AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG005160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005160 MtrunA17_Chr1g0205031 77.385 566 87 6 1 536 1 555 0.0 859
MsaG005160 MtrunA17_Chr5g0394661 36.423 615 278 16 5 516 13 617 3.83e-90 293
MsaG005160 MtrunA17_Chr1g0205021 39.739 307 80 8 16 295 2 230 1.71e-46 163
MsaG005160 MtrunA17_Chr1g0205001 38.521 257 91 8 190 433 18 220 6.76e-35 130
MsaG005160 MtrunA17_Chr1g0205001 71.429 42 12 0 15 56 61 102 2.40e-12 66.6
MsaG005160 MtrunA17_Chr1g0149101 38.764 178 100 5 357 531 474 645 7.91e-30 124
MsaG005160 MtrunA17_Chr1g0205011 47.771 157 46 6 236 371 4 145 5.83e-23 97.4
MsaG005160 MtrunA17_Chr8g0390351 41.481 135 69 4 386 516 83 211 6.77e-23 102
MsaG005160 MtrunA17_Chr6g0485811 42.222 135 68 4 386 516 128 256 7.01e-23 102
MsaG005160 MtrunA17_Chr3g0139951 43.200 125 68 3 386 510 148 269 2.08e-20 93.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005160 AT4G14770.1 31.636 550 288 24 3 516 7 504 5.58e-54 194
MsaG005160 AT3G22780.1 29.676 556 311 15 16 526 22 542 2.11e-52 190
MsaG005160 AT4G14770.3 31.343 536 281 23 16 516 2 485 3.31e-52 189
MsaG005160 AT4G14770.2 31.402 535 280 23 17 516 2 484 5.07e-52 188
MsaG005160 AT3G22760.1 29.981 537 264 17 16 528 21 469 4.47e-50 182
MsaG005160 AT3G22760.2 36.275 306 151 7 234 528 74 346 4.15e-49 177
MsaG005160 AT3G04850.1 39.147 258 130 7 267 510 332 576 9.93e-41 156
MsaG005160 AT5G25790.3 39.735 151 81 4 386 536 95 235 2.34e-24 106
MsaG005160 AT5G25790.1 37.748 151 88 3 386 536 95 239 1.85e-23 103
MsaG005160 AT5G25790.2 37.748 151 88 3 386 536 95 239 1.98e-23 103
MsaG005160 AT2G20110.3 38.272 162 88 5 353 510 88 241 1.15e-21 99.0
MsaG005160 AT2G20110.2 38.272 162 88 5 353 510 88 241 1.40e-21 99.0
MsaG005160 AT2G20110.1 38.272 162 88 5 353 510 88 241 1.43e-21 99.0
MsaG005160 AT4G29000.1 38.931 131 78 2 386 516 132 260 1.74e-20 95.5
MsaG005160 AT3G16160.1 42.276 123 66 3 386 508 66 183 2.69e-18 87.0

Find 92 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTGCCAATGTTGCTTTAA+TGG 0.092114 1:-78339642 MsaT005160.1:CDS
TATGCCTTCGTAATGATTTA+AGG 0.098318 1:+78338915 None:intergenic
CCAGAATTCTTTCGAACTTT+AGG 0.204484 1:+78337862 None:intergenic
CCTAAAGTTCGAAAGAATTC+TGG 0.241815 1:-78337862 MsaT005160.1:CDS
TTGCACTTCACTCGTCCTTT+TGG 0.274158 1:+78338696 None:intergenic
