AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0394740


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394740 MtrunA17_Chr3g0080411 94.025 318 5 2 1 304 8 325 0.0 612
Msa0394740 MtrunA17_Chr3g0108541 34.810 316 173 13 2 299 10 310 6.93e-36 131
Msa0394740 MtrunA17_Chr5g0432911 32.468 308 176 11 1 299 17 301 1.17e-35 130
Msa0394740 MtrunA17_Chr8g0358861 29.167 312 190 10 1 299 1 294 9.49e-26 103
Msa0394740 MtrunA17_Chr7g0245311 28.135 327 179 10 1 298 14 313 5.83e-25 102
Msa0394740 MtrunA17_Chr8g0347761 27.240 279 172 10 30 295 34 294 1.29e-18 84.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394740 AT4G22900.1 47.077 325 135 9 7 298 12 332 3.50e-92 277
Msa0394740 AT4G11950.1 43.168 322 148 8 7 298 10 326 1.38e-80 247
Msa0394740 AT1G62981.2 41.234 308 145 13 21 299 41 341 3.63e-57 187
Msa0394740 AT1G62981.1 41.234 308 145 13 21 299 41 341 3.63e-57 187
Msa0394740 AT3G08600.1 32.082 293 157 11 26 294 37 311 2.93e-21 92.4
Msa0394740 AT4G23720.1 26.990 289 178 13 19 294 38 306 2.64e-17 81.3
Msa0394740 AT4G01140.1 27.368 285 185 11 20 297 28 297 2.26e-16 78.6
Msa0394740 AT1G62981.3 39.098 133 67 6 177 299 80 208 6.79e-11 61.2

Find 42 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCATTGACTTAGTCTTAT+TGG 0.092073 3_2:+9895632 None:intergenic
GCTAAAACTCATGGACATTT+TGG 0.170821 3_2:-9895701 Msa0394740:CDS
AGTACTATTGGTGCTGCTTT+AGG 0.264423 3_2:-9895596 Msa0394740:CDS
TTATTGTCATTGAAATTTCA+TGG 0.299770 3_2:-9896401 Msa0394740:CDS
AAGCTACCTTCAAATTTATC+AGG 0.315618 3_2:-9896269 Msa0394740:CDS
CAACTTGTTTCTCCAATTGT+TGG 0.336972 3_2:-9896050 Msa0394740:CDS
TAAGCTAAAATTCCAACAAT+TGG 0.344113 3_2:+9896038 None:intergenic
GTTGGTGTTGTTCTAGTTCC+AGG 0.353242 3_2:+9895431 None:intergenic
TTATGAAGAAGAAGCACTTC+AGG 0.366104 3_2:-9895489 Msa0394740:CDS
GCATAGAGTATAATAATAAT+TGG 0.373049 3_2:-9896115 Msa0394740:CDS
AAGGTATGGTGCAAAATTAA+AGG 0.383254 3_2:-9896204 Msa0394740:CDS
AAGGAGTTTCATCTTGGTAT+TGG 0.399934 3_2:-9896185 Msa0394740:CDS
TTTCAAGAATCAAGAAGAAA+AGG 0.407881 3_2:-9895916 Msa0394740:CDS
TTGATGCCTGATAAATTTGA+AGG 0.417038 3_2:+9896263 None:intergenic
GCTTCAATTCCAAGTTGAAA+AGG 0.422597 3_2:+9895981 None:intergenic
ACACAAACATTTGTTGCTAA+AGG 0.423104 3_2:+9895725 None:intergenic
ATTGCTGTTGGGAGTACTAT+TGG 0.428321 3_2:-9895608 Msa0394740:CDS
GCACTTCAGGTTTCAATGGT+TGG 0.434477 3_2:-9895476 Msa0394740:CDS
AGAAGCACTTCAGGTTTCAA+TGG 0.442190 3_2:-9895480 Msa0394740:CDS
GAAGGTAGCTTCACAGATTG+AGG 0.451958 3_2:+9896281 None:intergenic
CTTCAATTCCAAGTTGAAAA+GGG 0.452206 3_2:+9895982 None:intergenic
