AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG002917

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002917 MtrunA17_Chr1g0179531 99.023 512 2 1 1 509 1 512 0.0 1056
MsaG002917 MtrunA17_Chr8g0384081 50.758 264 120 3 249 505 56 316 1.62e-87 272
MsaG002917 MtrunA17_Chr2g0283871 35.644 101 59 3 130 225 23 122 1.13e-15 78.2
MsaG002917 MtrunA17_Chr4g0041151 36.275 102 58 3 130 225 31 131 1.28e-15 77.8
MsaG002917 MtrunA17_Chr1g0164461 41.346 104 51 4 118 218 27 123 1.58e-15 75.1
MsaG002917 MtrunA17_Chr6g0485241 37.255 102 61 2 128 227 128 228 2.43e-15 77.8
MsaG002917 MtrunA17_Chr3g0082261 41.346 104 51 4 118 218 27 123 1.76e-14 74.7
MsaG002917 MtrunA17_Chr5g0402321 34.000 100 60 2 130 223 22 121 1.40e-13 70.5
MsaG002917 MtrunA17_Chr4g0066271 38.000 100 58 2 130 225 117 216 3.48e-12 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002917 AT3G10030.1 56.364 550 184 7 1 506 1 538 0.0 590
MsaG002917 AT3G10030.2 55.086 521 178 7 1 477 1 509 0.0 542
MsaG002917 AT3G18680.1 53.906 256 113 2 252 505 78 330 9.97e-91 281
MsaG002917 AT3G18680.2 47.751 289 113 3 252 505 78 363 1.64e-83 263
MsaG002917 AT3G54390.1 36.441 118 65 3 124 239 32 141 3.35e-17 82.8
MsaG002917 AT3G54390.2 36.441 118 65 3 124 239 48 157 3.76e-17 82.8
MsaG002917 AT3G58630.1 30.872 149 78 3 130 253 26 174 2.71e-16 80.5
MsaG002917 AT3G58630.2 30.872 149 78 3 130 253 26 174 3.07e-16 80.1
MsaG002917 AT3G14180.1 37.607 117 66 4 109 221 63 176 5.91e-16 80.5
MsaG002917 AT3G24490.1 31.667 120 73 3 102 218 64 177 1.42e-12 69.3
MsaG002917 AT2G44730.1 38.043 92 53 2 130 217 64 155 2.44e-12 68.9

Find 135 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGGAAGAGTTGTTATATT+TGG 0.225653 1:-49256722 MsaT002917.1:CDS
TTGACAATGCTTTGGACTTC+AGG 0.272821 1:+49258232 None:intergenic
CGACATATCTGCTGCTCTTC+GGG 0.289993 1:-49256660 MsaT002917.1:CDS
ATATTTGGTGGCATTGGTTT+TGG 0.302206 1:-49256707 MsaT002917.1:CDS
CTTTCGAGCACATATCCTTC+AGG 0.327576 1:-49256424 MsaT002917.1:CDS
GAACAACTCTCCGCCATCTA+AGG 0.331588 1:+49258208 None:intergenic
GGTGGTGAGGTGCGAAGGTT+TGG 0.337687 1:+49259728 None:intergenic
TGCGAGGAAAATGCCATTCC+TGG 0.369901 1:-49256350 MsaT002917.1:intron
CCGACATATCTGCTGCTCTT+CGG 0.371066 1:-49256661 MsaT002917.1:CDS
TATTGTTGGGAATTCGCTTC+CGG 0.371702 1:-49259161 MsaT002917.1:CDS
