AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1414540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1414540 MtrunA17_Chr4g0000481 91.176 204 16 2 1 204 1 202 4.48e-122 350
Msa1414540 MtrunA17_Chr6g0479211 38.547 179 99 5 33 204 6 180 2.32e-27 105
Msa1414540 MtrunA17_Chr2g0299991 38.462 130 73 3 81 204 65 193 5.16e-22 92.0
Msa1414540 MtrunA17_Chr6g0487231 41.935 124 65 3 87 204 70 192 3.09e-21 89.7
Msa1414540 MtrunA17_Chr4g0070851 39.815 108 58 3 103 204 87 193 1.60e-19 85.1
Msa1414540 MtrunA17_Chr6g0483151 31.092 119 75 3 92 204 20 137 2.86e-14 70.5
Msa1414540 MtrunA17_Chr5g0419441 35.156 128 78 2 82 204 235 362 2.81e-12 65.1
Msa1414540 MtrunA17_Chr2g0286421 33.333 126 77 4 86 204 102 227 3.09e-12 64.7
Msa1414540 MtrunA17_Chr8g0384301 32.824 131 78 3 83 204 296 425 3.86e-12 64.7
Msa1414540 MtrunA17_Chr1g0170551 32.203 118 74 3 92 204 13 129 1.20e-11 63.2
Msa1414540 MtrunA17_Chr4g0038501 32.000 125 72 3 90 204 24 145 8.75e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1414540 AT1G51660.1 59.048 210 67 3 1 204 1 197 3.73e-66 207
Msa1414540 AT3G21220.2 57.561 205 69 4 1 204 1 188 7.62e-60 191
Msa1414540 AT3G21220.1 57.561 205 69 4 1 204 1 188 7.62e-60 191
Msa1414540 AT1G73500.1 47.287 129 61 3 81 204 42 168 4.71e-31 115
Msa1414540 AT1G18350.1 40.556 180 84 6 30 204 5 166 1.64e-29 111
Msa1414540 AT3G06230.1 37.419 155 90 3 51 204 20 168 2.56e-24 97.4
Msa1414540 AT4G29810.3 38.462 130 73 3 81 204 74 202 1.31e-22 93.6
Msa1414540 AT4G29810.1 38.462 130 73 3 81 204 65 193 1.37e-22 94.0
Msa1414540 AT4G29810.2 38.462 130 73 3 81 204 74 202 1.48e-22 94.0
Msa1414540 AT4G26070.1 36.923 130 75 3 81 204 63 191 1.55e-22 92.8
Msa1414540 AT5G56580.1 41.732 127 66 4 85 204 69 194 3.04e-22 92.8
Msa1414540 AT4G26070.2 36.923 130 75 3 81 204 63 191 3.07e-22 92.8
Msa1414540 AT4G26070.3 36.923 130 75 3 81 204 63 191 3.07e-22 92.8
Msa1414540 AT4G26070.5 36.923 130 75 3 81 204 50 178 4.60e-22 92.0
Msa1414540 AT4G26070.4 36.923 130 75 3 81 204 62 190 4.65e-22 92.4
Msa1414540 AT1G32320.1 33.333 126 76 2 83 204 45 166 6.71e-16 74.7
Msa1414540 AT1G69220.1 35.938 128 77 2 82 204 245 372 1.37e-14 72.0
Msa1414540 AT1G66750.1 30.233 129 83 3 82 204 9 136 2.85e-13 67.8
Msa1414540 AT1G53570.2 32.450 151 81 4 64 204 201 340 2.19e-12 65.5
Msa1414540 AT1G53570.3 32.450 151 81 4 64 204 201 340 2.19e-12 65.5
Msa1414540 AT1G53570.1 32.450 151 81 4 64 204 201 340 2.25e-12 65.5
