AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG000242


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000242 MtrunA17_Chr1g0154211 94.697 396 21 0 7 402 4 399 0.0 781
MsaG000242 MtrunA17_Chr1g0154111 66.838 389 99 8 1 384 1 364 3.22e-173 496
MsaG000242 MtrunA17_Chr1g0154111 56.710 231 60 6 40 257 368 571 1.39e-68 227
MsaG000242 MtrunA17_Chr1g0154101 58.259 448 117 6 10 390 168 612 9.24e-169 493
MsaG000242 MtrunA17_Chr1g0154101 73.373 169 43 2 1 168 1 168 2.95e-77 255
MsaG000242 MtrunA17_Chr1g0154101 32.041 387 201 11 23 399 503 837 5.12e-42 157
MsaG000242 MtrunA17_Chr1g0154131 64.706 374 62 7 10 382 168 472 2.35e-159 457
MsaG000242 MtrunA17_Chr1g0154131 79.167 168 35 0 1 168 1 168 1.17e-89 279
MsaG000242 MtrunA17_Chr1g0154171 58.629 394 120 4 6 398 3 354 6.79e-152 434
MsaG000242 MtrunA17_Chr1g0154191 54.342 403 131 5 8 398 4 365 1.51e-143 413
MsaG000242 MtrunA17_Chr1g0154071 54.948 384 147 7 3 385 134 492 1.48e-133 392
MsaG000242 MtrunA17_Chr1g0154071 74.101 139 33 1 5 140 4 142 2.33e-63 211
MsaG000242 MtrunA17_Chr1g0154151 53.867 362 106 8 40 397 19 323 5.10e-120 352
MsaG000242 MtrunA17_Chr1g0154241 67.059 255 75 4 9 257 5 256 1.76e-114 335
MsaG000242 MtrunA17_Chr1g0154251 50.129 389 157 10 9 365 10 393 8.12e-112 337
MsaG000242 MtrunA17_Chr1g0154041 41.823 373 184 7 25 390 15 361 8.73e-82 262
MsaG000242 MtrunA17_Chr1g0154041 31.606 386 206 12 23 398 252 589 1.89e-38 145
MsaG000242 MtrunA17_Chr1g0154161 83.673 147 19 2 1 142 1 147 2.43e-81 252
MsaG000242 MtrunA17_Chr1g0154161 49.029 206 95 2 194 398 122 318 4.07e-55 184
MsaG000242 MtrunA17_Chr1g0154121 62.366 93 33 1 307 397 1 93 5.12e-35 124
MsaG000242 MtrunA17_Chr6g0464121 56.000 75 32 1 311 384 122 196 1.20e-21 95.1
MsaG000242 MtrunA17_Chr4g0033961 27.000 400 227 16 30 382 11 392 4.52e-19 88.6
MsaG000242 MtrunA17_Chr7g0233561 38.202 89 55 0 26 114 19 107 1.26e-14 74.3
MsaG000242 MtrunA17_Chr7g0233571 39.175 97 55 1 19 115 8 100 2.53e-14 72.0
MsaG000242 MtrunA17_Chr3g0131891 35.484 93 59 1 24 115 17 109 3.06e-14 73.2
MsaG000242 MtrunA17_Chr7g0233531 40.000 75 45 0 41 115 2 76 2.63e-13 69.7
MsaG000242 MtrunA17_Chr5g0419201 36.667 90 57 0 26 115 17 106 6.26e-13 67.0
MsaG000242 MtrunA17_Chr7g0233541 37.975 79 49 0 41 119 2 80 2.24e-12 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000242 AT4G33280.3 32.808 381 207 12 12 368 11 366 9.57e-49 170
MsaG000242 AT4G33280.1 32.410 361 174 10 12 368 11 305 6.20e-47 164
MsaG000242 AT4G33280.2 55.039 129 56 2 12 139 11 138 2.51e-43 153