CGAAGGTTTGGTGGAGGTGG+TGG 0.380551 1:+49259740 None:intergenic
TCAATCAACTTTAGAGAAGA+TGG 0.381962 1:-49256831 MsaT002917.1:CDS
AACCTTAGGGTCAATATTGC+AGG 0.385341 1:+49258149 None:intergenic
GTCTAGAGGTGTCACCTCTA+TGG 0.386263 1:-49256393 MsaT002917.1:CDS
TCTAAGGTTTGACAATGCTT+TGG 0.391295 1:+49258224 None:intergenic
TTTCTGCTAGTCATTGGCCT+TGG 0.394011 1:-49259201 MsaT002917.1:CDS
AGGTTTGGTGGAGGTGGTGG+TGG 0.399667 1:+49259743 None:intergenic
GGAGGTGGTGGTGGTGAGAG+TGG 0.404152 1:+49259752 None:intergenic
GTTGCATTTCTGCTAGTCAT+TGG 0.405063 1:-49259207 MsaT002917.1:CDS
GGCACACTTATTGACCAAAC+TGG 0.406605 1:-49255922 MsaT002917.1:CDS
GTTTACTTGACCTCCACTGC+TGG 0.412531 1:+49258257 None:intergenic
GTTAGCTTATTGCTCCAGTT+TGG 0.414252 1:+49255908 None:intergenic
AAGCATTGTCAAACCTTAGA+TGG 0.420124 1:-49258221 MsaT002917.1:CDS
ATTAGTGGATCGGCACTTAC+CGG 0.426477 1:-49258180 MsaT002917.1:CDS
CTTCAGGTAGCAATTGTTGT+TGG 0.428109 1:-49257843 MsaT002917.1:intron
CCACCGTTACCGCTAGAAAC+AGG 0.428189 1:+49259490 None:intergenic
AAGCAGATGGAACATATTGT+TGG 0.431908 1:-49259175 MsaT002917.1:CDS
GGTGAGGTGCGAAGGTTTGG+TGG 0.432109 1:+49259731 None:intergenic
GTGCGAAGGTTTGGTGGAGG+TGG 0.433564 1:+49259737 None:intergenic
GGAATCTAAGAGGAAGAGAT+TGG 0.434366 1:-49259354 MsaT002917.1:CDS
GGAAGAGTTGTTATATTTGG+TGG 0.436188 1:-49256719 MsaT002917.1:CDS
CTCAAAGGTACCAACGTAGA+TGG 0.437085 1:-49256482 MsaT002917.1:CDS
CGTTTGCTGAACCGTACAAT+AGG 0.437374 1:-49256769 MsaT002917.1:CDS
GTTGTTATATTTGGTGGCAT+TGG 0.439242 1:-49256713 MsaT002917.1:CDS
AGCAGATGGAACATATTGTT+GGG 0.444247 1:-49259174 MsaT002917.1:CDS
GACGGAGGTGGTGATGTGTT+TGG 0.447470 1:+49259666 None:intergenic
CTGCTCTGCAGTTAATGCTC+AGG 0.451851 1:-49256510 MsaT002917.1:intron
AGGTTGATAATTTGAAGAAA+AGG 0.452877 1:-49259261 MsaT002917.1:CDS
GATGTACTGCATACCAAGTT+GGG 0.454334 1:-49257767 MsaT002917.1:intron
ATAGAAAAGATCGAGAAGAA+TGG 0.456281 1:-49259441 MsaT002917.1:CDS
TCTATACTCTGCTCCTACTC+CGG 0.456827 1:+49259459 None:intergenic
GTCGTCGTCGGCGACGGCGG+CGG 0.456922 1:+49259642 None:intergenic
TTTATCATCATCAGCAAACT+TGG 0.459547 1:+49259138 None:intergenic
CATCTACGTTGGTACCTTTG+AGG 0.460201 1:+49256483 None:intergenic
GAGAGACATAGAATGAATAA+TGG 0.466819 1:-49259229 MsaT002917.1:CDS
