AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0792960

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0792960 MtrunA17_Chr1g0207451 71.523 151 39 2 1 149 81 229 3.95e-70 212
Msa0792960 MtrunA17_Chr3g0134711 49.587 121 52 2 1 115 84 201 7.38e-27 101
Msa0792960 MtrunA17_Chr1g0152661 47.107 121 52 4 1 115 79 193 2.11e-24 94.7
Msa0792960 MtrunA17_Chr7g0231181 38.136 118 50 4 4 117 241 339 1.80e-14 69.7
Msa0792960 MtrunA17_Chr7g0263121 44.444 72 38 2 4 75 45 114 2.36e-12 61.6
Msa0792960 MtrunA17_Chr4g0012691 30.769 130 70 4 4 117 221 346 5.92e-12 62.8
Msa0792960 MtrunA17_Chr1g0182161 35.652 115 45 4 5 115 41 130 3.37e-11 58.5
Msa0792960 MtrunA17_Chr5g0425411 38.462 91 41 2 5 80 121 211 7.60e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0792960 AT1G27730.1 50.394 127 51 4 1 120 78 199 2.34e-29 107
Msa0792960 AT5G04340.1 50.000 126 51 3 4 120 90 212 2.17e-26 100
Msa0792960 AT3G19580.1 45.600 125 57 3 1 114 104 228 8.51e-25 97.1
Msa0792960 AT3G19580.2 45.600 125 57 3 1 114 104 228 8.51e-25 97.1
Msa0792960 AT5G43170.1 48.739 119 40 5 4 120 76 175 5.85e-22 87.8
Msa0792960 AT5G67450.1 42.254 142 50 4 4 115 98 237 3.70e-20 84.3
Msa0792960 AT3G49930.1 52.564 78 32 1 4 76 95 172 3.02e-19 81.3
Msa0792960 AT3G60580.1 38.596 114 59 3 4 116 174 277 5.84e-18 79.0
Msa0792960 AT1G49900.1 46.753 77 39 1 4 78 194 270 2.29e-17 79.0
Msa0792960 AT1G49900.1 45.333 75 39 1 4 78 751 823 4.25e-15 72.4
Msa0792960 AT2G45120.1 38.596 114 62 4 4 116 195 301 9.09e-16 73.6
Msa0792960 AT5G56200.1 40.860 93 36 3 5 78 344 436 2.77e-13 67.0
Msa0792960 AT1G02030.1 34.821 112 56 3 5 116 162 256 3.27e-13 65.9
Msa0792960 AT3G46070.1 37.079 89 53 1 4 89 37 125 6.04e-11 58.2

Find 50 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACATTAACCTTGTTCTTCT+TGG 0.180001 5_3:-4817672 None:intergenic
TTTCCTACTGCCCAAGCTTT+TGG 0.259478 5_3:+4817464 Msa0792960:CDS
CTGTGCCTCTCACTAAATTC+TGG 0.264666 5_3:+4817621 Msa0792960:CDS
CACCTCTTGCTCATCCATTC+CGG 0.359071 5_3:-4817702 None:intergenic
AACATAGACGGTGTTGTTAA+TGG 0.362302 5_3:-4817387 None:intergenic
GATGAGCAAGAGGTGGAAAA+AGG 0.370532 5_3:+4817710 Msa0792960:CDS
GAACAAGGTTAATGTTAATC+TGG 0.395694 5_3:+4817679 Msa0792960:CDS
GTCAAAGCCACGGTGGTTGA+TGG 0.421188 5_3:-4817588 None:intergenic
TGTGCCTCTCACTAAATTCT+GGG 0.423468 5_3:+4817622 Msa0792960:CDS
AGATGAGGATTTACGGTGGC+TGG 0.430843 5_3:-4817348 None:intergenic
GGAACACACATGCATCTTAC+CGG 0.431723 5_3:-4817426 None:intergenic
CTATCTTATCTAGCACTTGG+TGG 0.445360 5_3:+4817317 Msa0792960:CDS