MsaG000242 AT3G18990.1 24.935 385 200 9 30 381 11 339 4.59e-22 96.7
MsaG000242 AT3G18990.2 24.873 394 221 9 30 401 11 351 5.25e-22 97.1
MsaG000242 AT4G34400.2 36.000 100 61 2 26 124 17 114 5.67e-17 82.4
MsaG000242 AT4G34400.1 36.000 100 61 2 26 124 17 114 5.67e-17 82.4
MsaG000242 AT3G06220.1 30.469 128 80 4 26 153 11 129 4.28e-14 70.5
MsaG000242 AT3G06160.1 27.103 214 132 7 26 238 26 216 1.56e-13 71.6
MsaG000242 AT3G06160.5 27.103 214 132 7 26 238 11 201 1.66e-13 71.2
MsaG000242 AT3G06160.4 27.103 214 132 7 26 238 11 201 1.66e-13 71.2
MsaG000242 AT3G06160.3 27.103 214 132 7 26 238 11 201 1.66e-13 71.2
MsaG000242 AT3G06160.2 27.103 214 132 7 26 238 70 260 2.31e-13 71.2
MsaG000242 AT3G53310.1 33.333 93 62 0 23 115 8 100 1.61e-12 68.2
MsaG000242 AT5G60130.5 38.462 91 51 2 37 122 25 115 1.33e-11 64.7
MsaG000242 AT5G66980.1 40.244 82 45 1 37 114 21 102 2.10e-11 65.1
MsaG000242 AT5G60130.3 39.326 89 49 2 39 122 1 89 2.28e-11 64.7
MsaG000242 AT5G60130.2 39.326 89 49 2 39 122 27 115 2.84e-11 64.3
MsaG000242 AT5G60130.1 38.462 91 51 2 37 122 25 115 3.43e-11 64.3
MsaG000242 AT5G60130.4 38.462 91 51 2 37 122 22 112 3.52e-11 64.3

Find 104 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCCAAGCTTTATGTTAT+TGG 0.166151 1:+3195606 None:intergenic
CAGCTCCACTAGGACCTTTA+AGG 0.180866 1:+3198044 None:intergenic
CCAGAAAATGTGACCCTTAA+AGG 0.236805 1:-3198058 MsaT000242.1:CDS
AACTTCATTAGCTGGCTTCT+TGG 0.255515 1:+3197565 None:intergenic
CCTTTGGCCGGTTGGTTGTT+TGG 0.258620 1:+3197589 None:intergenic
GAAAGTATTGATCATCAAAA+TGG 0.270213 1:-3195493 MsaT000242.1:CDS
TGGTTGTTTGGGAAAGTAGA+TGG 0.276616 1:+3197601 None:intergenic
CTTTGGCCGGTTGGTTGTTT+GGG 0.281327 1:+3197590 None:intergenic
TCACGAGAATTACCTTCTTT+TGG 0.284057 1:+3197509 None:intergenic
TGGTTCACCTGAGAGATTTC+GGG 0.291973 1:-3197729 MsaT000242.1:CDS
AGTGGAGCTGTGTGGGATAT+TGG 0.305311 1:-3198031 MsaT000242.1:CDS
GTGGTTCACCTGAGAGATTT+CGG 0.308902 1:-3197730 MsaT000242.1:CDS
TGTCGATGGTCCACGTATTC+TGG 0.310730 1:-3196359 MsaT000242.1:intron
AAGTAGATGGGGAGTTCCTT+AGG 0.312746 1:+3197614 None:intergenic
CTTGGGAGGAAGACATTTAC+TGG 0.335828 1:-3239786 MsaT000242.1:CDS
GTCTTCCTCGCTTCTTAGTC+TGG 0.344493 1:+3197534 None:intergenic
TAGCTGGCTTCTTGGTCCTT+TGG 0.354794 1:+3197573 None:intergenic
CACCTGAGAGATTTCGGGTT+CGG 0.376625 1:-3197724 MsaT000242.1:CDS
CTTGTATGCACTCTACTTCT+AGG 0.379008 1:+3195667 None:intergenic
ATTTCTTCAAACCACCCATT+TGG 0.379142 1:-3239734 MsaT000242.1:CDS
ATTGAGTGAAACGGATGAAC+TGG 0.387722 1:+3239755 None:intergenic
GTGGAGCTGTGTGGGATATT+GGG 0.390357 1:-3198030 MsaT000242.1:CDS