Msa1414540 AT1G53570.4 32.450 151 81 4 64 204 201 340 2.27e-12 65.5
Msa1414540 AT1G53570.5 32.450 151 81 4 64 204 201 340 2.31e-12 65.5
Msa1414540 AT1G53570.6 32.192 146 87 3 69 204 197 340 5.25e-12 64.3
Msa1414540 AT1G53570.7 32.192 146 87 3 69 204 197 340 5.31e-12 64.3
Msa1414540 AT3G48750.1 32.283 127 78 4 85 204 3 128 8.28e-12 63.2
Msa1414540 AT3G15220.1 34.127 126 76 2 83 204 15 137 1.00e-11 63.5
Msa1414540 AT1G70430.4 25.180 139 98 2 72 204 2 140 1.22e-11 63.5
Msa1414540 AT1G70430.1 25.180 139 98 2 72 204 2 140 1.41e-11 63.2
Msa1414540 AT1G70430.3 25.180 139 98 2 72 204 2 140 1.48e-11 63.2
Msa1414540 AT1G63700.1 31.690 142 87 3 72 204 386 526 2.89e-11 62.4
Msa1414540 AT1G63700.2 31.690 142 87 3 72 204 386 526 2.89e-11 62.4
Msa1414540 AT3G61960.2 34.167 120 72 3 91 204 15 133 3.67e-11 62.0
Msa1414540 AT1G69220.2 34.400 125 75 3 85 204 223 345 4.00e-11 62.0

Find 66 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATCACAACGCTGAGATTC+AGG 0.275280 tig0024129:+82625 Msa1414540:CDS
GAGCCGGTGGCGGTTGGTGG+TGG 0.347819 tig0024129:-82208 None:intergenic
AATCTTTCTAGCTCGGAAAA+AGG 0.354519 tig0024129:-82433 None:intergenic
TATGCTTTGAAGGTGATATA+CGG 0.382785 tig0024129:+82506 Msa1414540:CDS
GGCAGCGGTGGAAGCGGTGG+TGG 0.389943 tig0024129:+82347 Msa1414540:CDS
CGGTCGTGCTTATGCTTTGA+AGG 0.390747 tig0024129:+82496 Msa1414540:CDS
CTCCACTTCCGCTTCCGATC+CGG 0.391970 tig0024129:-82459 None:intergenic
GCTGAGCCGGTGGCGGTTGG+TGG 0.396621 tig0024129:-82211 None:intergenic
GTTGTTGTTGTTTGGTGAAC+CGG 0.397124 tig0024129:-82242 None:intergenic
GATCTTTGCGGCGGCGTTGA+GGG 0.403069 tig0024129:-82273 None:intergenic
CATCAACATCACGCAAGATC+TGG 0.410466 tig0024129:-82588 None:intergenic
CCGGACGGTGGCAGCGGCAG+TGG 0.412273 tig0024129:-82340 None:intergenic
GTTGGTGGTGGAAGCTGAAT+CGG 0.429270 tig0024129:-82196 None:intergenic
GGAGGAAACGGAAGCGGAAG+CGG 0.437055 tig0024129:+82368 Msa1414540:CDS
AACCGGATCGGAAGCGGAAG+TGG 0.437188 tig0024129:+82440 Msa1414540:CDS
GGAAGCGGTGGTGGAGGAAA+CGG 0.438980 tig0024129:+82356 Msa1414540:CDS
ACCGGCTCAGCCACCGCCTC+CGG 0.449426 tig0024129:+82206 Msa1414540:CDS
CTGCCACCGTCCGGTGGCAG+CGG 0.450286 tig0024129:+82332 Msa1414540:CDS
GTGGCTGAGCCGGTGGCGGT+TGG 0.454821 tig0024129:-82214 None:intergenic
ACCGGAGGCGGTGGCTGAGC+CGG 0.455721 tig0024129:-82224 None:intergenic
AGCGGTGGAAGCGGTGGTGG+AGG 0.463460 tig0024129:+82350 Msa1414540:CDS