GTTTGTGTCCACCAAAAGCT+TGG 0.450920 5_3:-4817475 None:intergenic
GACGGTGTTGTTAATGGTGG+TGG 0.454028 5_3:-4817381 None:intergenic
TTTGTGTCCACCAAAAGCTT+GGG 0.500676 5_3:-4817474 None:intergenic
CAGAATTTAGTGAGAGGCAC+AGG 0.504910 5_3:-4817620 None:intergenic
TTTCTATCTTATCTAGCACT+TGG 0.507254 5_3:+4817314 Msa0792960:CDS
TGTTGTTAATGGTGGTGGAT+TGG 0.511948 5_3:-4817376 None:intergenic
CCACCAAAAGCTTGGGCAGT+AGG 0.517458 5_3:-4817467 None:intergenic
AAGGTTAATGTTAATCTGGC+CGG 0.517608 5_3:+4817683 Msa0792960:CDS
TAATGTTAATCTGGCCGGAA+TGG 0.525751 5_3:+4817688 Msa0792960:CDS
TTGTCGTCGAGCTGAATGAC+AGG 0.529754 5_3:+4817270 None:intergenic
GCCACGGTGGTTGATGGAAG+AGG 0.538391 5_3:-4817582 None:intergenic
AGGAAAACTCTTGTGACAGT+TGG 0.541592 5_3:-4817447 None:intergenic
GTTTCCATCGCAACCGTCGC+CGG 0.550306 5_3:+4817407 Msa0792960:CDS
CTTACCGGCGACGGTTGCGA+TGG 0.561316 5_3:-4817411 None:intergenic
TCTCACTAAATTCTGGGCTC+CGG 0.563716 5_3:+4817628 Msa0792960:CDS
CTAGATAAGATAGAAAAGCT+TGG 0.571484 5_3:-4817307 None:intergenic
TGTTGTTACCGCCGTTGTAG+TGG 0.578897 5_3:-4817502 None:intergenic
TCTCCACTGTCGAATCTCGC+CGG 0.588418 5_3:-4817647 None:intergenic
CACAAACGGTGCCACTACAA+CGG 0.603038 5_3:+4817491 Msa0792960:CDS
GGCCGGAATGGATGAGCAAG+AGG 0.607481 5_3:+4817700 Msa0792960:CDS
TGAGAGGCACAGGTAAGTTG+AGG 0.611073 5_3:-4817610 None:intergenic
CACATGCATCTTACCGGCGA+CGG 0.623083 5_3:-4817420 None:intergenic
ATTTGAAGAAGAGAAACGCA+AGG 0.638030 5_3:-4817739 None:intergenic
GTCAAAGTTACTAACAGCGG+TGG 0.642956 5_3:+4817530 Msa0792960:CDS
TGGAGATTCCAAGAAGAACA+AGG 0.654591 5_3:+4817664 Msa0792960:CDS
AAACGGTGCCACTACAACGG+CGG 0.659288 5_3:+4817494 Msa0792960:CDS
CGGAATGGATGAGCAAGAGG+TGG 0.663787 5_3:+4817703 Msa0792960:CDS
GGTGGAGTTACAATCTCTGA+CGG 0.665727 5_3:+4817548 Msa0792960:CDS
GTAAGTTGAGGTCAAAGCCA+CGG 0.668476 5_3:-4817598 None:intergenic
AACGTCAAAGTTACTAACAG+CGG 0.669045 5_3:+4817527 Msa0792960:CDS
GTTGATGGAAGAGGACGCGA+CGG 0.682513 5_3:-4817573 None:intergenic
GGAGCCCAGAATTTAGTGAG+AGG 0.685772 5_3:-4817626 None:intergenic
TCCTCTTCCATCAACCACCG+TGG 0.689382 5_3:+4817581 Msa0792960:CDS
TTTCAGATGAGGATTTACGG+TGG 0.709487 5_3:-4817352 None:intergenic
GGTTGCGATGGAAACATAGA+CGG 0.712836 5_3:-4817399 None:intergenic
ATAGACGGTGTTGTTAATGG+TGG 0.733629 5_3:-4817384 None:intergenic
AGTTGAGGTCAAAGCCACGG+TGG 0.766971 5_3:-4817595 None:intergenic
GCTCCGGCGAGATTCGACAG+TGG 0.770708 5_3:+4817644 Msa0792960:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CTAGATAAGATAGAAAAGCT+TGG - chr5_3:4817310-4817329 None:intergenic 30.0%