ATAATCTTTATCTTGCCGTT+TGG 0.397078 1:+3195733 None:intergenic
GTGAGGGAGCACTTGATTTG+AGG 0.403845 1:-3197490 MsaT000242.1:CDS
TTACAAGTTGTTGTTCCAAA+TGG 0.406373 1:+3239719 None:intergenic
TGTTTACTTCGTGGGCGGTT+GGG 0.420992 1:-3197987 MsaT000242.1:CDS
TGAGGGAGCACTTGATTTGA+GGG 0.422320 1:-3197489 MsaT000242.1:CDS
CTGTTTACTTCGTGGGCGGT+TGG 0.428777 1:-3197988 MsaT000242.1:CDS
TTCTTGGTCCTTTGGCCGGT+TGG 0.434930 1:+3197581 None:intergenic
GGTTGTTTGGGAAAGTAGAT+GGG 0.439627 1:+3197602 None:intergenic
TGGCTTCTTGGTCCTTTGGC+CGG 0.440342 1:+3197577 None:intergenic
CCTCGCTTCTTAGTCTGGCC+AGG 0.449815 1:+3197539 None:intergenic
AGTAGATGGGGAGTTCCTTA+GGG 0.454636 1:+3197615 None:intergenic
TACAAGTTGTTGTTCCAAAT+GGG 0.455785 1:+3239720 None:intergenic
CACAAAACAGCAGCAGGTCT+TGG 0.458108 1:-3239804 MsaT000242.1:CDS
CCAGGTGTAACTTCATTAGC+TGG 0.461198 1:+3197557 None:intergenic
GATGCGCTATGGAAAATTGA+TGG 0.463928 1:+3195758 None:intergenic
AGCTCCACTAGGACCTTTAA+GGG 0.472647 1:+3198045 None:intergenic
CGCCGAACCCGAAATCTCTC+AGG 0.473424 1:+3197722 None:intergenic
TGAAACGGATGAACTGGAAA+TGG 0.476169 1:+3239761 None:intergenic
AAAGTATTGATCATCAAAAT+GGG 0.485102 1:-3195492 MsaT000242.1:CDS
GAAGTCAATACTGCTTCTAA+TGG 0.487691 1:-3197764 MsaT000242.1:CDS
GATGGTACTGTTTACTTCGT+GGG 0.490529 1:-3197995 MsaT000242.1:CDS
TACTTTCCCAAACAACCAAC+CGG 0.491088 1:-3197596 MsaT000242.1:CDS
ACAAAACAGCAGCAGGTCTT+GGG 0.491871 1:-3239803 MsaT000242.1:CDS
CAACGGTGAATCTCTCTTTG+AGG 0.491919 1:-3197909 MsaT000242.1:CDS
GATTATTCTTCGTAATTTGA+AGG 0.492590 1:-3195716 MsaT000242.1:CDS
TCCATAGCGCATCTTCCAAA+CGG 0.492621 1:-3195748 MsaT000242.1:CDS
CGAGGAAGACCGCCAAAAGA+AGG 0.494591 1:-3197521 MsaT000242.1:CDS
AAGAACACAAACACATCTGT+TGG 0.496016 1:-3197788 MsaT000242.1:CDS
GCTAGTCTCCGAGGTTCAAA+AGG 0.500197 1:-3195515 MsaT000242.1:CDS
TTGCTGAGGTCGACGAAGAC+GGG 0.500559 1:-3195537 MsaT000242.1:CDS
GGACATGCTCAAACTGAAGA+AGG 0.510328 1:-3197824 MsaT000242.1:CDS
ATTATTCTTCGTAATTTGAA+GGG 0.513122 1:-3195715 MsaT000242.1:CDS
GTTGCTGAGGTCGACGAAGA+CGG 0.514090 1:-3195538 MsaT000242.1:CDS
AACAAAATATGGAAAAGTTG+AGG 0.516177 1:+3196402 None:intergenic
TATTGAATCTGCTTCCCCTA+AGG 0.518194 1:-3197630 MsaT000242.1:CDS
GAAAAGTTGAGGTAAATGAC+TGG 0.520804 1:+3196413 None:intergenic
GAAACGGATGAACTGGAAAT+GGG 0.528881 1:+3239762 None:intergenic
CACCGTTGTACTTAAAGACA+AGG 0.534444 1:+3197924 None:intergenic
ATGCGCTATGGAAAATTGAT+GGG 0.534562 1:+3195759 None:intergenic
AGATGGTACTGTTTACTTCG+TGG 0.536376 1:-3197996 MsaT000242.1:CDS
