AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003894


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003894 MtrunA17_Chr1g0191021 89.362 376 34 2 1 376 1 370 0.0 605
MsaG003894 MtrunA17_Chr7g0273821 42.222 405 151 14 49 381 45 438 1.54e-85 267
MsaG003894 MtrunA17_Chr1g0191011 37.584 298 132 10 88 378 123 373 6.22e-48 167
MsaG003894 MtrunA17_Chr3g0113131 37.037 135 75 3 97 231 153 277 4.69e-16 79.0
MsaG003894 MtrunA17_Chr2g0280431 34.615 104 58 3 92 195 199 292 3.23e-11 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003894 AT5G28040.2 41.053 380 172 14 43 382 60 427 1.47e-69 225
MsaG003894 AT5G28040.1 41.053 380 172 14 43 382 60 427 1.47e-69 225
MsaG003894 AT3G04930.1 39.211 431 181 17 20 377 29 451 3.93e-59 199
MsaG003894 AT3G04930.2 38.841 345 146 15 20 307 29 365 2.75e-42 153
MsaG003894 AT4G00390.1 39.103 156 78 4 50 204 115 254 2.94e-22 97.4
MsaG003894 AT1G61730.1 37.342 158 89 3 38 194 100 248 7.21e-22 96.7
MsaG003894 AT4G25210.1 36.196 163 69 5 65 194 81 241 1.94e-20 92.4
MsaG003894 AT4G01260.1 38.994 159 70 7 61 194 51 207 5.54e-19 87.4
MsaG003894 AT4G00610.1 30.986 142 89 2 56 197 108 240 3.51e-17 82.4
MsaG003894 AT1G44810.1 38.889 108 60 2 92 199 117 218 2.12e-16 79.7
MsaG003894 AT5G14280.1 39.130 92 56 0 99 190 63 154 6.57e-15 75.1
MsaG003894 AT1G11510.2 33.544 158 78 2 97 254 109 239 7.65e-15 75.5
MsaG003894 AT1G11510.1 32.911 158 79 2 97 254 138 268 8.74e-15 75.5
MsaG003894 AT2G25650.1 36.458 96 61 0 96 191 64 159 1.86e-14 74.7
MsaG003894 AT4G00238.1 32.558 129 79 2 98 224 141 263 2.74e-14 73.9
MsaG003894 AT4G00250.1 37.037 108 62 1 98 205 116 217 3.43e-14 73.2
MsaG003894 AT2G01370.1 34.513 113 69 3 90 200 72 181 8.41e-14 71.2
MsaG003894 AT4G00270.1 35.417 96 62 0 96 191 63 158 1.77e-13 70.9
MsaG003894 AT1G66420.1 32.192 146 83 4 97 233 87 225 1.54e-11 65.1
MsaG003894 AT2G36340.1 30.108 93 65 0 101 193 63 155 6.15e-11 64.3

Find 114 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAATTAAATGAGAAGAATT+AGG 0.126474 1:-63365985 None:intergenic
TTGAAATTTCTCACAAAATC+TGG 0.161108 1:+63365884 MsaT003894.1:CDS
CCTTACCAGAATCAAATTTC+TGG 0.175110 1:-63365825 None:intergenic
TAGGGTTAGGGTTAGGGTTT+GGG 0.208114 1:-63365966 None:intergenic