TGTGATGCAACGACGTCGTA+TGG 0.469790 1:-49259535 MsaT002917.1:CDS
TCCTTTCTCAAGATGCCTGA+TGG 0.470108 1:+49256739 None:intergenic
GTCGGCGACGGCGGCGGAGA+CGG 0.470366 1:+49259648 None:intergenic
ACAATAGGCAACGGGCCATC+AGG 0.470864 1:-49256754 MsaT002917.1:CDS
TTGGCCTTGGTTTAAGCAGA+TGG 0.477301 1:-49259188 MsaT002917.1:CDS
GTTGCAATGGCTTCCCGTCT+TGG 0.480588 1:-49257957 MsaT002917.1:CDS
GTCTCCGTCGTCGTCGGCGA+CGG 0.482206 1:+49259636 None:intergenic
CAGGTAGCAATTGTTGTTGG+AGG 0.488440 1:-49257840 MsaT002917.1:CDS
GAATCTAAGAGGAAGAGATT+GGG 0.489819 1:-49259353 MsaT002917.1:CDS
TGGTGAGAGTGGTGGTGGTG+AGG 0.490505 1:+49259715 None:intergenic
ATTTCTTCTGTGGTGATGCA+TGG 0.491743 1:-49257812 MsaT002917.1:CDS
TGGAGAAGTGGTGGTGAGAG+TGG 0.496490 1:+49259704 None:intergenic
TGCTGCTCTTCGGGCTTCAG+AGG 0.502112 1:-49256651 MsaT002917.1:CDS
TTGGGAAGAAGTAGCTTCAA+TGG 0.503405 1:-49259335 MsaT002917.1:CDS
GATGCATGGGTAACTGCAAC+AGG 0.506168 1:-49257798 MsaT002917.1:CDS
TTTCGAGCACATATCCTTCA+GGG 0.508101 1:-49256423 MsaT002917.1:CDS
GACGGCGGCGGAGACGGAGG+TGG 0.510775 1:+49259654 None:intergenic
TAAAGTTGATTGAAGCAGTA+AGG 0.510796 1:+49256841 None:intergenic
TCTTAAATTTGTCAGCATGA+TGG 0.513943 1:-49256879 MsaT002917.1:intron
ATAGTATTGCTTACCAGGAA+TGG 0.515872 1:+49256337 None:intergenic
GTGATTAATCTTACCCAACT+TGG 0.518834 1:+49257754 None:intergenic
GCCATCAGGCATCTTGAGAA+AGG 0.521422 1:-49256740 MsaT002917.1:CDS
GGTGGTGGTGGTGAGAGTGG+TGG 0.521909 1:+49259755 None:intergenic
CTGTACCTCCACACCAAGAC+GGG 0.522588 1:+49257944 None:intergenic
ATGGCCCGTTGCCTATTGTA+CGG 0.527865 1:+49256758 None:intergenic
GGCTTCCCGTCTTGGTGTGG+AGG 0.530692 1:-49257949 MsaT002917.1:intron
TCCGTCGTCGTCGGCGACGG+CGG 0.535708 1:+49259639 None:intergenic
AGATGTACTGCATACCAAGT+TGG 0.537226 1:-49257768 MsaT002917.1:CDS
AACATTTCAAAAGCTTTGTG+TGG 0.537883 1:-49255955 MsaT002917.1:CDS
TCATCATCAGCAAACTTGGC+CGG 0.538573 1:+49259142 None:intergenic
AATATTGCAGGTATCGGATC+CGG 0.539941 1:+49258161 None:intergenic
TACCTGCAATATTGACCCTA+AGG 0.540236 1:-49258151 MsaT002917.1:intron
CTACCAGCGTCATCGTCGAA+TGG 0.542605 1:+49259592 None:intergenic
CAATCAACTTTAGAGAAGAT+GGG 0.544338 1:-49256830 MsaT002917.1:CDS
TGCCTAGGTGAAATTGAAGC+AGG 0.547449 1:+49259106 None:intergenic
AGTGGTGGTGAGAGTGGTGG+TGG 0.547464 1:+49259710 None:intergenic