CGTGCCAATAACATAAAGCT+TGG 0.537860 1:-3195610 MsaT000242.1:CDS
GACATGCTCAAACTGAAGAA+GGG 0.539180 1:-3197823 MsaT000242.1:CDS
GCTTCTAACAAGGAACTCTC+AGG 0.540714 1:-3197467 MsaT000242.1:intron
ATCAAAACATTCAATGTCGA+TGG 0.543207 1:-3196373 MsaT000242.1:CDS
GCCGTTTGGAAGATGCGCTA+TGG 0.543496 1:+3195747 None:intergenic
GAAGAACACAAAACAGCAGC+AGG 0.549527 1:-3239810 MsaT000242.1:CDS
CCAGCTAATGAAGTTACACC+TGG 0.556435 1:-3197557 MsaT000242.1:CDS
TTCCTTGTCTTTAAGTACAA+CGG 0.557608 1:-3197926 MsaT000242.1:CDS
TGGAGTTAGTTTCTGTGAGA+AGG 0.558125 1:-3197873 MsaT000242.1:CDS
TTTGAAGAAATTGAGTGAAA+CGG 0.560139 1:+3239746 None:intergenic
AGGTCCTAGTGGAGCTGTGT+GGG 0.568073 1:-3198038 MsaT000242.1:CDS
TGATTTGAGGGCTTCTAACA+AGG 0.574575 1:-3197477 MsaT000242.1:CDS
AAGTTGTTGTTCCAAATGGG+TGG 0.583718 1:+3239723 None:intergenic
CCAAACAACCAACCGGCCAA+AGG 0.585015 1:-3197589 MsaT000242.1:CDS
ATATCCCACACAGCTCCACT+AGG 0.588180 1:+3198034 None:intergenic
GTTGTTTGGGAAAGTAGATG+GGG 0.591431 1:+3197603 None:intergenic
GTCAATACTGCTTCTAATGG+TGG 0.601970 1:-3197761 MsaT000242.1:CDS
CATACAAGTCACACTTTGTG+TGG 0.602821 1:-3195652 MsaT000242.1:CDS
TCTAATGGTGGCGTTGACTG+TGG 0.604326 1:-3197749 MsaT000242.1:CDS
GTCAAGGTTATCGTCAGCAA+AGG 0.607838 1:-3196452 MsaT000242.1:CDS
GTCACACTTTGTGTGGAGGA+TGG 0.614641 1:-3195645 MsaT000242.1:CDS
AAAAGTTGAGGTAAATGACT+GGG 0.616205 1:+3196414 None:intergenic
AAGGTCCTAGTGGAGCTGTG+TGG 0.617527 1:-3198039 MsaT000242.1:CDS
ATTACGTGTCCGTGTTGCTG+AGG 0.620142 1:-3195551 MsaT000242.1:CDS
ACATGCTCAAACTGAAGAAG+GGG 0.624407 1:-3197822 MsaT000242.1:CDS
AAAAGAAGGTAATTCTCGTG+AGG 0.624894 1:-3197507 MsaT000242.1:CDS
GTGACCCTTAAAGGTCCTAG+TGG 0.630968 1:-3198049 MsaT000242.1:CDS
GAACAACTCACCAGAATACG+TGG 0.631909 1:+3196349 None:intergenic
AAAGAAGGTAATTCTCGTGA+GGG 0.632567 1:-3197506 MsaT000242.1:CDS
CCACAGAGGCAGCACAGTCA+AGG 0.637815 1:-3196468 MsaT000242.1:intron
AAACAGCAGCAGGTCTTGGG+AGG 0.639430 1:-3239800 MsaT000242.1:CDS
ATTGGGTTGACAACTAGAGA+TGG 0.647577 1:-3198013 MsaT000242.1:CDS
ACTGTGTTAATTCAAATGGG+AGG 0.654200 1:-3239832 None:intergenic
GTAATTTGAAGGGAGAACAG+TGG 0.655181 1:-3195705 MsaT000242.1:CDS
GGTACTGTTTACTTCGTGGG+CGG 0.659429 1:-3197992 MsaT000242.1:CDS
CTTCGTCGACCTCAGCAACA+CGG 0.662749 1:+3195542 None:intergenic
CGAAGACGGGCTAGTCTCCG+AGG 0.666474 1:-3195524 MsaT000242.1:CDS
TGCGCTATGGAAAATTGATG+GGG 0.667850 1:+3195760 None:intergenic
ACAAGTCACACTTTGTGTGG+AGG 0.672770 1:-3195649 MsaT000242.1:CDS
GTAGATGGGGAGTTCCTTAG+GGG 0.675019 1:+3197616 None:intergenic
CATGCTCAAACTGAAGAAGG+GGG 0.720080 1:-3197821 MsaT000242.1:CDS
