13 64.7
MS.gene95990.t1 AT3G58100 33.333 87 56 1 8 92 39 125 1.78e-13 62.8
MS.gene95990.t1 AT4G26830 39.286 84 49 1 9 90 370 453 1.91e-13 64.3
MS.gene95990.t1 AT5G55180 39.506 81 47 1 8 86 370 450 2.20e-13 64.3
MS.gene95990.t1 AT1G79480 36.905 84 52 1 10 92 311 394 3.22e-13 63.9
MS.gene95990.t1 AT1G29380 37.931 87 49 3 10 93 148 232 3.27e-13 63.2
MS.gene95990.t1 AT2G01630 37.037 81 49 1 8 86 358 438 3.38e-13 63.9
MS.gene95990.t1 AT1G79480 36.905 84 52 1 10 92 310 393 3.48e-13 63.5
MS.gene95990.t1 AT2G29735 38.043 92 54 2 4 92 25 116 3.60e-13 60.5
MS.gene95990.t1 AT5G64790 34.483 87 55 2 7 92 366 451 4.25e-13 63.5
MS.gene95990.t1 AT5G63250 36.782 87 51 1 10 92 42 128 4.38e-13 60.8
MS.gene95990.t1 AT1G11820 39.506 81 47 1 8 86 379 459 4.81e-13 63.2
MS.gene95990.t1 AT3G58100 33.333 87 56 1 8 92 115 201 5.91e-13 62.4
MS.gene95990.t1 AT2G30933 37.079 89 53 2 6 92 78 165 6.25e-13 62.0
MS.gene95990.t1 AT1G29380 38.372 86 48 3 10 92 148 231 6.30e-13 62.8
MS.gene95990.t1 AT5G24318 33.735 83 54 1 5 86 367 449 7.06e-13 62.8
MS.gene95990.t1 AT2G16230 34.524 84 54 1 10 92 366 449 7.14e-13 62.8
MS.gene95990.t1 AT5G35740 34.091 88 55 2 8 92 28 115 9.02e-13 59.7
MS.gene95990.t1 AT4G13600 36.905 84 52 1 10 92 61 144 2.08e-12 60.8
MS.gene95990.t1 AT5G56590 35.294 85 53 1 10 92 369 453 2.80e-12 61.2
MS.gene95990.t1 AT3G24330 39.286 84 49 2 8 90 380 462 4.97e-12 60.5
MS.gene95990.t1 AT5G67460 35.714 84 52 1 5 86 288 371 5.93e-12 60.1
MS.gene95990.t1 AT4G17180 38.554 83 50 1 10 92 359 440 1.30e-11 59.3
MS.gene95990.t1 AT1G29380 38.750 80 44 3 10 86 148 225 1.49e-11 58.2
MS.gene95990.t1 AT1G29380 38.750 80 44 3 10 86 148 225 1.49e-11 58.2
MS.gene95990.t1 AT2G42930 39.744 78 45 2 10 86 40 116 5.29e-11 55.5