CTTTGAAGCTGGAGCTTTGT+TGG 0.274516 1:+78337729 None:intergenic
TAAGTGCAGCTCGGTGATTC+AGG 0.293566 1:+78338862 None:intergenic
TACTGGTAGATTGTGGTAAC+AGG 0.297737 1:+78339780 None:intergenic
TTTGAAGCTGGAGCTTTGTT+GGG 0.308021 1:+78337730 None:intergenic
TTTCTGTCTGTTGCGGCTAT+TGG 0.313269 1:+78339680 None:intergenic
GAATATGGACTCGTCGTTAA+AGG 0.316508 1:+78340200 None:intergenic
ACACCAAAGTTCGACTTTGC+AGG 0.317208 1:-78338429 MsaT005160.1:intron
TTGAAGGTGGAACATTTATT+CGG 0.321966 1:-78339856 MsaT005160.1:CDS
AATGTTGACCCACTTGCTTT+TGG 0.345110 1:-78339737 MsaT005160.1:CDS
CACCCTTCACATTTACAACT+TGG 0.349859 1:+78337535 None:intergenic
CAAGTACCTCGTGAGGAATA+TGG 0.357398 1:+78340185 None:intergenic
CACCAATGGAGACACATTTA+CGG 0.379389 1:-78338789 MsaT005160.1:CDS
ACAGCCTCAGATGAAAGTTC+AGG 0.391141 1:+78340058 None:intergenic
CTGCGTCGTCGCTTTGAAGC+TGG 0.396100 1:+78337718 None:intergenic
TGAAATTGAAGACAATCCTT+TGG 0.408389 1:-78339705 MsaT005160.1:CDS
AAGTCATCAGTTCACATTCC+TGG 0.424450 1:-78338742 MsaT005160.1:CDS
AGAGTTGCTCCTTTGCATAC+TGG 0.425375 1:+78339026 None:intergenic
AATTGTGGCTGCTTTGCTGC+TGG 0.427566 1:-78338000 MsaT005160.1:CDS
AAGTATCTTCTTGAATTACT+TGG 0.428004 1:-78339932 MsaT005160.1:CDS
AAGTTATTGTAATCACAATC+TGG 0.434332 1:+78339827 None:intergenic
ACCCTTCACATTTACAACTT+GGG 0.434704 1:+78337536 None:intergenic
TGAAGGTGGAACATTTATTC+GGG 0.437173 1:-78339855 MsaT005160.1:CDS
TAGTTTCTGACCACAATTTG+AGG 0.447183 1:+78337832 None:intergenic
CTCCTACTCGCAGTGGTGGC+AGG 0.454782 1:-78337276 MsaT005160.1:intron
CCCTTCACATTTACAACTTG+GGG 0.459373 1:+78337537 None:intergenic
TTAAATATTTCTGTAAGTCA+AGG 0.471447 1:-78338835 MsaT005160.1:CDS
TCTTGTACATCCGTACCATC+TGG 0.499848 1:+78339899 None:intergenic
CCTTCGTAATGATTTAAGGC+TGG 0.512377 1:+78338919 None:intergenic
GCTATCCATTAAAGCAACAT+TGG 0.513739 1:+78339637 None:intergenic
TAAATATTTCTGTAAGTCAA+GGG 0.524834 1:-78338834 MsaT005160.1:CDS
TGGTTCCTCACCTCAAATTG+TGG 0.524835 1:-78337842 MsaT005160.1:intron
GCAGAATACGATGCAAGTGC+AGG 0.525356 1:-78337699 MsaT005160.1:CDS
CGAACTTTAGGAACAAATGC+AGG 0.526329 1:+78337874 None:intergenic
GGAACAAGTCAGATCTAACT+AGG 0.530885 1:-78338408 MsaT005160.1:CDS
CGAAAATATACATGGTAGGA+AGG 0.533470 1:-78337512 MsaT005160.1:CDS
TGCTTGATTTCTGTCTGTTG+CGG 0.536356 1:+78339673 None:intergenic
CACACTTCTGTGAATCACTA+GGG 0.539386 1:+78338977 None:intergenic