AAATTAAAGGAGTTTCATCT+TGG 0.452708 3_2:-9896191 Msa0394740:CDS
AACATTACTCTTTCAATACA+TGG 0.463603 3_2:+9896149 None:intergenic
GTCAATGGAAAATTGCTGTT+GGG 0.471587 3_2:-9895619 Msa0394740:CDS
TTTCAACTTGGAATTGAAGC+TGG 0.480245 3_2:-9895978 Msa0394740:CDS
TTAGACAAAGATTTCAAGAC+AGG 0.484697 3_2:-9896308 Msa0394740:CDS
GTTCTAGTTCCAGGTGCAGT+AGG 0.488529 3_2:+9895440 None:intergenic
TGAATGTGTAATCTCTTATG+AGG 0.490113 3_2:+9896336 None:intergenic
GGTTAAGAAAAGGTCAAGAA+TGG 0.493692 3_2:-9895531 Msa0394740:CDS
AGCCAATAAGACTAAGTCAA+TGG 0.499042 3_2:-9895634 Msa0394740:CDS
GTTTGTGTTGCTAAAACTCA+TGG 0.503467 3_2:-9895710 Msa0394740:CDS
TGTGGAAGTTTAACAAGGTA+TGG 0.509899 3_2:-9896218 Msa0394740:CDS
AGTCAATGGAAAATTGCTGT+TGG 0.510007 3_2:-9895620 Msa0394740:CDS
TTCAAGAATCAAGAAGAAAA+GGG 0.519947 3_2:-9895915 Msa0394740:intron
AAGGTCAAGAATGGTTCAGA+TGG 0.524303 3_2:-9895522 Msa0394740:CDS
TGGTTGTTAGGGTTAAGAAA+AGG 0.555158 3_2:-9895541 Msa0394740:CDS
GTGAGAGCTCCTACTGCACC+TGG 0.585262 3_2:-9895449 Msa0394740:CDS
TTAGATGTGGAAGTTTAACA+AGG 0.623871 3_2:-9896223 Msa0394740:CDS
GATACTGTGAGATTTAGATG+TGG 0.646729 3_2:-9896236 Msa0394740:CDS
TAGTCATGTTGCTCAAGTGT+TGG 0.655160 3_2:+9895413 None:intergenic
ATGTGTAATCTCTTATGAGG+AGG 0.665772 3_2:+9896339 None:intergenic
TGCAGTAAACCTTATCAACG+AGG 0.756012 3_2:+9895377 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTGTCATTGAAATTTCA+TGG - chr3_2:9895409-9895428 Msa0394740:CDS 20.0%
!! GCATAGAGTATAATAATAAT+TGG - chr3_2:9895695-9895714 Msa0394740:CDS 20.0%
!!! NNNNNAAGTTTTGAAGGAAA+TGG - chr3_2:9896037-9896056 Msa0394740:CDS 20.0%
!! TTATTGTCATTGAAATTTCA+TGG - chr3_2:9895409-9895428 Msa0394740:CDS 20.0%
!! GCATAGAGTATAATAATAAT+TGG - chr3_2:9895695-9895714 Msa0394740:CDS 20.0%
!!! NNNNNAAGTTTTGAAGGAAA+TGG - chr3_2:9896037-9896056 Msa0394740:CDS 20.0%
! AAATTAAAGGAGTTTCATCT+TGG - chr3_2:9895619-9895638 Msa0394740:CDS 25.0%
! AACATTACTCTTTCAATACA+TGG + chr3_2:9895664-9895683 None:intergenic 25.0%
! TAAGCTAAAATTCCAACAAT+TGG + chr3_2:9895775-9895794 None:intergenic 25.0%
! TTTCAAGAATCAAGAAGAAA+AGG - chr3_2:9895894-9895913 Msa0394740:intron 25.0%
! TTCAAGAATCAAGAAGAAAA+GGG - chr3_2:9895895-9895914 Msa0394740:intron 25.0%
! AAATTAAAGGAGTTTCATCT+TGG - chr3_2:9895619-9895638 Msa0394740:CDS 25.0%
! AACATTACTCTTTCAATACA+TGG + chr3_2:9895664-9895683 None:intergenic 25.0%
! TAAGCTAAAATTCCAACAAT+TGG + chr3_2:9895775-9895794 None:intergenic 25.0%
! TTTCAAGAATCAAGAAGAAA+AGG - chr3_2:9895894-9895913 Msa0394740:intron 25.0%
! TTCAAGAATCAAGAAGAAAA+GGG - chr3_2:9895895-9895914 Msa0394740:intron 25.0%
TGAATGTGTAATCTCTTATG+AGG + chr3_2:9895477-9895496 None:intergenic 30.0%