GGCGGTGGCTGAGCCGGTGG+CGG 0.470478 tig0024129:-82218 None:intergenic
CCACCGTCCGGTGGCAGCGG+TGG 0.471680 tig0024129:+82335 Msa1414540:CDS
TCCGGTGGCAGCGGTGGAAG+CGG 0.472400 tig0024129:+82341 Msa1414540:CDS
CTGCCACCGGACGGTGGCAG+CGG 0.475182 tig0024129:-82346 None:intergenic
ACCGCTTCCACCGCTGCCAC+CGG 0.483888 tig0024129:-82359 None:intergenic
CCGAGCTAGAAAGATTGAAC+CGG 0.484264 tig0024129:+82423 Msa1414540:CDS
CGAAGGGAACATATTTCCTC+AGG 0.488646 tig0024129:+82679 Msa1414540:CDS
TGATCTTTGCGGCGGCGTTG+AGG 0.488743 tig0024129:-82274 None:intergenic
CCACTGCCGCTGCCACCGTC+CGG 0.500585 tig0024129:+82323 Msa1414540:CDS
AGATTGAACCGGATCGGAAG+CGG 0.504319 tig0024129:+82434 Msa1414540:CDS
CCGGTTCAATCTTTCTAGCT+CGG 0.509178 tig0024129:-82440 None:intergenic
CTTCCACCACCAACCGCCAC+CGG 0.521484 tig0024129:+82188 Msa1414540:CDS
GTTTGGTGAACCGGAGGCGG+TGG 0.527198 tig0024129:-82233 None:intergenic
GATGTGACGACGGTGGAGAT+AGG 0.529462 tig0024129:-82764 None:intergenic
GGTGGCAGCGGTGGAAGCGG+TGG 0.536898 tig0024129:+82344 Msa1414540:CDS
TTTGTGTCACGCTGTGGAAG+CGG 0.539623 tig0024129:-82307 None:intergenic
CTTTGCGGCGGCGTTGAGGG+CGG 0.540631 tig0024129:-82270 None:intergenic
GGAAACGGAAGCGGAAGCGG+AGG 0.553349 tig0024129:+82371 Msa1414540:CDS
GGAGGCGGTGGCTGAGCCGG+TGG 0.556776 tig0024129:-82221 None:intergenic
GGTGGTGGAGGAAACGGAAG+CGG 0.578311 tig0024129:+82362 Msa1414540:CDS
CGGATCGGAAGCGGAAGTGG+AGG 0.579984 tig0024129:+82443 Msa1414540:CDS
CACGATGAACGATGTGACGA+CGG 0.588271 tig0024129:-82774 None:intergenic
GTTGTTTGGTGAACCGGAGG+CGG 0.589676 tig0024129:-82236 None:intergenic
CTTCCACCGCTGCCACCGGA+CGG 0.592453 tig0024129:-82355 None:intergenic
GTAGAGTTAGATGATCTTTG+CGG 0.593178 tig0024129:-82285 None:intergenic
CCACCGCTGCCACCGGACGG+TGG 0.593208 tig0024129:-82352 None:intergenic
CTGCCGCTGCCACCGTCCGG+TGG 0.596926 tig0024129:+82326 Msa1414540:CDS
CTAGAAAGATTGAACCGGAT+CGG 0.605491 tig0024129:+82428 Msa1414540:CDS
GGTGGAGATAGGCGAGTCCA+CGG 0.618681 tig0024129:-82753 None:intergenic
GGAAAATCACATCGCTGACG+TGG 0.622002 tig0024129:+82700 Msa1414540:CDS
TTGCTTGAATACATGGACGG+TGG 0.624571 tig0024129:+82650 Msa1414540:CDS
AAAGTAGTTCACAAAATCAA+CGG 0.625254 tig0024129:+82476 Msa1414540:CDS
GCGAGGTTTGTGTCACGCTG+TGG 0.631274 tig0024129:-82313 None:intergenic
CGGAAGCGGAAGTGGAGGAA+CGG 0.639226 tig0024129:+82448 Msa1414540:CDS
ATGGACGGTGGATCTCTCGA+AGG 0.650167 tig0024129:+82662 Msa1414540:CDS