TCTTCCATTGGCTCCCGTTT+TGG 0.265008 1:-63365577 None:intergenic
AAGAATTAGGGTTAGGGTTA+GGG 0.289966 1:-63365972 None:intergenic
GAAGAATTAGGGTTAGGGTT+AGG 0.292949 1:-63365973 None:intergenic
TTCATCCACATTGCTGCTAT+TGG 0.293962 1:-63366109 None:intergenic
ACCATGAGTGGGAGTCCTTT+TGG 0.299111 1:+63366249 MsaT003894.1:CDS
CTTATCAACAAGCTGGTTCT+TGG 0.314691 1:-63365767 None:intergenic
CAATTAAATGAGAAGAATTA+GGG 0.319988 1:-63365984 None:intergenic
CAATGAATACTGTGCCATTT+GGG 0.343845 1:+63366307 MsaT003894.1:CDS
AAATGAGAAGAATTAGGGTT+AGG 0.345124 1:-63365979 None:intergenic
GCTCTCCAGAAATTTGATTC+TGG 0.345969 1:+63365820 MsaT003894.1:CDS
TTAGGGTTAGGGTTAGGGTT+TGG 0.348108 1:-63365967 None:intergenic
TCAATGAATACTGTGCCATT+TGG 0.350621 1:+63366306 MsaT003894.1:CDS
ATTGCTGCTATTGGTATTAC+CGG 0.365150 1:-63366100 None:intergenic
TGAAATTTCTCACAAAATCT+GGG 0.377801 1:+63365885 MsaT003894.1:CDS
GCTGGAGCTGGAGCCGGAGC+TGG 0.383081 1:+63366471 MsaT003894.1:CDS
TCGTCTTATCATAACGATAC+TGG 0.386458 1:+63365700 MsaT003894.1:CDS
GGAGGTGGGGACAGCGGCGG+TGG 0.386670 1:-63365494 None:intergenic
TGATAGTGGTGGTCGGTGTT+TGG 0.389979 1:-63365445 None:intergenic
GTGGCGGAAGCAGCAGATCT+TGG 0.391074 1:+63366371 MsaT003894.1:CDS
ATATGATATTATCTATTGAT+TGG 0.394784 1:-63366511 None:intergenic
GACGAGATTACGATTCTTCA+AGG 0.409728 1:+63365649 MsaT003894.1:CDS
AATGAGAAGAATTAGGGTTA+GGG 0.412685 1:-63365978 None:intergenic
CGGTGTCAAACAGCTCTTCA+TGG 0.416968 1:-63366202 None:intergenic
CGGCTCCCCTGAACCAAAAC+GGG 0.425461 1:+63365564 MsaT003894.1:CDS
GGAGCCGGAGCTGGAGGTAG+TGG 0.425950 1:+63366480 MsaT003894.1:CDS
ATTTCCTCCTCTTCATCAAC+AGG 0.428859 1:-63365940 None:intergenic
ACCAGCTTGTTGATAAGCTT+CGG 0.431916 1:+63365773 MsaT003894.1:CDS
TCGCTGGTCTTCTCTTCCAT+TGG 0.435468 1:-63365589 None:intergenic
GGGGACAGCGGCGGTGGCGA+AGG 0.444218 1:-63365488 None:intergenic
CCAGAAATTTGATTCTGGTA+AGG 0.445820 1:+63365825 MsaT003894.1:CDS
GAAGGTTGACGGAGATTGTT+CGG 0.453008 1:-63365470 None:intergenic
ATGGTCTCTTCGATTAATCC+AGG 0.453758 1:-63366183 None:intergenic
CTGTTTGACACCGGTGTTGA+AGG 0.458464 1:+63366212 MsaT003894.1:CDS
CTGATGCGGAGGCGTGTGGT+AGG 0.462324 1:-63365528 None:intergenic
AACGGTAATTCAACGCCAAT+TGG 0.467910 1:+63365913 MsaT003894.1:CDS