TTAGACAAAGATTTCAAGAC+AGG - chr3_2:9895502-9895521 Msa0394740:CDS 30.0%
AAGCTACCTTCAAATTTATC+AGG - chr3_2:9895541-9895560 Msa0394740:CDS 30.0%
TTGATGCCTGATAAATTTGA+AGG + chr3_2:9895550-9895569 None:intergenic 30.0%
TTAGATGTGGAAGTTTAACA+AGG - chr3_2:9895587-9895606 Msa0394740:CDS 30.0%
AAGGTATGGTGCAAAATTAA+AGG - chr3_2:9895606-9895625 Msa0394740:CDS 30.0%
! CTTCAATTCCAAGTTGAAAA+GGG + chr3_2:9895831-9895850 None:intergenic 30.0%
! ACACAAACATTTGTTGCTAA+AGG + chr3_2:9896088-9896107 None:intergenic 30.0%
!! TTCCATTGACTTAGTCTTAT+TGG + chr3_2:9896181-9896200 None:intergenic 30.0%
!!! AGGTTTACTTTTTGTAGCAA+TGG - chr3_2:9896249-9896268 Msa0394740:CDS 30.0%
! TTTTTGTAGCAATGGTTGTT+AGG - chr3_2:9896257-9896276 Msa0394740:CDS 30.0%
! TTTTGTAGCAATGGTTGTTA+GGG - chr3_2:9896258-9896277 Msa0394740:CDS 30.0%
TGAATGTGTAATCTCTTATG+AGG + chr3_2:9895477-9895496 None:intergenic 30.0%
TTAGACAAAGATTTCAAGAC+AGG - chr3_2:9895502-9895521 Msa0394740:CDS 30.0%
AAGCTACCTTCAAATTTATC+AGG - chr3_2:9895541-9895560 Msa0394740:CDS 30.0%
TTGATGCCTGATAAATTTGA+AGG + chr3_2:9895550-9895569 None:intergenic 30.0%
TTAGATGTGGAAGTTTAACA+AGG - chr3_2:9895587-9895606 Msa0394740:CDS 30.0%
AAGGTATGGTGCAAAATTAA+AGG - chr3_2:9895606-9895625 Msa0394740:CDS 30.0%
! CTTCAATTCCAAGTTGAAAA+GGG + chr3_2:9895831-9895850 None:intergenic 30.0%
! ACACAAACATTTGTTGCTAA+AGG + chr3_2:9896088-9896107 None:intergenic 30.0%
!! TTCCATTGACTTAGTCTTAT+TGG + chr3_2:9896181-9896200 None:intergenic 30.0%
!!! AGGTTTACTTTTTGTAGCAA+TGG - chr3_2:9896249-9896268 Msa0394740:CDS 30.0%
! TTTTTGTAGCAATGGTTGTT+AGG - chr3_2:9896257-9896276 Msa0394740:CDS 30.0%
! TTTTGTAGCAATGGTTGTTA+GGG - chr3_2:9896258-9896277 Msa0394740:CDS 30.0%
ATGTGTAATCTCTTATGAGG+AGG + chr3_2:9895474-9895493 None:intergenic 35.0%
GATACTGTGAGATTTAGATG+TGG - chr3_2:9895574-9895593 Msa0394740:CDS 35.0%
TGTGGAAGTTTAACAAGGTA+TGG - chr3_2:9895592-9895611 Msa0394740:CDS 35.0%
AAGGAGTTTCATCTTGGTAT+TGG - chr3_2:9895625-9895644 Msa0394740:CDS 35.0%
! CAACTTGTTTCTCCAATTGT+TGG - chr3_2:9895760-9895779 Msa0394740:CDS 35.0%
! AGTAGTAACCCTTTTCAACT+TGG - chr3_2:9895820-9895839 Msa0394740:intron 35.0%
! GCTTCAATTCCAAGTTGAAA+AGG + chr3_2:9895832-9895851 None:intergenic 35.0%
TTTCAACTTGGAATTGAAGC+TGG - chr3_2:9895832-9895851 Msa0394740:intron 35.0%
! GTTTGTGTTGCTAAAACTCA+TGG - chr3_2:9896100-9896119 Msa0394740:CDS 35.0%
! GCTAAAACTCATGGACATTT+TGG - chr3_2:9896109-9896128 Msa0394740:CDS 35.0%
!!! AACTCATGGACATTTTGGTT+TGG - chr3_2:9896114-9896133 Msa0394740:CDS 35.0%
AGCCAATAAGACTAAGTCAA+TGG - chr3_2:9896176-9896195 Msa0394740:CDS 35.0%
