AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003879

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003879 MtrunA17_Chr1g0190851 95.616 479 15 4 1 478 84 557 0.0 929
MsaG003879 MtrunA17_Chr7g0273941 46.712 441 153 16 3 428 106 479 1.23e-105 323
MsaG003879 MtrunA17_Chr1g0201941 35.374 294 159 7 146 426 266 541 1.08e-47 174
MsaG003879 MtrunA17_Chr1g0201941 40.000 100 57 2 326 425 46 142 2.27e-16 82.0
MsaG003879 MtrunA17_Chr1g0201941 44.706 85 42 1 21 100 58 142 7.32e-15 77.0
MsaG003879 MtrunA17_Chr2g0290511 34.043 282 154 6 174 449 117 372 2.28e-37 140
MsaG003879 MtrunA17_Chr1g0201911 34.363 259 136 4 171 428 236 461 3.37e-35 138
MsaG003879 MtrunA17_Chr1g0201911 40.217 92 52 2 337 428 55 143 2.63e-14 75.1
MsaG003879 MtrunA17_Chr1g0201911 44.706 85 42 1 21 100 56 140 2.90e-14 75.1
MsaG003879 MtrunA17_Chr6g0463941 59.783 92 35 1 337 428 464 553 7.91e-28 117
MsaG003879 MtrunA17_Chr6g0463941 40.860 93 52 2 335 427 53 142 1.22e-15 79.7
MsaG003879 MtrunA17_Chr6g0463941 41.176 85 45 1 21 100 56 140 1.24e-13 73.2
MsaG003879 MtrunA17_Chr7g0265831 28.358 268 161 7 21 262 116 378 3.21e-20 93.2
MsaG003879 MtrunA17_Chr7g0265831 39.785 93 52 3 337 428 115 204 7.63e-13 70.5
MsaG003879 MtrunA17_Chr1g0179191 29.707 239 149 7 21 244 132 366 6.11e-19 89.4
MsaG003879 MtrunA17_Chr1g0179191 39.785 93 52 3 337 428 131 220 8.44e-13 70.5
MsaG003879 MtrunA17_Chr1g0198171 36.090 133 72 4 300 422 68 197 2.05e-15 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003879 AT5G28300.1 42.617 535 200 17 20 473 102 610 1.55e-102 319
MsaG003879 AT1G76890.2 38.806 268 130 4 162 428 252 486 2.44e-47 172
MsaG003879 AT1G76890.2 46.591 88 44 2 335 422 39 123 1.65e-16 82.8
MsaG003879 AT1G76890.2 46.988 83 39 1 21 98 42 124 1.96e-14 76.3
MsaG003879 AT1G76880.1 58.696 92 36 1 337 428 408 497 2.56e-28 118
MsaG003879 AT1G76880.1 39.048 105 61 2 335 439 59 160 2.92e-15 79.0
MsaG003879 AT1G76880.1 45.882 85 41 1 21 100 62 146 4.39e-13 72.0
MsaG003879 AT1G33240.3 51.786 112 43 2 337 439 435 544 8.84e-27 114
MsaG003879 AT1G33240.3 43.820 89 47 2 337 425 62 147 3.29e-17 84.7
MsaG003879 AT1G33240.3 47.059 85 40 1 21 100 63 147 7.13e-17 84.0