TTGAAGCTGGAGCTTTGTTG+GGG 0.541047 1:+78337731 None:intergenic
GTTGCGGCTATTGGTTCCAA+AGG 0.544179 1:+78339689 None:intergenic
TTAAAGGAGATAGAGTATTG+AGG 0.545460 1:+78340310 None:intergenic
ATACAGTTCTGCAAGCTCGC+AGG 0.548799 1:-78337918 MsaT005160.1:CDS
ACACACTTCTGTGAATCACT+AGG 0.552964 1:+78338976 None:intergenic
TCCGTCAGAGTACTCCCAAA+AGG 0.555631 1:-78338711 MsaT005160.1:CDS
CCTCTCGTGAGTTGGAAACA+AGG 0.556689 1:+78340570 None:intergenic
ACTGAGACGCTGAACTCACT+TGG 0.558175 1:-78340258 MsaT005160.1:CDS
ATCTCAAGTCTCTGCACCAA+TGG 0.560130 1:-78338803 MsaT005160.1:CDS
ATGAAAAGATGTCTTCTCAA+AGG 0.565868 1:-78338888 MsaT005160.1:CDS
GCTGCTGGAGTCTACTGCAC+AGG 0.566140 1:-78337985 MsaT005160.1:CDS
CTCTGACGGAAATCTTCACC+AGG 0.567030 1:+78338724 None:intergenic
CAGATCTAACTAGGAAAGGA+GGG 0.570663 1:-78338399 MsaT005160.1:CDS
AAGTCAGATCTAACTAGGAA+AGG 0.571577 1:-78338403 MsaT005160.1:CDS
AGCCGTAAATGTGTCTCCAT+TGG 0.572557 1:+78338787 None:intergenic
CTCTCGTGAGTTGGAAACAA+GGG 0.577501 1:+78340571 None:intergenic
TCAGATCTAACTAGGAAAGG+AGG 0.580562 1:-78338400 MsaT005160.1:CDS
CTACAGATTCAACTCATGCA+TGG 0.581951 1:-78340006 MsaT005160.1:CDS
CAAGCAAGAACCAGATGGTA+CGG 0.582545 1:-78339909 MsaT005160.1:CDS
AGTATACAGATGAGCTGTCA+AGG 0.583545 1:-78339066 MsaT005160.1:CDS
TTGCTATTACTGGTAGATTG+TGG 0.588055 1:+78339773 None:intergenic
GACGCTGAACTCACTTGGCA+TGG 0.589852 1:-78340253 MsaT005160.1:CDS
AAATCCTGAACTTTCATCTG+AGG 0.591883 1:-78340062 MsaT005160.1:CDS
GGTGGAACATTTATTCGGGA+AGG 0.592387 1:-78339851 MsaT005160.1:CDS
ACATCGAGTGATGTGAAAAG+AGG 0.592896 1:+78340225 None:intergenic
GATAGCAATCAAATTAAGAG+AGG 0.597084 1:-78339620 MsaT005160.1:CDS
CAACAGACAGAAATCAAGCA+CGG 0.597880 1:-78339670 MsaT005160.1:CDS
ATAGCAATCAAATTAAGAGA+GGG 0.602322 1:-78339619 MsaT005160.1:CDS
TCTGACCACAATTTGAGGTG+AGG 0.607327 1:+78337837 None:intergenic
CCTTGTTTCCAACTCACGAG+AGG 0.612973 1:-78340570 MsaT005160.1:intron
TCCCCAAGTTGTAAATGTGA+AGG 0.615749 1:-78337538 MsaT005160.1:CDS
CATGCATGAGTTGAATCTGT+AGG 0.615864 1:+78340007 None:intergenic
GGTGCGAAAATATACATGGT+AGG 0.616427 1:-78337516 MsaT005160.1:CDS
GTCACAGATGTAGTTGAAGG+TGG 0.621901 1:-78339869 MsaT005160.1:CDS
AGGAATGTGAACTGATGACT+TGG 0.627401 1:+78338744 None:intergenic
TTTAAAGAATAAGTGCAGCT+CGG 0.628487 1:+78338853 None:intergenic
ACTTTAGGAACAAATGCAGG+TGG 0.632470 1:+78337877 None:intergenic