Find 18 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAATATGATCATGGTTAA+TGG 0.289090 2.4:+23709285 None:intergenic
AGATCGATAATAGAGATTCA+TGG 0.408516 2.4:-23709558 None:intergenic
GGAATATGATCATGGTTAAT+GGG 0.423180 2.4:+23709286 None:intergenic
AATCTCTATTATCGATCTAA+AGG 0.467046 2.4:+23709563 MS.gene95990:CDS
TATGATCATGGTTAATGGGC+AGG 0.497346 2.4:+23709290 None:intergenic
GATCTAAAGGAACGGACCAT+TGG 0.511484 2.4:+23709576 MS.gene95990:CDS
CGTGGGAGCAAGCATAATTG+AGG 0.528871 2.4:-23709463 None:intergenic
GATTGCAGATTTCTTCAGAA+AGG 0.533309 2.4:+23709488 MS.gene95990:CDS
AGTGTTGCTTGATCTGATGA+AGG 0.538388 2.4:-23709431 None:intergenic
CTCTGAAATCGCAGTTCCAA+TGG 0.540263 2.4:-23709592 None:intergenic
CATTGGAACTGCGATTTCAG+AGG 0.562954 2.4:+23709593 MS.gene95990:CDS
TGCAGGAGGGAATATGATCA+TGG 0.565880 2.4:+23709278 None:intergenic
ATAATAGAGATTCATGGCGA+TGG 0.571419 2.4:-23709552 None:intergenic
GATTCATGGCGATGGAAGCG+CGG 0.609487 2.4:-23709544 None:intergenic
CTATTATCGATCTAAAGGAA+CGG 0.620629 2.4:+23709568 MS.gene95990:CDS
AACACAGAAAACTTGGTGCG+TGG 0.648923 2.4:+23709403 MS.gene95990:intron
AAGAAATCTGCAATCAACGT+GGG 0.663490 2.4:-23709480 None:intergenic
GAAGAAATCTGCAATCAACG+TGG 0.692599 2.4:-23709481 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACTTTATGTAATTTAT+TGG - chr2.4:23709347-23709366 None:intergenic 10.0%
! AATCTCTATTATCGATCTAA+AGG + chr2.4:23709563-23709582 MS.gene95990:CDS 25.0%
! GTCATATCAAACTTGTAAAT+TGG - chr2.4:23709907-23709926 None:intergenic 25.0%
! TATGAAAAACACAGAAAACT+TGG + chr2.4:23709396-23709415 MS.gene95990:intron 25.0%
!!! CCAATCATAGTTCTAATTTT+CGG + chr2.4:23709736-23709755 MS.gene95990:intron 25.0%
AATGAGTTATGTGACTTACT+TGG - chr2.4:23709644-23709663 None:intergenic 30.0%
AGATCGATAATAGAGATTCA+TGG - chr2.4:23709561-23709580 None:intergenic 30.0%
CAAACTTGTAAATTGGTTGA+TGG - chr2.4:23709900-23709919 None:intergenic 30.0%
CAACATTGTAACTGCAATTA+TGG + chr2.4:23709787-23709806 MS.gene95990:intron 30.0%
CCATAATATTGATGTTCACA+TGG + chr2.4:23709839-23709858 MS.gene95990:intron 30.0%
CCATGTGAACATCAATATTA+TGG - chr2.4:23709842-23709861 None:intergenic 30.0%
CCGAAAATTAGAACTATGAT+TGG - chr2.4:23709739-23709758 None:intergenic 30.0%
CTATTATCGATCTAAAGGAA+CGG + chr2.4:23709568-23709587 MS.gene95990:CDS 30.0%
! TTTTTCTCATTCTGAATTGC+AGG + chr2.4:23709947-23709966 MS.gene95990:intron 30.0%
!!! TGGTTGATGGTTTTAAATTG+CGG - chr2.4:23709887-23709906 None:intergenic 30.0%
AAGAAATCTGCAATCAACGT+GGG - chr2.4:23709483-23709502 None:intergenic 35.0%
ATAATAGAGATTCATGGCGA+TGG - chr2.4:23709555-23709574 None:intergenic 35.0%
GATTGCAGATTTCTTCAGAA+AGG + chr2.4:23709488-23709507 MS.gene95990:CDS 35.0%
TCATTCTGAATTGCAGGTTA+TGG + chr2.4:23709953-23709972 MS.gene95990:intron 35.0%
!! TATGATTGGTTTCGATGTCA+AGG - chr2.4:23709725-23709744 None:intergenic 35.0%
ACAAGCAAATGAAGTCGATG+CGG - chr2.4:23709813-23709832 None:intergenic 40.0%
GAAGAAATCTGCAATCAACG+TGG - chr2.4:23709484-23709503 None:intergenic 40.0%
GTTCACATGGTAACTACAAC+TGG + chr2.4:23709852-23709871 MS.gene95990:intron 40.0%
TGTTGCATAGACCGCAATTA+TGG - chr2.4:23709769-23709788 None:intergenic 40.0%
!! AGTGTTGCTTGATCTGATGA+AGG - chr2.4:23709434-23709453 None:intergenic 40.0%
CACATGGTAACTACAACTGG+TGG + chr2.4:23709855-23709874 MS.gene95990:intron 45.0%
CATTGGAACTGCGATTTCAG+AGG + chr2.4:23709593-23709612 MS.gene95990:CDS 45.0%
GATCTAAAGGAACGGACCAT+TGG + chr2.4:23709576-23709595 MS.gene95990:CDS 45.0%
TCGGACTGCAACCATAATTG+CGG + chr2.4:23709755-23709774 MS.gene95990:intron 45.0%
! CGCGGTTCATGAGATTTTCA+GGG - chr2.4:23709529-23709548 None:intergenic 45.0%
!! AACACAGAAAACTTGGTGCG+TGG + chr2.4:23709403-23709422 MS.gene95990:intron 45.0%
!! AGATTTTCAGGGCTAGAGCA+GGG - chr2.4:23709518-23709537 None:intergenic 45.0%
!! CTCTGAAATCGCAGTTCCAA+TGG - chr2.4:23709595-23709614 None:intergenic 45.0%
CGTGGGAGCAAGCATAATTG+AGG - chr2.4:23709466-23709485 None:intergenic 50.0%
! GCGCGGTTCATGAGATTTTC+AGG - chr2.4:23709530-23709549 None:intergenic 50.0%
!! GAGATTTTCAGGGCTAGAGC+AGG - chr2.4:23709519-23709538 None:intergenic 50.0%
!! GATTTTCAGGGCTAGAGCAG+GGG - chr2.4:23709517-23709536 None:intergenic 50.0%
GATTCATGGCGATGGAAGCG+CGG - chr2.4:23709547-23709566 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 23709291 23709994 23709291 ID=MS.gene95990
chr2.4 mRNA 23709291 23709994 23709291 ID=MS.gene95990.t1;Parent=MS.gene95990
chr2.4 exon 23709291 23709311 23709291 ID=MS.gene95990.t1.exon1;Parent=MS.gene95990.t1
chr2.4 CDS 23709291 23709311 23709291 ID=cds.MS.gene95990.t1;Parent=MS.gene95990.t1
chr2.4 exon 23709410 23709644 23709410 ID=MS.gene95990.t1.exon2;Parent=MS.gene95990.t1
chr2.4 CDS 23709410 23709644 23709410 ID=cds.MS.gene95990.t1;Parent=MS.gene95990.t1
chr2.4 exon 23709969 23709994 23709969 ID=MS.gene95990.t1.exon3;Parent=MS.gene95990.t1
chr2.4 CDS 23709969 23709994 23709969 ID=cds.MS.gene95990.t1;Parent=MS.gene95990.t1
Gene Sequence