MsaG003879 AT1G33240.1 51.786 112 43 2 337 439 435 544 9.92e-27 114
MsaG003879 AT1G33240.1 43.820 89 47 2 337 425 62 147 3.43e-17 85.1
MsaG003879 AT1G33240.1 47.059 85 40 1 21 100 63 147 9.18e-17 83.6
MsaG003879 AT1G33240.2 51.786 112 43 2 337 439 396 505 1.10e-26 114
MsaG003879 AT5G47660.1 33.582 268 130 12 159 426 169 388 7.98e-20 91.7
MsaG003879 AT3G10000.1 27.841 176 113 5 257 430 17 180 1.14e-14 76.6
MsaG003879 AT5G03680.1 42.857 91 48 3 337 426 119 206 1.01e-13 73.9
MsaG003879 AT3G10000.2 25.714 175 108 5 257 430 17 170 8.65e-12 67.4

Find 90 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATAGATTTGAAGTGTTTA+AGG 0.195477 1:-63236971 MsaT003879.1:CDS
GTCTTTGATCTCTTTCAATT+TGG 0.216907 1:+63237873 None:intergenic
ATAAGGCTATATGAAGAAAT+AGG 0.236435 1:+63236511 None:intergenic
CTCTCTCGCTGCTCGATATA+AGG 0.299308 1:+63236494 None:intergenic
TCCTTCTTCTTCTACTACTT+TGG 0.306363 1:-63236557 MsaT003879.1:CDS
AATGCCAACACTTCATCTTT+TGG 0.317647 1:+63236451 None:intergenic
AATCATAATCAAAATAGTTT+TGG 0.326250 1:-63237225 MsaT003879.1:CDS
TTTCAAGAGTTTCCGGATTA+GGG 0.337138 1:+63236620 None:intergenic
TCACAAGGAATGTTGGAGTT+AGG 0.345818 1:-63236349 MsaT003879.1:CDS
GAGCTAGGGTTTACCGGTAT+TGG 0.348770 1:+63236586 None:intergenic
ACATGTTCCCAAGTGAAATC+TGG 0.352061 1:+63237764 None:intergenic
GAACGAGGTGCAAGACAAAA+TGG 0.355649 1:-63237112 MsaT003879.1:CDS
GAACAAAGAGCTTGAGTTGA+TGG 0.361917 1:-63236809 MsaT003879.1:CDS
GATAGATTTGAAGTGTTTAA+GGG 0.370463 1:-63236970 MsaT003879.1:CDS
AGCAGCGAGAGAGACGATAT+TGG 0.377007 1:-63236484 MsaT003879.1:CDS
GAAGAAGGAAGGGTTGAGCT+AGG 0.386310 1:+63236571 None:intergenic
CAACAACAAGGCACCACTTT+GGG 0.393210 1:-63236380 MsaT003879.1:CDS
TTCTTCTTCTACTACTTTGG+TGG 0.410965 1:-63236554 MsaT003879.1:CDS
AGGGTTGAGCTAGGGTTTAC+CGG 0.424547 1:+63236580 None:intergenic
AGTTTAGTAGAGAAGAAGCT+TGG 0.425700 1:-63236855 MsaT003879.1:CDS
TTGAGCAATCTTTATAATCA+AGG 0.426028 1:-63236202 MsaT003879.1:CDS
GAGAAGAAGAGGAAAAGATC+AGG 0.430204 1:-63236997 MsaT003879.1:CDS
TAAGGCTATATGAAGAAATA+GGG 0.437015 1:+63236512 None:intergenic
GAGAATTTCACAAGGAATGT+TGG 0.441400 1:-63236356 MsaT003879.1:CDS
TTCCTCAACTCATTGATCCT+TGG 0.453786 1:-63237844 MsaT003879.1:CDS