CTGAGATGACCAGTATGCAA+AGG 0.633227 1:-78339035 MsaT005160.1:CDS
ACTGGTAGATTGTGGTAACA+GGG 0.636581 1:+78339781 None:intergenic
TCTGTCACAGATGTAGTTGA+AGG 0.639278 1:-78339872 MsaT005160.1:CDS
AATTAAGAGAGGGGATGATG+AGG 0.639810 1:-78339609 MsaT005160.1:intron
AGATCTAACTAGGAAAGGAG+GGG 0.643115 1:-78338398 MsaT005160.1:CDS
GAAGGGTGCGAAAATATACA+TGG 0.643125 1:-78337520 MsaT005160.1:CDS
CTTGGCAAGCAAGAACCAGA+TGG 0.652633 1:-78339914 MsaT005160.1:CDS
AAGCAGTCTTGACATGAGCA+AGG 0.654291 1:+78337961 None:intergenic
AAAGGAGCAACTCTGATGAG+AGG 0.655315 1:-78339017 MsaT005160.1:CDS
TAGCAATCAAATTAAGAGAG+GGG 0.656836 1:-78339618 MsaT005160.1:CDS
CCCCAAGTTGTAAATGTGAA+GGG 0.657560 1:-78337537 MsaT005160.1:CDS
CCAGCCTTAAATCATTACGA+AGG 0.687773 1:-78338919 MsaT005160.1:CDS
ACGAGTCCATATTCCTCACG+AGG 0.713943 1:-78340191 MsaT005160.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 78337263 78340618 78337263 ID=MsaG005160
Chr1 mRNA 78337263 78340618 78337263 ID=MsaT005160.1;Parent=MsaG005160
Chr1 exon 78337263 78337285 78337263 ID=MsaT005160.1.exon9;Parent=MsaT005160.1
Chr1 CDS 78337263 78337285 78337263 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78337446 78337575 78337446 ID=MsaT005160.1.exon8;Parent=MsaT005160.1
Chr1 CDS 78337446 78337575 78337446 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78337660 78337758 78337660 ID=MsaT005160.1.exon7;Parent=MsaT005160.1
Chr1 CDS 78337660 78337758 78337660 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78337843 78338023 78337843 ID=MsaT005160.1.exon6;Parent=MsaT005160.1
Chr1 CDS 78337843 78338023 78337843 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78338355 78338442 78338355 ID=MsaT005160.1.exon5;Parent=MsaT005160.1
Chr1 CDS 78338355 78338442 78338355 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78338707 78339106 78338707 ID=MsaT005160.1.exon4;Parent=MsaT005160.1
Chr1 CDS 78338707 78339106 78338707 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78339610 78340105 78339610 ID=MsaT005160.1.exon3;Parent=MsaT005160.1
Chr1 CDS 78339610 78340105 78339610 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78340192 78340352 78340192 ID=MsaT005160.1.exon2;Parent=MsaT005160.1
Chr1 CDS 78340192 78340352 78340192 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Chr1 exon 78340571 78340618 78340571 ID=MsaT005160.1.exon1;Parent=MsaT005160.1