GAGTTAGATGATCTTTGCGG+CGG 0.661602 tig0024129:-82282 None:intergenic
TGGACGGTGGATCTCTCGAA+GGG 0.662436 tig0024129:+82663 Msa1414540:CDS
GTTGTTGTTTGGTGAACCGG+AGG 0.677745 tig0024129:-82239 None:intergenic
GCAAGATCTGGATTTCACGA+TGG 0.678526 tig0024129:-82576 None:intergenic
GGTGATATACGGACATCACG+AGG 0.687802 tig0024129:+82517 Msa1414540:CDS
GATGAACGATGTGACGACGG+TGG 0.689960 tig0024129:-82771 None:intergenic
GTGGCACGTCAGATCCTCCG+TGG 0.705559 tig0024129:+82719 Msa1414540:CDS
GCAGCGGCAGTGGTACAGCG+AGG 0.715731 tig0024129:-82330 None:intergenic
TGATGTTGATGATGTTAACG+TGG 0.747936 tig0024129:+82583 Msa1414540:CDS
GGAGATAGGCGAGTCCACGG+AGG 0.785591 tig0024129:-82750 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGTAGTTCACAAAATCAA+CGG + tig0024129:82476-82495 Msa1414540:CDS 25.0%
!! TATGCTTTGAAGGTGATATA+CGG + tig0024129:82506-82525 Msa1414540:CDS 30.0%
GTAGAGTTAGATGATCTTTG+CGG - tig0024129:82271-82290 None:intergenic 35.0%
!! AATCTTTCTAGCTCGGAAAA+AGG - tig0024129:82419-82438 None:intergenic 35.0%
!! TGATGTTGATGATGTTAACG+TGG + tig0024129:82583-82602 Msa1414540:CDS 35.0%
! TCAGGTTTTGCTTGAATACA+TGG + tig0024129:82643-82662 Msa1414540:CDS 35.0%
! GTTTTGCTTGAATACATGGA+CGG + tig0024129:82647-82666 Msa1414540:CDS 35.0%
!! GTTGTTGTTGTTTGGTGAAC+CGG - tig0024129:82228-82247 None:intergenic 40.0%
CTAGAAAGATTGAACCGGAT+CGG + tig0024129:82428-82447 Msa1414540:CDS 40.0%
! CGGCTGTTGTTGTTGTTGTT+TGG - tig0024129:82236-82255 None:intergenic 45.0%
GAGTTAGATGATCTTTGCGG+CGG - tig0024129:82268-82287 None:intergenic 45.0%
!! CCGGTTCAATCTTTCTAGCT+CGG - tig0024129:82426-82445 None:intergenic 45.0%
CCGAGCTAGAAAGATTGAAC+CGG + tig0024129:82423-82442 Msa1414540:CDS 45.0%
GCAAGATCTGGATTTCACGA+TGG - tig0024129:82562-82581 None:intergenic 45.0%
CATCAACATCACGCAAGATC+TGG - tig0024129:82574-82593 None:intergenic 45.0%
TTGCTTGAATACATGGACGG+TGG + tig0024129:82650-82669 Msa1414540:CDS 45.0%
CGAAGGGAACATATTTCCTC+AGG + tig0024129:82679-82698 Msa1414540:CDS 45.0%
! TCAGCGATGTGATTTTCCTG+AGG - tig0024129:82698-82717 None:intergenic 45.0%
!! GTTGGTGGTGGAAGCTGAAT+CGG - tig0024129:82182-82201 None:intergenic 50.0%
!! GTTGTTGTTTGGTGAACCGG+AGG - tig0024129:82225-82244 None:intergenic 50.0%
TTTGTGTCACGCTGTGGAAG+CGG - tig0024129:82293-82312 None:intergenic 50.0%
AGATTGAACCGGATCGGAAG+CGG + tig0024129:82434-82453 Msa1414540:CDS 50.0%
CGGTCGTGCTTATGCTTTGA+AGG + tig0024129:82496-82515 Msa1414540:CDS 50.0%