AGTCAATGGAAAATTGCTGT+TGG - chr3_2:9896190-9896209 Msa0394740:CDS 35.0%
! GTCAATGGAAAATTGCTGTT+GGG - chr3_2:9896191-9896210 Msa0394740:CDS 35.0%
!! GCTTTAGGTGCTTTTCTTTT+AGG - chr3_2:9896229-9896248 Msa0394740:CDS 35.0%
TGGTTGTTAGGGTTAAGAAA+AGG - chr3_2:9896269-9896288 Msa0394740:CDS 35.0%
GGTTAAGAAAAGGTCAAGAA+TGG - chr3_2:9896279-9896298 Msa0394740:CDS 35.0%
!! TTATGAAGAAGAAGCACTTC+AGG - chr3_2:9896321-9896340 Msa0394740:CDS 35.0%
ATGTGTAATCTCTTATGAGG+AGG + chr3_2:9895474-9895493 None:intergenic 35.0%
GATACTGTGAGATTTAGATG+TGG - chr3_2:9895574-9895593 Msa0394740:CDS 35.0%
TGTGGAAGTTTAACAAGGTA+TGG - chr3_2:9895592-9895611 Msa0394740:CDS 35.0%
AAGGAGTTTCATCTTGGTAT+TGG - chr3_2:9895625-9895644 Msa0394740:CDS 35.0%
! CAACTTGTTTCTCCAATTGT+TGG - chr3_2:9895760-9895779 Msa0394740:CDS 35.0%
! AGTAGTAACCCTTTTCAACT+TGG - chr3_2:9895820-9895839 Msa0394740:intron 35.0%
! GCTTCAATTCCAAGTTGAAA+AGG + chr3_2:9895832-9895851 None:intergenic 35.0%
TTTCAACTTGGAATTGAAGC+TGG - chr3_2:9895832-9895851 Msa0394740:intron 35.0%
! GTTTGTGTTGCTAAAACTCA+TGG - chr3_2:9896100-9896119 Msa0394740:CDS 35.0%
! GCTAAAACTCATGGACATTT+TGG - chr3_2:9896109-9896128 Msa0394740:CDS 35.0%
!!! AACTCATGGACATTTTGGTT+TGG - chr3_2:9896114-9896133 Msa0394740:CDS 35.0%
AGCCAATAAGACTAAGTCAA+TGG - chr3_2:9896176-9896195 Msa0394740:CDS 35.0%
AGTCAATGGAAAATTGCTGT+TGG - chr3_2:9896190-9896209 Msa0394740:CDS 35.0%
! GTCAATGGAAAATTGCTGTT+GGG - chr3_2:9896191-9896210 Msa0394740:CDS 35.0%
!! GCTTTAGGTGCTTTTCTTTT+AGG - chr3_2:9896229-9896248 Msa0394740:CDS 35.0%
TGGTTGTTAGGGTTAAGAAA+AGG - chr3_2:9896269-9896288 Msa0394740:CDS 35.0%
GGTTAAGAAAAGGTCAAGAA+TGG - chr3_2:9896279-9896298 Msa0394740:CDS 35.0%
!! TTATGAAGAAGAAGCACTTC+AGG - chr3_2:9896321-9896340 Msa0394740:CDS 35.0%
!! ATTGCTGTTGGGAGTACTAT+TGG - chr3_2:9896202-9896221 Msa0394740:CDS 40.0%
!! AGTACTATTGGTGCTGCTTT+AGG - chr3_2:9896214-9896233 Msa0394740:CDS 40.0%
AAGGTCAAGAATGGTTCAGA+TGG - chr3_2:9896288-9896307 Msa0394740:CDS 40.0%
!! AGAAGCACTTCAGGTTTCAA+TGG - chr3_2:9896330-9896349 Msa0394740:CDS 40.0%
TAGTCATGTTGCTCAAGTGT+TGG + chr3_2:9896400-9896419 None:intergenic 40.0%
!! ATTGCTGTTGGGAGTACTAT+TGG - chr3_2:9896202-9896221 Msa0394740:CDS 40.0%
!! AGTACTATTGGTGCTGCTTT+AGG - chr3_2:9896214-9896233 Msa0394740:CDS 40.0%
AAGGTCAAGAATGGTTCAGA+TGG - chr3_2:9896288-9896307 Msa0394740:CDS 40.0%
!! AGAAGCACTTCAGGTTTCAA+TGG - chr3_2:9896330-9896349 Msa0394740:CDS 40.0%
TAGTCATGTTGCTCAAGTGT+TGG + chr3_2:9896400-9896419 None:intergenic 40.0%
GAAGGTAGCTTCACAGATTG+AGG + chr3_2:9895532-9895551 None:intergenic 45.0%