>MS.gene95990

ATGATCATGGTTAATGGGCAGGTAAATATTAATTTCTCTTGTAATTTCTAGAACCAATAAATTACATAAAGTTTTTTTTTTATCTAATTAAATTGTGTAATGATTTATGAAAAACACAGAAAACTTGGTGCGTGGCAAAGCCTTCATCAGATCAAGCAACACTTTTATCAAACCTCAATTATGCTTGCTCCCACGTTGATTGCAGATTTCTTCAGAAAGGATGCCCCTGCTCTAGCCCTGAAAATCTCATGAACCGCGCTTCCATCGCCATGAATCTCTATTATCGATCTAAAGGAACGGACCATTGGAACTGCGATTTCAGAGGATCTGCTCTGATTGTTGTGACTGATCCAAGTAAGTCACATAACTCATTGTGTTGTTTCATGTTCTAGATTAAATAATTGTTCTTCTAAAATCTAAATGAAACATTGCCTTGACATCGAAACCAATCATAGTTCTAATTTTCGGACTGCAACCATAATTGCGGTCTATGCAACAACATTGTAACTGCAATTATGGCCGCATCGACTTCATTTGCTTGTATTTTTCCATAATATTGATGTTCACATGGTAACTACAACTGGTGGTTGCAACCGCAATTTAAAACCATCAACCAATTTACAAGTTTGATATGACTTTCTAATGTGACATTAATCTTTTTCTCATTCTGAATTGCAGGTTATGGTAACTGCATTTATGCATAG
Protein sequence

>MS.gene95990.t1

MIMVNGQKTWCVAKPSSDQATLLSNLNYACSHVDCRFLQKGCPCSSPENLMNRASIAMNLYYRSKGTDHWNCDFRGSALIVVTDPSYGNCIYA