AGGGTCAATATTGCAGGTAT+CGG 0.548147 1:+49258155 None:intergenic
TTTCTTCTGTGGTGATGCAT+GGG 0.549335 1:-49257811 MsaT002917.1:CDS
AAACCTGTTTCTAGCGGTAA+CGG 0.550390 1:-49259493 MsaT002917.1:CDS
AGGTGGTGATGTGTTTGGAT+TGG 0.554894 1:+49259671 None:intergenic
GTTTCTAGCGGTAACGGTGG+AGG 0.556622 1:-49259487 MsaT002917.1:CDS
TTTCACCTAGGCAATCTAAG+AGG 0.557596 1:-49259096 MsaT002917.1:intron
CTGAATCGAGGGAATCTAAG+AGG 0.560567 1:-49259364 MsaT002917.1:CDS
AGAAGTGGTGGTGAGAGTGG+TGG 0.560608 1:+49259707 None:intergenic
GTGGTGGTGGTGAGGTGCGA+AGG 0.560743 1:+49259723 None:intergenic
TGAACCGTACAATAGGCAAC+GGG 0.562366 1:-49256762 MsaT002917.1:CDS
GATATGTCGGTTGAGAAAAG+TGG 0.562539 1:+49256674 None:intergenic
GGCGACGGCGGCGGAGACGG+AGG 0.562987 1:+49259651 None:intergenic
AGTTTCAAATGAAGTTGCAA+TGG 0.565412 1:-49257970 MsaT002917.1:CDS
AATGCTCAGGCTGTCCTCAA+AGG 0.568956 1:-49256497 MsaT002917.1:CDS
GCTGCTCTTCGGGCTTCAGA+GGG 0.570088 1:-49256650 MsaT002917.1:intron
CGTATGGATTCAACAACAAA+CGG 0.572327 1:-49259519 MsaT002917.1:CDS
ACAAACTTCAGTTTCAATGC+AGG 0.580585 1:-49256792 MsaT002917.1:CDS
GGTGGAGGAAGCGCCGGAGT+AGG 0.580586 1:-49259472 MsaT002917.1:CDS
GGTGTCGTCTCCGTCGTCGT+CGG 0.581790 1:+49259630 None:intergenic
AACTTCATTTGAAACTAACA+TGG 0.586306 1:+49257977 None:intergenic
GTCATATACGCCATCTACGT+TGG 0.587713 1:+49256472 None:intergenic
GGAGGTCGTAATTTCTTCTG+TGG 0.589587 1:-49257822 MsaT002917.1:CDS
TTAAACCTCTTAGATTGCCT+AGG 0.591137 1:+49259091 None:intergenic
GCCGCCGTCGCCGACGACGA+CGG 0.592641 1:-49259640 MsaT002917.1:CDS
GTGGCTACGTCCAGCAGTGG+AGG 0.596879 1:-49258267 MsaT002917.1:CDS
AATCCATTCGACGATGACGC+TGG 0.603457 1:-49259595 MsaT002917.1:CDS
GGTAACGGTGGAGGAAGCGC+CGG 0.603519 1:-49259478 MsaT002917.1:CDS
GAGGTGCGAAGGTTTGGTGG+AGG 0.605729 1:+49259734 None:intergenic
TTCAGGGAGCTAGTGTCTAG+AGG 0.610453 1:-49256407 MsaT002917.1:CDS
CAGGGCTGACATATCCATAG+AGG 0.610631 1:+49256379 None:intergenic
CTGAACCGTACAATAGGCAA+CGG 0.610750 1:-49256763 MsaT002917.1:CDS
TGAGAATCAATCGAAGAGTG+TGG 0.613705 1:-49259299 MsaT002917.1:CDS
TGTTCCATCTGCTTAAACCA+AGG 0.614998 1:+49259184 None:intergenic
GGAGACGACACCGATGACTA+CGG 0.620045 1:-49259619 MsaT002917.1:CDS
GGAGTGGCTACGTCCAGCAG+TGG 0.623352 1:-49258270 MsaT002917.1:CDS
GAATGGATTACCGTAGTCAT+CGG 0.625254 1:+49259609 None:intergenic