Chr1 CDS 78340571 78340618 78340571 ID=cds.MsaT005160.1;Parent=MsaT005160.1
Gene Sequence

>MsaT005160.1

ATGGCGGCACTAGATCAAAAGAACACCCTTGTTTCCAACTCACGAGAGGATGATTCTTTCTTTGACTACCTCAATACTCTATCTCCTTTAAACACCAAAAAGTATGTTGGAGTTGGAGCTACTGAGACGCTGAACTCACTTGGCATGGCTTATCCTCTTTTCACATCACTCGATGTGACCTTTAACGACGAGTCCATATTCCTCACGAGGAATAATCTTTTGTACACATCAAATCCTGAACTTTCATCTGAGGCTGTAAATAACACATATTCACATGAAGAAGCTCCTACAGATTCAACTCATGCATGGATTGACACAAGTCAGCTACATGATCTTCAAATCTCAAGTGATGATGATGCTAAGTATCTTCTTGAATTACTTGGCAAGCAAGAACCAGATGGTACGGATGTACAAGATGACTCTGTCACAGATGTAGTTGAAGGTGGAACATTTATTCGGGAAGGACCAGATTGTGATTACAATAACTTAATTAGTGCAACACAATCTGTGACCCTGTTACCACAATCTACCAGTAATAGCAATTATAAAATGAAAAATGTTGACCCACTTGCTTTTGGCTCAAAACATGAAATTGAAGACAATCCTTTGGAACCAATAGCCGCAACAGACAGAAATCAAGCACGGAACAATCTTGCCAATGTTGCTTTAATGGATAGCAATCAAATTAAGAGAGGGGATGATGAGCTTGCACGTATTAGACGCAGTATACAGATGAGCTGTCAAGGCTATGAGTCTGAGATGACCAGTATGCAAAGGAGCAACTCTGATGAGAGGAATGCTATTAACAAAAACCCTAGTGATTCACAGAAGTGTGTTTTGCAAGGAAATGGTTTTTACTGGAATGCACTTCCAGCCTTAAATCATTACGAAGGCATAGAAAATGAAAAGATGTCTTCTCAAAGGAAACCTGAATCACCGAGCTGCACTTATTCTTTAAATATTTCTGTAAGTCAAGGGTATCAACTATCTCAAGTCTCTGCACCAATGGAGACACATTTACGGCTATCTGAGAATGAAGATGTCACCAAGTCATCAGTTCACATTCCTGGTGAAGATTTCCGTCAGAGTACTCCCAAAAGGACGATTCGACTTTGCAGGAACAAGTCAGATCTAACTAGGAAAGGAGGGGCATGCAAACACTGTAAATGTAAAAAATCAAAGTGTTTGAAACTTAATTGTGGCTGCTTTGCTGCTGGAGTCTACTGCACAGGACCTTGCTCATGTCAAGACTGCTTGAATAAACATATTAATGAAGATACAGTTCTGCAAGCTCGCAGGATGATTGAGTATCGTAATCCACCTGCATTTGTTCCTAAAGTTCGAAAGAATTCTGGTTCCTCACCTCAAATTGTGGATGACCCCAACAAAGCTCCAGCTTCAAAGCGACGACGCAGAATACGATGCAAGTGCAGGAAATCAAGCTGCATGAATAAACGTTGTGAATGTTTTAAGGGTGGTGTCGCTTGTTCCCCAAGTTGTAAATGTGAAGGGTGCGAAAATATACATGGTAGGAAGGATAGTGCAGCTGAAACTAAATCTGAGCTTGAAGAAACAGAAGCATCACAGATAAAGCTACAAATTTTGGTGGCAGGAACTCGACATTAG

Protein sequence

>MsaT005160.1

MAALDQKNTLVSNSREDDSFFDYLNTLSPLNTKKYVGVGATETLNSLGMAYPLFTSLDVTFNDESIFLTRNNLLYTSNPELSSEAVNNTYSHEEAPTDSTHAWIDTSQLHDLQISSDDDAKYLLELLGKQEPDGTDVQDDSVTDVVEGGTFIREGPDCDYNNLISATQSVTLLPQSTSNSNYKMKNVDPLAFGSKHEIEDNPLEPIAATDRNQARNNLANVALMDSNQIKRGDDELARIRRSIQMSCQGYESEMTSMQRSNSDERNAINKNPSDSQKCVLQGNGFYWNALPALNHYEGIENEKMSSQRKPESPSCTYSLNISVSQGYQLSQVSAPMETHLRLSENEDVTKSSVHIPGEDFRQSTPKRTIRLCRNKSDLTRKGGACKHCKCKKSKCLKLNCGCFAAGVYCTGPCSCQDCLNKHINEDTVLQARRMIEYRNPPAFVPKVRKNSGSSPQIVDDPNKAPASKRRRRIRCKCRKSSCMNKRCECFKGGVACSPSCKCEGCENIHGRKDSAAETKSELEETEASQIKLQILVAGTRH*