GGTGATATACGGACATCACG+AGG + tig0024129:82517-82536 Msa1414540:CDS 50.0%
CGATCACAACGCTGAGATTC+AGG + tig0024129:82625-82644 Msa1414540:CDS 50.0%
GGAAAATCACATCGCTGACG+TGG + tig0024129:82700-82719 Msa1414540:CDS 50.0%
CACGATGAACGATGTGACGA+CGG - tig0024129:82760-82779 None:intergenic 50.0%
! GTTGTTTGGTGAACCGGAGG+CGG - tig0024129:82222-82241 None:intergenic 55.0%
ATGGACGGTGGATCTCTCGA+AGG + tig0024129:82662-82681 Msa1414540:CDS 55.0%
TGGACGGTGGATCTCTCGAA+GGG + tig0024129:82663-82682 Msa1414540:CDS 55.0%
GATGTGACGACGGTGGAGAT+AGG - tig0024129:82750-82769 None:intergenic 55.0%
GATGAACGATGTGACGACGG+TGG - tig0024129:82757-82776 None:intergenic 55.0%
! GATCTTTGCGGCGGCGTTGA+GGG - tig0024129:82259-82278 None:intergenic 60.0%
TGATCTTTGCGGCGGCGTTG+AGG - tig0024129:82260-82279 None:intergenic 60.0%
GCGAGGTTTGTGTCACGCTG+TGG - tig0024129:82299-82318 None:intergenic 60.0%
!! GGAAGCGGTGGTGGAGGAAA+CGG + tig0024129:82356-82375 Msa1414540:CDS 60.0%
!! GGTGGTGGAGGAAACGGAAG+CGG + tig0024129:82362-82381 Msa1414540:CDS 60.0%
GGAGGAAACGGAAGCGGAAG+CGG + tig0024129:82368-82387 Msa1414540:CDS 60.0%
AACCGGATCGGAAGCGGAAG+TGG + tig0024129:82440-82459 Msa1414540:CDS 60.0%
CTCCACTTCCGCTTCCGATC+CGG - tig0024129:82445-82464 None:intergenic 60.0%
CGGAAGCGGAAGTGGAGGAA+CGG + tig0024129:82448-82467 Msa1414540:CDS 60.0%
GGTGGAGATAGGCGAGTCCA+CGG - tig0024129:82739-82758 None:intergenic 60.0%
CTTCCACCACCAACCGCCAC+CGG + tig0024129:82188-82207 Msa1414540:CDS 65.0%
! GTTTGGTGAACCGGAGGCGG+TGG - tig0024129:82219-82238 None:intergenic 65.0%
GGAAACGGAAGCGGAAGCGG+AGG + tig0024129:82371-82390 Msa1414540:CDS 65.0%
CGGATCGGAAGCGGAAGTGG+AGG + tig0024129:82443-82462 Msa1414540:CDS 65.0%
GTGGCACGTCAGATCCTCCG+TGG + tig0024129:82719-82738 Msa1414540:CDS 65.0%
GGAGATAGGCGAGTCCACGG+AGG - tig0024129:82736-82755 None:intergenic 65.0%
! CTTTGCGGCGGCGTTGAGGG+CGG - tig0024129:82256-82275 None:intergenic 70.0%
GCAGCGGCAGTGGTACAGCG+AGG - tig0024129:82316-82335 None:intergenic 70.0%
CTTCCACCGCTGCCACCGGA+CGG - tig0024129:82341-82360 None:intergenic 70.0%
TCCGGTGGCAGCGGTGGAAG+CGG + tig0024129:82341-82360 Msa1414540:CDS 70.0%
ACCGCTTCCACCGCTGCCAC+CGG - tig0024129:82345-82364 None:intergenic 70.0%
! AGCGGTGGAAGCGGTGGTGG+AGG + tig0024129:82350-82369 Msa1414540:CDS 70.0%
!! GAGCCGGTGGCGGTTGGTGG+TGG - tig0024129:82194-82213 None:intergenic 75.0%