CAACAACAACAATGAAGAAA+AGG 0.456418 1:-63236413 MsaT003879.1:CDS
CACCTGCACCAGCACCATCT+TGG 0.460031 1:+63236083 None:intergenic
AAATCTAGTTGAGGCTGAAA+AGG 0.460400 1:-63237136 MsaT003879.1:CDS
AAGAAGGAAGGGTTGAGCTA+GGG 0.460441 1:+63236572 None:intergenic
TTGCTCAATAGATGAAAGTA+AGG 0.463276 1:+63236217 None:intergenic
GAGGTTTATCAAGGTGGTGG+GGG 0.479843 1:-63237171 MsaT003879.1:CDS
CTCAAGTGGGGCCTCCAAGC+TGG 0.484767 1:-63236054 MsaT003879.1:CDS
TTCAAGAATGGATGATGTAT+TGG 0.485834 1:-63237070 MsaT003879.1:CDS
CAAAGGATGCTAATAGGAAA+AGG 0.488346 1:-63236261 MsaT003879.1:CDS
GCAACAACAAGGCACCACTT+TGG 0.490808 1:-63236381 MsaT003879.1:CDS
GTCAAAGAAAAGTGAAGAAG+AGG 0.493141 1:-63237046 MsaT003879.1:CDS
TGAAGATGACATTGAAGCTA+AGG 0.499602 1:+63236702 None:intergenic
GAAGAAGAGGTAGTTGAGAA+AGG 0.502624 1:-63237033 MsaT003879.1:CDS
GCACATGAACAAGCTATTGC+TGG 0.507249 1:-63236787 MsaT003879.1:CDS
CATGTTCCCAAGTGAAATCT+GGG 0.514235 1:+63237765 None:intergenic
GCAGGTGAGTCTTCTCAAGT+GGG 0.514949 1:-63236067 MsaT003879.1:CDS
GTTGGTTCCCAGATTTCACT+TGG 0.516402 1:-63237772 MsaT003879.1:CDS
GCACTCACAAAACCCTAATC+CGG 0.519084 1:-63236632 MsaT003879.1:CDS
GAAGAGGTTTATCAAGGTGG+TGG 0.520513 1:-63237174 MsaT003879.1:CDS
AACCAAGATGGTGCTGGTGC+AGG 0.525566 1:-63236085 MsaT003879.1:CDS
GTTTGTTACTGAGCTGGAAG+AGG 0.529219 1:-63237190 MsaT003879.1:CDS
TGCAGGTGAGTCTTCTCAAG+TGG 0.532154 1:-63236068 MsaT003879.1:CDS
AAGTAGTAGAAGAAGAAGGA+AGG 0.534716 1:+63236560 None:intergenic
GAGACGATATTGGTAGAAGA+TGG 0.544390 1:-63236474 MsaT003879.1:CDS
TGGGAACCAACTCTCCATGC+TGG 0.546340 1:+63237784 None:intergenic
CAAAGAGGTGCAAAGAGAAG+TGG 0.549838 1:-63236312 MsaT003879.1:CDS
TGTAGAGGAGGATTCAAGAA+TGG 0.554166 1:-63237082 MsaT003879.1:CDS
AGAGGTTTATCAAGGTGGTG+GGG 0.556530 1:-63237172 MsaT003879.1:CDS
TAGTGAAATTACCAGCTTGG+AGG 0.560803 1:+63236043 None:intergenic
CACAGGAAGCTAGCTGAGGT+TGG 0.561113 1:-63237321 MsaT003879.1:intron
TCAGATCCAGCATGGAGAGT+TGG 0.563903 1:-63237790 MsaT003879.1:CDS
CTACAAATGATGAGAAGAAG+AGG 0.565637 1:-63237008 MsaT003879.1:CDS
ACCAAAGTAGTAGAAGAAGA+AGG 0.573800 1:+63236556 None:intergenic
ATGGCCAAAAGATGAAGTGT+TGG 0.578682 1:-63236455 MsaT003879.1:CDS
AAGAGGTTTATCAAGGTGGT+GGG 0.581021 1:-63237173 MsaT003879.1:CDS