TTTCTATCTTATCTAGCACT+TGG + chr5_3:4817314-4817333 Msa0792960:CDS 30.0%
AACATTAACCTTGTTCTTCT+TGG - chr5_3:4817675-4817694 None:intergenic 30.0%
GAACAAGGTTAATGTTAATC+TGG + chr5_3:4817679-4817698 Msa0792960:CDS 30.0%
! GGTTTTCAGATGAGGATTTA+CGG - chr5_3:4817358-4817377 None:intergenic 35.0%
!! AACATAGACGGTGTTGTTAA+TGG - chr5_3:4817390-4817409 None:intergenic 35.0%
AACGTCAAAGTTACTAACAG+CGG + chr5_3:4817527-4817546 Msa0792960:CDS 35.0%
AAGGTTAATGTTAATCTGGC+CGG + chr5_3:4817683-4817702 Msa0792960:CDS 35.0%
ATTTGAAGAAGAGAAACGCA+AGG - chr5_3:4817742-4817761 None:intergenic 35.0%
CTATCTTATCTAGCACTTGG+TGG + chr5_3:4817317-4817336 Msa0792960:CDS 40.0%
TTTCAGATGAGGATTTACGG+TGG - chr5_3:4817355-4817374 None:intergenic 40.0%
!! TGTTGTTAATGGTGGTGGAT+TGG - chr5_3:4817379-4817398 None:intergenic 40.0%
!! ATAGACGGTGTTGTTAATGG+TGG - chr5_3:4817387-4817406 None:intergenic 40.0%
AGGAAAACTCTTGTGACAGT+TGG - chr5_3:4817450-4817469 None:intergenic 40.0%
TTTGTGTCCACCAAAAGCTT+GGG - chr5_3:4817477-4817496 None:intergenic 40.0%
!! AAGCTTTTGGTGGACACAAA+CGG + chr5_3:4817477-4817496 Msa0792960:CDS 40.0%
TGTGCCTCTCACTAAATTCT+GGG + chr5_3:4817622-4817641 Msa0792960:CDS 40.0%
TGGAGATTCCAAGAAGAACA+AGG + chr5_3:4817664-4817683 Msa0792960:CDS 40.0%
TAATGTTAATCTGGCCGGAA+TGG + chr5_3:4817688-4817707 Msa0792960:CDS 40.0%
!!! GGTGGATTGGTTTTCAGATG+AGG - chr5_3:4817366-4817385 None:intergenic 45.0%
GGTTGCGATGGAAACATAGA+CGG - chr5_3:4817402-4817421 None:intergenic 45.0%
GGAACACACATGCATCTTAC+CGG - chr5_3:4817429-4817448 None:intergenic 45.0%
! TTTCCTACTGCCCAAGCTTT+TGG + chr5_3:4817464-4817483 Msa0792960:CDS 45.0%
GTTTGTGTCCACCAAAAGCT+TGG - chr5_3:4817478-4817497 None:intergenic 45.0%
GTCAAAGTTACTAACAGCGG+TGG + chr5_3:4817530-4817549 Msa0792960:CDS 45.0%
GGTGGAGTTACAATCTCTGA+CGG + chr5_3:4817548-4817567 Msa0792960:CDS 45.0%
! GTAAGTTGAGGTCAAAGCCA+CGG - chr5_3:4817601-4817620 None:intergenic 45.0%
! CAGAATTTAGTGAGAGGCAC+AGG - chr5_3:4817623-4817642 None:intergenic 45.0%
CTGTGCCTCTCACTAAATTC+TGG + chr5_3:4817621-4817640 Msa0792960:CDS 45.0%
TCTCACTAAATTCTGGGCTC+CGG + chr5_3:4817628-4817647 Msa0792960:CDS 45.0%
GATGAGCAAGAGGTGGAAAA+AGG + chr5_3:4817710-4817729 Msa0792960:CDS 45.0%
AGATGAGGATTTACGGTGGC+TGG - chr5_3:4817351-4817370 None:intergenic 50.0%
!! GACGGTGTTGTTAATGGTGG+TGG - chr5_3:4817384-4817403 None:intergenic 50.0%
!! CACAAACGGTGCCACTACAA+CGG + chr5_3:4817491-4817510 Msa0792960:CDS 50.0%
TGTTGTTACCGCCGTTGTAG+TGG - chr5_3:4817505-4817524 None:intergenic 50.0%