TCATCAACAGGTACACCAAT+TGG 0.471428 1:-63365928 None:intergenic
CACAAAATCTGGGGCAGTAA+CGG 0.472372 1:+63365895 MsaT003894.1:CDS
GCGGCGGTGGCGAAGGTTGA+CGG 0.475689 1:-63365481 None:intergenic
TGGTTCAGGGGAGCCGTCGA+TGG 0.476050 1:-63365557 None:intergenic
GAGATTGTTCGGTTTGATAG+TGG 0.479733 1:-63365459 None:intergenic
GAAAAGCTTCCGCGAATCGC+TGG 0.482525 1:-63365605 None:intergenic
TTGAGATCGAATGCTGGAGC+TGG 0.483868 1:+63366459 MsaT003894.1:CDS
TCGAATGCTGGAGCTGGAGC+CGG 0.484287 1:+63366465 MsaT003894.1:CDS
ATTTCCACTACCTCCAGCTC+CGG 0.484287 1:-63366484 None:intergenic
TAGGGCTAAGATGACGGAGG+TGG 0.485162 1:-63365509 None:intergenic
GAAGCAGCAGATCTTGGAGC+TGG 0.497446 1:+63366377 MsaT003894.1:CDS
CGCAATCTCGCAAGAGATCG+CGG 0.499446 1:+63366019 MsaT003894.1:CDS
AAGAGAAGACCAGCGATTCG+CGG 0.508453 1:+63365596 MsaT003894.1:CDS
GAGATCGCGGGCAGCTGAGG+AGG 0.510050 1:+63366032 MsaT003894.1:CDS
ACGGCTCCCCTGAACCAAAA+CGG 0.512535 1:+63365563 MsaT003894.1:CDS
GAAGCGGTTGGAGCTGGTGC+AGG 0.515736 1:+63366410 MsaT003894.1:CDS
CTCATGGCATTCTCTCGAAA+CGG 0.520566 1:+63365334 None:intergenic
ATTAATCCAGGGATTAATCC+AGG 0.522199 1:-63366171 None:intergenic
AGGGCTAAGATGACGGAGGT+GGG 0.524316 1:-63365508 None:intergenic
CAAGAGATCGCGGGCAGCTG+AGG 0.524761 1:+63366029 MsaT003894.1:CDS
GTATTCGAAGCGGTTGGAGC+TGG 0.525755 1:+63366404 MsaT003894.1:CDS
CGACGACGATTTAGCAGAAG+AGG 0.541523 1:+63365405 MsaT003894.1:CDS
AGTGGTGGTCGGTGTTTGGT+TGG 0.541859 1:-63365441 None:intergenic
TCGGCGTAATCATCGTGGGT+GGG 0.542069 1:-63365367 None:intergenic
TTCAATAACTCCTTCAACAC+CGG 0.545324 1:-63366222 None:intergenic
TTCGGTTTGATAGTGGTGGT+CGG 0.548380 1:-63365452 None:intergenic
GCAATCTCGCAAGAGATCGC+GGG 0.549804 1:+63366020 MsaT003894.1:CDS
CGGCGTAATCATCGTGGGTG+GGG 0.551271 1:-63365366 None:intergenic
TGAACCAAAACGGGAGCCAA+TGG 0.551623 1:+63365573 MsaT003894.1:CDS
GGAGCTGGAGCCGGAGCTGG+AGG 0.552899 1:+63366474 MsaT003894.1:CDS
TGAAATCAAGGTTGCGATCG+AGG 0.554388 1:+63366434 MsaT003894.1:CDS
AATGTACCTGGATTAATCCC+TGG 0.555659 1:+63366165 MsaT003894.1:CDS
GATGACGGAGGTGGGGACAG+CGG 0.558674 1:-63365500 None:intergenic
CAAATTTCTGGAGAGCAGTA+CGG 0.563493 1:-63365813 None:intergenic
GAGGAGTTGAGATCGAATGC+TGG 0.564654 1:+63366453 MsaT003894.1:CDS
GTCGGCGTAATCATCGTGGG+TGG 0.567951 1:-63365368 None:intergenic