CTTGAATCCTCCTCTACATG+AGG 0.583768 1:+63237087 None:intergenic
AAAGAGGTGCAAAGAGAAGT+GGG 0.586402 1:-63236311 MsaT003879.1:CDS
GAGCTGGAAGAGGTTTATCA+AGG 0.586678 1:-63237180 MsaT003879.1:CDS
ATATAGTGAAATTACCAGCT+TGG 0.588322 1:+63236040 None:intergenic
AGTAGTAGAAGAAGAAGGAA+GGG 0.592188 1:+63236561 None:intergenic
GAGTGTGGTGAAGAAAATGA+TGG 0.595280 1:-63236938 MsaT003879.1:CDS
GTCCAAGGATCAATGAGTTG+AGG 0.597929 1:+63237842 None:intergenic
GAAATAGGGTTGTTCTTGCG+AGG 0.598239 1:+63236526 None:intergenic
TGTGAAATTCTCTCCCAAAG+TGG 0.599247 1:+63236367 None:intergenic
AGCTTGGAAGAAACAAGAGA+TGG 0.599559 1:-63236839 MsaT003879.1:CDS
TTTGAAGATCAGATCCAGCA+TGG 0.607084 1:-63237798 MsaT003879.1:CDS
CTTTGGGAGAGAATTTCACA+AGG 0.610777 1:-63236364 MsaT003879.1:CDS
CAAAATGGACCCTCATGTAG+AGG 0.618548 1:-63237097 MsaT003879.1:CDS
GATGAAAACCAAGATGGTGC+TGG 0.618902 1:-63236091 MsaT003879.1:CDS
TCACTTGGGAACATGTCTCA+AGG 0.620742 1:-63237757 MsaT003879.1:intron
AACAACAATGAAGAAAAGGA+AGG 0.621045 1:-63236409 MsaT003879.1:CDS
AGAACTTCATCATTAGTCCA+AGG 0.625382 1:+63237827 None:intergenic
AGAAAGCAATAACGTGAATG+TGG 0.625602 1:-63236149 MsaT003879.1:CDS
CAGGTGAGTCTTCTCAAGTG+GGG 0.628435 1:-63236066 MsaT003879.1:CDS
TTGAATCCTCCTCTACATGA+GGG 0.632417 1:+63237088 None:intergenic
TTGGTTCCCAGATTTCACTT+GGG 0.635745 1:-63237771 MsaT003879.1:CDS
ACACAAGATGAAAACCAAGA+TGG 0.647031 1:-63236097 MsaT003879.1:CDS
AATGGACCCTCATGTAGAGG+AGG 0.651973 1:-63237094 MsaT003879.1:CDS
CTGGAAGAGGTTTATCAAGG+TGG 0.657958 1:-63237177 MsaT003879.1:CDS
TGAGGCTGAAAAGGCGAACG+AGG 0.666720 1:-63237127 MsaT003879.1:CDS
TGTTGGCATTGATAAACTTG+AGG 0.669533 1:-63236438 MsaT003879.1:CDS
GATACAAGAGAAGTGCAAAG+AGG 0.678975 1:-63236327 MsaT003879.1:CDS
GGAAGGAAATAGCAACAACA+AGG 0.682423 1:-63236392 MsaT003879.1:CDS
GAATGTGGCTGAAGAAAATG+TGG 0.683811 1:-63236134 MsaT003879.1:CDS
TGTGCACAGGAAGCTAGCTG+AGG 0.710431 1:-63237325 MsaT003879.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 63236051 63237906 63236051 ID=MsaG003879
Chr1 mRNA 63236051 63237906 63236051 ID=MsaT003879.1;Parent=MsaG003879
Chr1 exon 63236051 63237338 63236051 ID=MsaT003879.1.exon2;Parent=MsaT003879.1
Chr1 CDS 63236051 63237338 63236051 ID=cds.MsaT003879.1;Parent=MsaT003879.1