! GCTGAGCCGGTGGCGGTTGG+TGG - tig0024129:82197-82216 None:intergenic 75.0%
! GTGGCTGAGCCGGTGGCGGT+TGG - tig0024129:82200-82219 None:intergenic 75.0%
! ACCGGCTCAGCCACCGCCTC+CGG + tig0024129:82206-82225 Msa1414540:CDS 75.0%
ACCGGAGGCGGTGGCTGAGC+CGG - tig0024129:82210-82229 None:intergenic 75.0%
CCACTGCCGCTGCCACCGTC+CGG + tig0024129:82323-82342 Msa1414540:CDS 75.0%
CTGCCACCGGACGGTGGCAG+CGG - tig0024129:82332-82351 None:intergenic 75.0%
CTGCCACCGTCCGGTGGCAG+CGG + tig0024129:82332-82351 Msa1414540:CDS 75.0%
GGTGGCAGCGGTGGAAGCGG+TGG + tig0024129:82344-82363 Msa1414540:CDS 75.0%
GGCAGCGGTGGAAGCGGTGG+TGG + tig0024129:82347-82366 Msa1414540:CDS 75.0%
! GGCGGTGGCTGAGCCGGTGG+CGG - tig0024129:82204-82223 None:intergenic 80.0%
! GGAGGCGGTGGCTGAGCCGG+TGG - tig0024129:82207-82226 None:intergenic 80.0%
! CCGGACGGTGGCAGCGGCAG+TGG - tig0024129:82326-82345 None:intergenic 80.0%
! CTGCCGCTGCCACCGTCCGG+TGG + tig0024129:82326-82345 Msa1414540:CDS 80.0%
! CCACCGCTGCCACCGGACGG+TGG - tig0024129:82338-82357 None:intergenic 80.0%
! CCACCGTCCGGTGGCAGCGG+TGG + tig0024129:82335-82354 Msa1414540:CDS 80.0%
Chromosome Type Strat End Strand Name
tig0024129 gene 82173 82784 82173 ID=Msa1414540;Name=Msa1414540
tig0024129 mRNA 82173 82784 82173 ID=Msa1414540-mRNA-1;Parent=Msa1414540;Name=Msa1414540-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|204
tig0024129 exon 82173 82784 82173 ID=Msa1414540-mRNA-1:exon:21825;Parent=Msa1414540-mRNA-1
tig0024129 CDS 82173 82784 82173 ID=Msa1414540-mRNA-1:cds;Parent=Msa1414540-mRNA-1
Gene Sequence

>Msa1414540

ATGAGGCCGATTCAGCTTCCACCACCAACCGCCACCGGCTCAGCCACCGCCTCCGGTTCACCAAACAACAACAACAACAGCCGCCCTCAACGCCGCCGCAAAGATCATCTAACTCTACCGCTTCCACAGCGTGACACAAACCTCGCTGTACCACTGCCGCTGCCACCGTCCGGTGGCAGCGGTGGAAGCGGTGGTGGAGGAAACGGAAGCGGAAGCGGAGGAGCGAGTCAACAGCTAGTGATTCCTTTTTCCGAGCTAGAAAGATTGAACCGGATCGGAAGCGGAAGTGGAGGAACGGTTTACAAAGTAGTTCACAAAATCAACGGTCGTGCTTATGCTTTGAAGGTGATATACGGACATCACGAGGAATCAGTTCGTCGTCAGATCCATCGTGAAATCCAGATCTTGCGTGATGTTGATGATGTTAACGTGGTCAAGTGTCATGAGATGTACGATCACAACGCTGAGATTCAGGTTTTGCTTGAATACATGGACGGTGGATCTCTCGAAGGGAACATATTTCCTCAGGAAAATCACATCGCTGACGTGGCACGTCAGATCCTCCGTGGACTCGCCTATCTCCACCGTCGTCACATCGTTCATCGTGATATC
Protein sequence

>Msa1414540

MRPIQLPPPTATGSATASGSPNNNNNSRPQRRRKDHLTLPLPQRDTNLAVPLPLPPSGGSGGSGGGGNGSGSGGASQQLVIPFSELERLNRIGSGSGGTVYKVVHKINGRAYALKVIYGHHEESVRRQIHREIQILRDVDDVNVVKCHEMYDHNAEIQVLLEYMDGGSLEGNIFPQENHIADVARQILRGLAYLHRRHIVHRDI