! GCACTTCAGGTTTCAATGGT+TGG - chr3_2:9896334-9896353 Msa0394740:CDS 45.0%
!! GTTGGTGTTGTTCTAGTTCC+AGG + chr3_2:9896382-9896401 None:intergenic 45.0%
GAAGGTAGCTTCACAGATTG+AGG + chr3_2:9895532-9895551 None:intergenic 45.0%
! GCACTTCAGGTTTCAATGGT+TGG - chr3_2:9896334-9896353 Msa0394740:CDS 45.0%
!! GTTGGTGTTGTTCTAGTTCC+AGG + chr3_2:9896382-9896401 None:intergenic 45.0%
!! GTTCTAGTTCCAGGTGCAGT+AGG + chr3_2:9896373-9896392 None:intergenic 50.0%
!! GTTCTAGTTCCAGGTGCAGT+AGG + chr3_2:9896373-9896392 None:intergenic 50.0%
GTGAGAGCTCCTACTGCACC+TGG - chr3_2:9896361-9896380 Msa0394740:CDS 60.0%
GTGAGAGCTCCTACTGCACC+TGG - chr3_2:9896361-9896380 Msa0394740:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 9895391 9896441 9895391 ID=Msa0394740;Name=Msa0394740
chr3_2 mRNA 9895391 9896441 9895391 ID=Msa0394740-mRNA-1;Parent=Msa0394740;Name=Msa0394740-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|304
chr3_2 exon 9895916 9896441 9895916 ID=Msa0394740-mRNA-1:exon:2607;Parent=Msa0394740-mRNA-1
chr3_2 exon 9895391 9895779 9895391 ID=Msa0394740-mRNA-1:exon:2606;Parent=Msa0394740-mRNA-1
chr3_2 CDS 9895916 9896441 9895916 ID=Msa0394740-mRNA-1:cds;Parent=Msa0394740-mRNA-1
chr3_2 CDS 9895391 9895779 9895391 ID=Msa0394740-mRNA-1:cds;Parent=Msa0394740-mRNA-1
Gene Sequence

>Msa0394740

ATGTTGATGACACTTTCATTATTGTCATTGAAATTTCATGGATCTTATGCTCAGAATATCAAATCAGTTCATGTTCTTGACCTCCTCATAAGAGATTACACATTCAAGTCATTAGACAAAGATTTCAAGACAGGAATACCTCAATCTGTGAAGCTACCTTCAAATTTATCAGGCATCAAAGTAGATACTGTGAGATTTAGATGTGGAAGTTTAACAAGGTATGGTGCAAAATTAAAGGAGTTTCATCTTGGTATTGGTGTTTCTATTCATCCATGTATTGAAAGAGTAATGTTGATAAGACAAAGCATAGAGTATAATAATAATTGGTCTTCTATATATTATGCAAACTATAATGATCTATCTAAGTATCAACTTGTTTCTCCAATTGTTGGAATTTTAGCTTACAATGCTGATGAAGATTCAAATTCTAGTAGTAACCCTTTTCAACTTGGAATTGAAGCTGGTGAAAAACTCATCACAATTGATTTCAACAATGCTACAAATTTCAAGAATCAAGAAGAAAAGGGAAATGGAAAAATGACACTTGCAATAACAAAACCTTTAGCAACAAATGTTTGTGTTGCTAAAACTCATGGACATTTTGGTTTGGTTGTTGAGTCTTTACAACATCAAGATGATGAGTATAAAAAGCCAATAAGACTAAGTCAATGGAAAATTGCTGTTGGGAGTACTATTGGTGCTGCTTTAGGTGCTTTTCTTTTAGGTTTACTTTTTGTAGCAATGGTTGTTAGGGTTAAGAAAAGGTCAAGAATGGTTCAGATGGAAAGAAGAGCTTATGAAGAAGAAGCACTTCAGGTTTCAATGGTTGGACATGTGAGAGCTCCTACTGCACCTGGAACTAGAACAACACCAACACTTGAGCAACATGACTATATAACTCGACATCCTCGTTGA

Protein sequence

>Msa0394740

MLMTLSLLSLKFHGSYAQNIKSVHVLDLLIRDYTFKSLDKDFKTGIPQSVKLPSNLSGIKVDTVRFRCGSLTRYGAKLKEFHLGIGVSIHPCIERVMLIRQSIEYNNNWSSIYYANYNDLSKYQLVSPIVGILAYNADEDSNSSSNPFQLGIEAGEKLITIDFNNATNFKNQEEKGNGKMTLAITKPLATNVCVAKTHGHFGLVVESLQHQDDEYKKPIRLSQWKIAVGSTIGAALGAFLLGLLFVAMVVRVKKRSRMVQMERRAYEEEALQVSMVGHVRAPTAPGTRTTPTLEQHDYITRHPR*