Chr1 exon 63237758 63237906 63237758 ID=MsaT003879.1.exon1;Parent=MsaT003879.1
Chr1 CDS 63237758 63237906 63237758 ID=cds.MsaT003879.1;Parent=MsaT003879.1
Gene Sequence

>MsaT003879.1

ATGAACAACTTCCAAATTGAAAGAGATCAAAGACAAATACTTCCTCAACTCATTGATCCTTGGACTAATGATGAAGTTCTTGCACTTTTGAAGATCAGATCCAGCATGGAGAGTTGGTTCCCAGATTTCACTTGGGAACATGTCTCAAGGAAGCTAGCTGAGGTTGGTTATAAACGTAGTGCTGAAAAATGCAAGGAAAAATTTGAAGAAGAAAGCAGATTCTTCAACAACATTAATAATAATCATAATCAAAATAGTTTTGGTAAGAATTTTAGGTTTGTTACTGAGCTGGAAGAGGTTTATCAAGGTGGTGGGGGTGAGAATAACAAAAATCTAGTTGAGGCTGAAAAGGCGAACGAGGTGCAAGACAAAATGGACCCTCATGTAGAGGAGGATTCAAGAATGGATGATGTATTGGTGTCAAAGAAAAGTGAAGAAGAGGTAGTTGAGAAAGGTACTACAAATGATGAGAAGAAGAGGAAAAGATCAGGTGATGATAGATTTGAAGTGTTTAAGGGTTTTTGTGAGAGTGTGGTGAAGAAAATGATGGATCAACAAGAAGAAATGCACAACAAGCTTATTGAAGATATGATTAAAAGAGATGAAGAGAAGTTTAGTAGAGAAGAAGCTTGGAAGAAACAAGAGATGGAGAAAATGAACAAAGAGCTTGAGTTGATGGCACATGAACAAGCTATTGCTGGTGATAGACAATCACGTATAATTCAATTCTTGAACAAATTCTCAACAAGTGCTAATTCTTCTTCCTTAGCTTCAATGTCATCTTCACTTCAAGCTTATTTAGCAACATTAACTTCAAACTCTTCTTCTACATTGCACTCACAAAACCCTAATCCGGAAACTCTTGAAAAAACTCTTCAACCAATACCGGTAAACCCTAGCTCAACCCTTCCTTCTTCTTCTACTACTTTGGTGGCTCAGCCTCGCAAGAACAACCCTATTTCTTCATATAGCCTTATATCGAGCAGCGAGAGAGACGATATTGGTAGAAGATGGCCAAAAGATGAAGTGTTGGCATTGATAAACTTGAGGTGCAACAACAACAATGAAGAAAAGGAAGGAAATAGCAACAACAAGGCACCACTTTGGGAGAGAATTTCACAAGGAATGTTGGAGTTAGGATACAAGAGAAGTGCAAAGAGGTGCAAAGAGAAGTGGGAGAATATAAACAAGTACTTCAGAAAAACAAAGGATGCTAATAGGAAAAGGTCACTTGATTCAAGAACTTGTCCTTACTTTCATCTATTGAGCAATCTTTATAATCAAGGTAAGCTTGTTCTTCAATCTGATCAAAAGCAAGAAAGCAATAACGTGAATGTGGCTGAAGAAAATGTGGTTCAAGAGAAAGCAACACAAGATGAAAACCAAGATGGTGCTGGTGCAGGTGAGTCTTCTCAAGTGGGGCCTCCAAGCTGGTAA
Protein sequence

>MsaT003879.1

MNNFQIERDQRQILPQLIDPWTNDEVLALLKIRSSMESWFPDFTWEHVSRKLAEVGYKRSAEKCKEKFEEESRFFNNINNNHNQNSFGKNFRFVTELEEVYQGGGGENNKNLVEAEKANEVQDKMDPHVEEDSRMDDVLVSKKSEEEVVEKGTTNDEKKRKRSGDDRFEVFKGFCESVVKKMMDQQEEMHNKLIEDMIKRDEEKFSREEAWKKQEMEKMNKELELMAHEQAIAGDRQSRIIQFLNKFSTSANSSSLASMSSSLQAYLATLTSNSSSTLHSQNPNPETLEKTLQPIPVNPSSTLPSSSTTLVAQPRKNNPISSYSLISSSERDDIGRRWPKDEVLALINLRCNNNNEEKEGNSNNKAPLWERISQGMLELGYKRSAKRCKEKWENINKYFRKTKDANRKRSLDSRTCPYFHLLSNLYNQGKLVLQSDQKQESNNVNVAEENVVQEKATQDENQDGAGAGESSQVGPPSW*