AATTTACTCAGCTGAATCGA+GGG 0.625957 1:-49259375 MsaT002917.1:CDS
AAATTTACTCAGCTGAATCG+AGG 0.626415 1:-49259376 MsaT002917.1:CDS
CCGAAGAGCAGCAGATATGT+CGG 0.627184 1:+49256661 None:intergenic
GGACTGAAGCTGTGGAGAAG+TGG 0.627526 1:+49259692 None:intergenic
TCTAGACACTAGCTCCCTGA+AGG 0.629448 1:+49256409 None:intergenic
ACTGTACCTCCACACCAAGA+CGG 0.637094 1:+49257943 None:intergenic
TTTGGATTGGACTGAAGCTG+TGG 0.637149 1:+49259684 None:intergenic
CCTGTTTCTAGCGGTAACGG+TGG 0.645172 1:-49259490 MsaT002917.1:CDS
GCTTTGTGTGGAGAACAAGT+TGG 0.647871 1:-49255943 MsaT002917.1:CDS
AATGGCTTCCCGTCTTGGTG+TGG 0.649204 1:-49257952 MsaT002917.1:CDS
CTGAAGCTGTGGAGAAGTGG+TGG 0.656134 1:+49259695 None:intergenic
TTCCTGCTTCAATTTCACCT+AGG 0.664237 1:-49259108 MsaT002917.1:CDS
CGGTCAAAACCTGTTTCTAG+CGG 0.664935 1:-49259499 MsaT002917.1:CDS
GGTGGTTGTTATCGTCGTGG+AGG 0.671957 1:+49259773 None:intergenic
CATTGTCAAACCTTAGATGG+CGG 0.680970 1:-49258218 MsaT002917.1:CDS
TGTGGAACAGTGTAAGAACA+AGG 0.689866 1:-49259281 MsaT002917.1:CDS
AGTGGTGGTTGTTATCGTCG+TGG 0.691782 1:+49259770 None:intergenic
GTCAGCCCTGACATTCTGCG+AGG 0.718203 1:-49256366 MsaT002917.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 49255909 49259830 49255909 ID=MsaG002917
Chr1 mRNA 49255909 49259830 49255909 ID=MsaT002917.1;Parent=MsaG002917
Chr1 exon 49255909 49256006 49255909 ID=MsaT002917.1.exon7;Parent=MsaT002917.1
Chr1 CDS 49255909 49256006 49255909 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49256351 49256521 49256351 ID=MsaT002917.1.exon6;Parent=MsaT002917.1
Chr1 CDS 49256351 49256521 49256351 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49256651 49256886 49256651 ID=MsaT002917.1.exon5;Parent=MsaT002917.1
Chr1 CDS 49256651 49256886 49256651 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49257768 49257859 49257768 ID=MsaT002917.1.exon4;Parent=MsaT002917.1
Chr1 CDS 49257768 49257859 49257768 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49257950 49258003 49257950 ID=MsaT002917.1.exon3;Parent=MsaT002917.1
Chr1 CDS 49257950 49258003 49257950 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49258152 49258296 49258152 ID=MsaT002917.1.exon2;Parent=MsaT002917.1
Chr1 CDS 49258152 49258296 49258152 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Chr1 exon 49259097 49259830 49259097 ID=MsaT002917.1.exon1;Parent=MsaT002917.1