CCTGGCCAGACTAAGAAGCG+AGG 0.722966 1:-3197539 MsaT000242.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 3195477 3239839 3195477 ID=MsaG000242
Chr1 mRNA 3195477 3239839 3195477 ID=MsaT000242.1;Parent=MsaG000242
Chr1 exon 3195477 3195788 3195477 ID=MsaT000242.1.exon4;Parent=MsaT000242.1
Chr1 CDS 3195477 3195788 3195477 ID=cds.MsaT000242.1;Parent=MsaT000242.1
Chr1 exon 3196360 3196484 3196360 ID=MsaT000242.1.exon3;Parent=MsaT000242.1
Chr1 CDS 3196360 3196484 3196360 ID=cds.MsaT000242.1;Parent=MsaT000242.1
Chr1 exon 3197468 3198122 3197468 ID=MsaT000242.1.exon2;Parent=MsaT000242.1
Chr1 CDS 3197468 3198122 3197468 ID=cds.MsaT000242.1;Parent=MsaT000242.1
Chr1 exon 3239723 3239839 3239723 ID=MsaT000242.1.exon1;Parent=MsaT000242.1
Chr1 CDS 3239723 3239839 3239723 ID=cds.MsaT000242.1;Parent=MsaT000242.1
Gene Sequence

>MsaT000242.1

ATGGGAGGAAGAACACAAAACAGCAGCAGGTCTTGGGAGGAAGACATTTACTGGACCCATTTCCAGTTCATCCGTTTCACTCAATTTCTTCAAACCACCCATTTGGAACAACAACTTGCACTTCCTAAAACATTTTCAGACAATTTAAAAAAGAAGTTGCCAGAAAATGTGACCCTTAAAGGTCCTAGTGGAGCTGTGTGGGATATTGGGTTGACAACTAGAGATGGTACTGTTTACTTCGTGGGCGGTTGGGAGCAATTCGTGAAAGATCACTCTTTGAAAGAGAATGATTTCCTTGTCTTTAAGTACAACGGTGAATCTCTCTTTGAGGTTTTAATCTTTGATGGAGTTAGTTTCTGTGAGAAGGCAGCTTCTTATTTTGTTAGAAAATGTGGACATGCTCAAACTGAAGAAGGGGGTAGCAAGGTAAAGAACACAAACACATCTGTTGGAGAAGTCAATACTGCTTCTAATGGTGGCGTTGACTGTGGTTCACCTGAGAGATTTCGGGTTCGGCGTCTTGACAGTATAAGAACACCATTAGCTGTACCTGTCAAAACTACTGATAAAATGACTTTAAATGCTTTTATTGAATCTGCTTCCCCTAAGGAACTCCCCATCTACTTTCCCAAACAACCAACCGGCCAAAGGACCAAGAAGCCAGCTAATGAAGTTACACCTGGCCAGACTAAGAAGCGAGGAAGACCGCCAAAAGAAGGTAATTCTCGTGAGGGAGCACTTGATTTGAGGGCTTCTAACAAGGAACTCTCAGAGGCAGCACAGTCAAGGTTATCGTCAGCAAAGGATGAGAAAAAGTTAGCCCAGTCATTTACCTCAACTTTTCCATATTTTGTTAAAATAATCAAAACATTCAATGTCGATGGTCCACGTATTCTGAATATACCCCATCAATTTTCCATAGCGCATCTTCCAAACGGCAAGATAAAGATTATTCTTCGTAATTTGAAGGGAGAACAGTGGACTGCTAATTCTGTTCCTAGAAGTAGAGTGCATACAAGTCACACTTTGTGTGGAGGATGGATGTCTTTTGTTCGTGCCAATAACATAAAGCTTGGAGATGTCTGCATTTTCGAACTTATAAATGACTGTGAATTACGTGTCCGTGTTGCTGAGGTCGACGAAGACGGGCTAGTCTCCGAGGTTCAAAAGGAAAGTATTGATCATCAAAATGGGAGTTGTGAAACTTAA

Protein sequence

>MsaT000242.1

MGGRTQNSSRSWEEDIYWTHFQFIRFTQFLQTTHLEQQLALPKTFSDNLKKKLPENVTLKGPSGAVWDIGLTTRDGTVYFVGGWEQFVKDHSLKENDFLVFKYNGESLFEVLIFDGVSFCEKAASYFVRKCGHAQTEEGGSKVKNTNTSVGEVNTASNGGVDCGSPERFRVRRLDSIRTPLAVPVKTTDKMTLNAFIESASPKELPIYFPKQPTGQRTKKPANEVTPGQTKKRGRPPKEGNSREGALDLRASNKELSEAAQSRLSSAKDEKKLAQSFTSTFPYFVKIIKTFNVDGPRILNIPHQFSIAHLPNGKIKIILRNLKGEQWTANSVPRSRVHTSHTLCGGWMSFVRANNIKLGDVCIFELINDCELRVRVAEVDEDGLVSEVQKESIDHQNGSCET*