! TGAGAGGCACAGGTAAGTTG+AGG - chr5_3:4817613-4817632 None:intergenic 50.0%
GGAGCCCAGAATTTAGTGAG+AGG - chr5_3:4817629-4817648 None:intergenic 50.0%
CACCTCTTGCTCATCCATTC+CGG - chr5_3:4817705-4817724 None:intergenic 50.0%
CACATGCATCTTACCGGCGA+CGG - chr5_3:4817423-4817442 None:intergenic 55.0%
CCACCAAAAGCTTGGGCAGT+AGG - chr5_3:4817470-4817489 None:intergenic 55.0%
! CCTACTGCCCAAGCTTTTGG+TGG + chr5_3:4817467-4817486 Msa0792960:CDS 55.0%
!! AAACGGTGCCACTACAACGG+CGG + chr5_3:4817494-4817513 Msa0792960:CDS 55.0%
! GTTGATGGAAGAGGACGCGA+CGG - chr5_3:4817576-4817595 None:intergenic 55.0%
TCCTCTTCCATCAACCACCG+TGG + chr5_3:4817581-4817600 Msa0792960:CDS 55.0%
GTCAAAGCCACGGTGGTTGA+TGG - chr5_3:4817591-4817610 None:intergenic 55.0%
AGTTGAGGTCAAAGCCACGG+TGG - chr5_3:4817598-4817617 None:intergenic 55.0%
TCTCCACTGTCGAATCTCGC+CGG - chr5_3:4817650-4817669 None:intergenic 55.0%
CGGAATGGATGAGCAAGAGG+TGG + chr5_3:4817703-4817722 Msa0792960:CDS 55.0%
GTTTCCATCGCAACCGTCGC+CGG + chr5_3:4817407-4817426 Msa0792960:CDS 60.0%
!! GCCACGGTGGTTGATGGAAG+AGG - chr5_3:4817585-4817604 None:intergenic 60.0%
GGCCGGAATGGATGAGCAAG+AGG + chr5_3:4817700-4817719 Msa0792960:CDS 60.0%
CTTACCGGCGACGGTTGCGA+TGG - chr5_3:4817414-4817433 None:intergenic 65.0%
GCTCCGGCGAGATTCGACAG+TGG + chr5_3:4817644-4817663 Msa0792960:CDS 65.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 4817281 4817784 4817281 ID=Msa0792960;Name=Msa0792960
chr5_3 mRNA 4817281 4817784 4817281 ID=Msa0792960-mRNA-1;Parent=Msa0792960;Name=Msa0792960-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|-1|0|1|-1|1|1|0|167
chr5_3 exon 4817281 4817784 4817281 ID=Msa0792960-mRNA-1:exon:1864;Parent=Msa0792960-mRNA-1
chr5_3 CDS 4817281 4817784 4817281 ID=Msa0792960-mRNA-1:cds;Parent=Msa0792960-mRNA-1
Gene Sequence

>Msa0792960

CTGAATGACAGGTGCAGTGTTTGCAACCAAGCTTTTCTATCTTATCTAGCACTTGGTGGTCACAAAGCCAGCCACCGTAAATCCTCATCTGAAAACCAATCCACCACCATTAACAACACCGTCTATGTTTCCATCGCAACCGTCGCCGGTAAGATGCATGTGTGTTCCAACTGTCACAAGAGTTTTCCTACTGCCCAAGCTTTTGGTGGACACAAACGGTGCCACTACAACGGCGGTAACAACAACAACGTCAAAGTTACTAACAGCGGTGGAGTTACAATCTCTGACGGCGCCGTCGCGTCCTCTTCCATCAACCACCGTGGCTTTGACCTCAACTTACCTGTGCCTCTCACTAAATTCTGGGCTCCGGCGAGATTCGACAGTGGAGATTCCAAGAAGAACAAGGTTAATGTTAATCTGGCCGGAATGGATGAGCAAGAGGTGGAAAAAGGAAAGTTCCTTGCGTTTCTCTTCTTCAAATCTATATGTCCTTTTATTAATTAA
Protein sequence

>Msa0792960

LNDRCSVCNQAFLSYLALGGHKASHRKSSSENQSTTINNTVYVSIATVAGKMHVCSNCHKSFPTAQAFGGHKRCHYNGGNNNNVKVTNSGGVTISDGAVASSSINHRGFDLNLPVPLTKFWAPARFDSGDSKKNKVNVNLAGMDEQEVEKGKFLAFLFFKSICPFIN*