CATGAAGGGGAAGATTCAGC+TGG 0.569578 1:+63365738 MsaT003894.1:CDS
GTCGTCTTCTCCCTCGATGT+CGG 0.573199 1:-63365386 None:intergenic
AATCATGCACATAATGTACC+TGG 0.574034 1:+63366153 MsaT003894.1:CDS
ATTGTTCGGTTTGATAGTGG+TGG 0.575227 1:-63365456 None:intergenic
TGGTCTCTTCGATTAATCCA+GGG 0.577535 1:-63366182 None:intergenic
GTGTGGTAGGGCTAAGATGA+CGG 0.582706 1:-63365515 None:intergenic
GGAGGTGTATTCGAAGCGGT+TGG 0.582984 1:+63366398 MsaT003894.1:CDS
TGATGCGGAGGCGTGTGGTA+GGG 0.584219 1:-63365527 None:intergenic
GCCGAAGCTTATCAACAAGC+TGG 0.585703 1:-63365774 None:intergenic
CTTCTTCAGTCCAGATACGC+TGG 0.591258 1:-63365627 None:intergenic
GTCGATGGTTGTTGCTGATG+CGG 0.592509 1:-63365542 None:intergenic
AAAAGGCGCTGGATGAAAAG+TGG 0.594253 1:+63366352 MsaT003894.1:CDS
GATAATCATCAGAATAACTC+CGG 0.596997 1:+63366081 MsaT003894.1:CDS
ACCAAAAGGACTCCCACTCA+TGG 0.598783 1:-63366250 None:intergenic
GCTGGTGCAGGATGAAATCA+AGG 0.598958 1:+63366422 MsaT003894.1:CDS
CGATGTCGGCGTAATCATCG+TGG 0.600774 1:-63365372 None:intergenic
GAAATTTCTCACAAAATCTG+GGG 0.604849 1:+63365886 MsaT003894.1:CDS
GAAAATCGTGATAAAAGTAA+CGG 0.608736 1:+63366129 MsaT003894.1:CDS
GCTGAATCTTCCCCTTCATG+TGG 0.609274 1:-63365735 None:intergenic
GGGCTAAGATGACGGAGGTG+GGG 0.612836 1:-63365507 None:intergenic
TTATTGAATGCTACCATGAG+TGG 0.614451 1:+63366237 MsaT003894.1:CDS
GACGGAGGTGGGGACAGCGG+CGG 0.622679 1:-63365497 None:intergenic
AGCTGGAGGTGTATTCGAAG+CGG 0.623559 1:+63366394 MsaT003894.1:CDS
TATTGAATGCTACCATGAGT+GGG 0.627706 1:+63366238 MsaT003894.1:CDS
TGGTGTACCTGTTGATGAAG+AGG 0.630690 1:+63365933 MsaT003894.1:CDS
GTTGCTGATGCGGAGGCGTG+TGG 0.634510 1:-63365532 None:intergenic
GATGTCGGCGTAATCATCGT+GGG 0.636913 1:-63365371 None:intergenic
GATGATTACGCCGACATCGA+GGG 0.637383 1:+63365376 MsaT003894.1:CDS
GGCATTCTCTCGAAACGGCG+TGG 0.645669 1:+63365339 MsaT003894.1:CDS
CATGAAGAGCTGTTTGACAC+CGG 0.646198 1:+63366203 MsaT003894.1:CDS
GCAGCAGATCTTGGAGCTGG+AGG 0.646814 1:+63366380 MsaT003894.1:CDS
GCATCAGCAACAACCATCGA+CGG 0.685479 1:+63365544 MsaT003894.1:CDS
AGGCGCTGGATGAAAAGTGG+CGG 0.689339 1:+63366355 MsaT003894.1:CDS
TAATACCAATAGCAGCAATG+TGG 0.690177 1:+63366104 MsaT003894.1:CDS
AGCTTGTTGATAAGCTTCGG+CGG 0.690763 1:+63365776 MsaT003894.1:CDS