Chr1 CDS 49259097 49259830 49259097 ID=cds.MsaT002917.1;Parent=MsaT002917.1
Gene Sequence

>MsaT002917.1

ATGGCTTCTTGCGACGACGACGACGATTTCTCTCTCCTCCACGACGATAACAACCACCACTCTCACCACCACCACCTCCACCAAACCTTCGCACCTCACCACCACCACTCTCACCACCACTTCTCCACAGCTTCAGTCCAATCCAAACACATCACCACCTCCGTCTCCGCCGCCGTCGCCGACGACGACGGAGACGACACCGATGACTACGGTAATCCATTCGACGATGACGCTGGTAGCGAGAAACGTAAAGATCGAGATCGCGATGAGATCTGTGATGCAACGACGTCGTATGGATTCAACAACAAACGGTCAAAACCTGTTTCTAGCGGTAACGGTGGAGGAAGCGCCGGAGTAGGAGCAGAGTATAGAAAAGATCGAGAAGAATGGAGTGATACAGCGATAGTGTGTTTACTCGAAGCTTATACAGAGAAATTTACTCAGCTGAATCGAGGGAATCTAAGAGGAAGAGATTGGGAAGAAGTAGCTTCAATGGTGAGTGAAAGATGTGAGAATCAATCGAAGAGTGTGGAACAGTGTAAGAACAAGGTTGATAATTTGAAGAAAAGGTATAAGCTAGAGAGACATAGAATGAATAATGGTTGCATTTCTGCTAGTCATTGGCCTTGGTTTAAGCAGATGGAACATATTGTTGGGAATTCGCTTCCGGCCAAGTTTGCTGATGATGATAAAGCTATTGTTCCTGCTTCAATTTCACCTAGGCAATCTAAGAGATATGGAGTGGCTACGTCCAGCAGTGGAGGTCAAGTAAACAGCCTGAAGTCCAAAGCATTGTCAAACCTTAGATGGCGGAGAGTTGTTCTAAAAATTAGTGGATCGGCACTTACCGGATCCGATACCTGCAATATTGACCCTAAGGTCGCCATGTTAGTTTCAAATGAAGTTGCAATGGCTTCCCGTCTTGGTGTGGAGGTAGCAATTGTTGTTGGAGGTCGTAATTTCTTCTGTGGTGATGCATGGGTAACTGCAACAGGTTTAGAAAGATGTACTGCATACCAAGTTGGCATGATGGCAACTGTGATGAACTCCTTACTGCTTCAATCAACTTTAGAGAAGATGGGTGTTCAGACTCGTGTACAAACTTCAGTTTCAATGCAGGCGTTTGCTGAACCGTACAATAGGCAACGGGCCATCAGGCATCTTGAGAAAGGAAGAGTTGTTATATTTGGTGGCATTGGTTTTGGTGCTGGTAATCCACTTTTCTCAACCGACATATCTGCTGCTCTTCGGGCTTCAGAGGTTAATGCTCAGGCTGTCCTCAAAGGTACCAACGTAGATGGCGTATATGACTGCAACTCACGAGACAACAATTTCACTTTCGAGCACATATCCTTCAGGGAGCTAGTGTCTAGAGGTGTCACCTCTATGGATATGTCAGCCCTGACATTCTGCGAGGAAAATGCCATTCCTGTTGTAGTTTTTAATCTATTGGCACCCGGGAACATTTCAAAAGCTTTGTGTGGAGAACAAGTTGGCACACTTATTGACCAAACTGGAGCAATAAGCTAA
Protein sequence

>MsaT002917.1

MASCDDDDDFSLLHDDNNHHSHHHHLHQTFAPHHHHSHHHFSTASVQSKHITTSVSAAVADDDGDDTDDYGNPFDDDAGSEKRKDRDRDEICDATTSYGFNNKRSKPVSSGNGGGSAGVGAEYRKDREEWSDTAIVCLLEAYTEKFTQLNRGNLRGRDWEEVASMVSERCENQSKSVEQCKNKVDNLKKRYKLERHRMNNGCISASHWPWFKQMEHIVGNSLPAKFADDDKAIVPASISPRQSKRYGVATSSSGGQVNSLKSKALSNLRWRRVVLKISGSALTGSDTCNIDPKVAMLVSNEVAMASRLGVEVAIVVGGRNFFCGDAWVTATGLERCTAYQVGMMATVMNSLLLQSTLEKMGVQTRVQTSVSMQAFAEPYNRQRAIRHLEKGRVVIFGGIGFGAGNPLFSTDISAALRASEVNAQAVLKGTNVDGVYDCNSRDNNFTFEHISFRELVSRGVTSMDMSALTFCEENAIPVVVFNLLAPGNISKALCGEQVGTLIDQTGAIS*