GATGGTTGTTGCTGATGCGG+AGG 0.694249 1:-63365539 None:intergenic
TGTACCTGTTGATGAAGAGG+AGG 0.712098 1:+63365936 MsaT003894.1:CDS
CGATGATTACGCCGACATCG+AGG 0.729131 1:+63365375 MsaT003894.1:CDS
TGGTAGGGCTAAGATGACGG+AGG 0.739720 1:-63365512 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 63365337 63366521 63365337 ID=MsaG003894
Chr1 mRNA 63365337 63366521 63365337 ID=MsaT003894.1;Parent=MsaG003894
Chr1 exon 63365337 63366521 63365337 ID=MsaT003894.1.exon1;Parent=MsaT003894.1
Chr1 CDS 63365337 63366521 63365337 ID=cds.MsaT003894.1;Parent=MsaT003894.1
Gene Sequence

>MsaT003894.1

ATGGCATTCTCTCGAAACGGCGTGGTTATCCCCACCCACGATGATTACGCCGACATCGAGGGAGAAGACGACGACGATTTAGCAGAAGAGGACAACTATTTTGTCCAACCAAACACCGACCACCACTATCAAACCGAACAATCTCCGTCAACCTTCGCCACCGCCGCTGTCCCCACCTCCGTCATCTTAGCCCTACCACACGCCTCCGCATCAGCAACAACCATCGACGGCTCCCCTGAACCAAAACGGGAGCCAATGGAAGAGAAGACCAGCGATTCGCGGAAGCTTTTCCAGCGTATCTGGACTGAAGAAGACGAGATTACGATTCTTCAAGGTTTTCTCGATTACAACGCGAATCGTGAATCGTCTTATCATAACGATACTGGATCGTTTTATGACCACATGAAGGGGAAGATTCAGCTGGATTTCACCAAGAACCAGCTTGTTGATAAGCTTCGGCGGTTGAAGAAGAAATACCGTACTGCTCTCCAGAAATTTGATTCTGGTAAGGATTTTGTTTTCAAGAGTGCTCATGATCAAGCTACTTTTGAAATTTCTCACAAAATCTGGGGCAGTAACGGTAATTCAACGCCAATTGGTGTACCTGTTGATGAAGAGGAGGAAATGAGCCCAAACCCTAACCCTAACCCTAATTCTTCTCATTTAATTGAGAAGAAAGCTGCGCAATCTCGCAAGAGATCGCGGGCAGCTGAGGAGGAAAAGTGTGAGTTGACTGATTCTAGAGATAATCATCAGAATAACTCCGGTAATACCAATAGCAGCAATGTGGATGAAAATCGTGATAAAAGTAACGGTAATCATGCACATAATGTACCTGGATTAATCCCTGGATTAATCGAAGAGACCATGAAGAGCTGTTTGACACCGGTGTTGAAGGAGTTATTGAATGCTACCATGAGTGGGAGTCCTTTTGGTCTTGGGGGAAGAGGGTTTGGAGCTGGAGCTTTTTCAATGAATACTGTGCCATTTGGGTTTTTGAATTTGGGGGGCAGAGAAAAGGCGCTGGATGAAAAGTGGCGGAAGCAGCAGATCTTGGAGCTGGAGGTGTATTCGAAGCGGTTGGAGCTGGTGCAGGATGAAATCAAGGTTGCGATCGAGGAGTTGAGATCGAATGCTGGAGCTGGAGCCGGAGCTGGAGGTAGTGGAAATAATACCAATCAATAG

Protein sequence

>MsaT003894.1

MAFSRNGVVIPTHDDYADIEGEDDDDLAEEDNYFVQPNTDHHYQTEQSPSTFATAAVPTSVILALPHASASATTIDGSPEPKREPMEEKTSDSRKLFQRIWTEEDEITILQGFLDYNANRESSYHNDTGSFYDHMKGKIQLDFTKNQLVDKLRRLKKKYRTALQKFDSGKDFVFKSAHDQATFEISHKIWGSNGNSTPIGVPVDEEEEMSPNPNPNPNSSHLIEKKAAQSRKRSRAAEEEKCELTDSRDNHQNNSGNTNSSNVDENRDKSNGNHAHNVPGLIPGLIEETMKSCLTPVLKELLNATMSGSPFGLGGRGFGAGAFSMNTVPFGFLNLGGREKALDEKWRKQQILELEVYSKRLELVQDEIKVAIEELRSNAGAGAGAGGSGNNTNQ*