AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1244460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1244460 MtrunA17_Chr2g0296781 94.783 230 12 0 1 230 348 577 1.33e-158 456
Msa1244460 MtrunA17_Chr6g0477261 91.739 230 19 0 1 230 237 466 2.49e-154 443
Msa1244460 MtrunA17_Chr1g0196541 73.568 227 60 0 1 227 348 574 2.00e-109 330
Msa1244460 MtrunA17_Chr5g0441581 49.302 215 108 1 2 216 377 590 4.20e-66 216
Msa1244460 MtrunA17_Chr6g0476441 91.463 82 7 0 149 230 1 82 5.53e-49 162
Msa1244460 MtrunA17_Chr1g0207551 41.784 213 113 4 1 211 388 591 1.45e-43 155
Msa1244460 MtrunA17_Chr2g0291581 36.792 212 131 2 1 210 412 622 1.40e-41 149
Msa1244460 MtrunA17_Chr3g0080351 37.915 211 124 2 1 211 422 625 1.09e-40 147
Msa1244460 MtrunA17_Chr5g0448761 37.850 214 127 3 1 214 423 630 3.76e-39 143
Msa1244460 MtrunA17_Chr5g0440451 37.500 232 133 5 1 230 404 625 4.50e-39 143
Msa1244460 MtrunA17_Chr3g0118611 37.321 209 123 3 1 209 301 501 7.38e-35 131
Msa1244460 MtrunA17_Chr2g0329031 33.645 214 134 3 1 214 361 566 2.64e-34 129
Msa1244460 MtrunA17_Chr1g0202341 36.792 212 124 5 1 210 407 610 5.52e-34 128
Msa1244460 MtrunA17_Chr5g0448511 32.536 209 135 3 1 209 195 397 8.16e-31 119
Msa1244460 MtrunA17_Chr2g0287061 33.493 209 123 5 5 209 505 701 8.58e-23 96.3
Msa1244460 MtrunA17_Chr2g0276841 30.047 213 124 8 1 206 432 626 1.59e-19 87.0
Msa1244460 MtrunA17_Chr2g0291591 31.655 139 95 0 1 139 415 553 5.72e-18 82.4
Msa1244460 MtrunA17_Chr1g0198761 30.213 235 146 7 1 229 414 636 7.83e-18 82.0
Msa1244460 MtrunA17_Chr2g0287651 28.505 214 138 6 1 209 429 632 9.98e-18 81.6
Msa1244460 MtrunA17_Chr8g0363841 27.556 225 127 6 1 209 373 577 1.67e-17 80.9
Msa1244460 MtrunA17_Chr1g0203051 28.141 199 121 4 1 190 431 616 1.07e-16 78.6
Msa1244460 MtrunA17_Chr3g0082121 30.583 206 131 6 5 209 396 590 9.70e-16 75.9
Msa1244460 MtrunA17_Chr1g0172041 35.417 96 61 1 121 216 1 95 7.84e-15 68.6
Msa1244460 MtrunA17_Chr2g0324011 24.299 214 146 4 1 209 366 568 8.49e-15 73.2
Msa1244460 MtrunA17_Chr2g0308841 27.830 212 136 5 1 206 24 224 2.98e-14 70.1
Msa1244460 MtrunA17_Chr6g0458391 25.592 211 146 4 1 209 564 765 3.24e-14 71.2
Msa1244460 MtrunA17_Chr2g0290391 27.753 227 141 8 1 225 421 626 7.45e-14 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1244460 AT4G15090.1 38.288 222 129 3 1 222 408 621 1.40e-42 153
Msa1244460 AT4G15090.5 38.288 222 129 3 1 222 408 621 1.40e-42 153
Msa1244460 AT4G15090.3 38.288 222 129 3 1 222 408 621 1.40e-42 153
Msa1244460 AT4G15090.2 38.288 222 129 3 1 222 408 621 1.40e-42 153
Msa1244460 AT4G15090.4 38.288 222 129 3 1 222 408 621 1.40e-42 153
Msa1244460 AT3G22170.2 38.942 208 120 3 5 212 421 621 3.32e-41 149
Msa1244460 AT3G22170.1 38.942 208 120 3 5 212 421 621 3.32e-41 149
Msa1244460 AT4G38180.1 36.364 209 127 3 1 209 432 634 5.86e-38 140
Msa1244460 AT1G52520.1 36.406 217 126 7 1 210 428 639 1.63e-37 139
Msa1244460 AT4G19990.1 34.579 214 135 2 1 214 299 507 7.28e-35 131
Msa1244460 AT4G19990.3 34.579 214 135 2 1 214 356 564 8.01e-35 131
Msa1244460 AT4G19990.4 34.579 214 135 2 1 214 356 564 8.01e-35 131
Msa1244460 AT4G19990.5 34.579 214 135 2 1 214 356 564 8.15e-35 131
Msa1244460 AT4G19990.7 34.579 214 135 2 1 214 370 578 8.56e-35 131
Msa1244460 AT4G19990.6 34.579 214 135 2 1 214 356 564 9.71e-35 131
Msa1244460 AT4G19990.2 34.579 214 135 2 1 214 356 564 9.71e-35 131
Msa1244460 AT1G76320.3 34.667 225 132 4 1 219 345 560 7.08e-34 128
Msa1244460 AT1G76320.2 34.667 225 132 4 1 219 345 560 7.48e-34 128
Msa1244460 AT1G76320.1 34.667 225 132 4 1 219 345 560 7.57e-34 128
Msa1244460 AT1G76320.4 34.667 225 132 4 1 219 345 560 7.57e-34 128
Msa1244460 AT4G38170.1 30.986 213 141 2 1 213 197 403 5.98e-31 119
Msa1244460 AT1G80010.1 32.189 233 149 6 1 229 453 680 6.25e-29 114
Msa1244460 AT2G32250.5 33.495 206 130 2 1 206 352 550 1.06e-28 114
Msa1244460 AT2G32250.2 33.495 206 130 2 1 206 352 550 1.10e-28 114
Msa1244460 AT2G32250.4 33.495 206 130 2 1 206 352 550 1.10e-28 114
Msa1244460 AT2G32250.6 33.495 206 130 2 1 206 352 550 1.15e-28 114
Msa1244460 AT2G32250.1 33.495 206 130 2 1 206 352 550 1.15e-28 114
Msa1244460 AT2G32250.3 33.495 206 130 2 1 206 352 550 1.15e-28 114
Msa1244460 AT2G32250.8 33.495 206 130 2 1 206 311 509 1.18e-28 114
Msa1244460 AT2G32250.7 33.495 206 130 2 1 206 311 509 1.28e-28 113
Msa1244460 AT2G27110.3 34.597 211 126 6 1 209 234 434 8.83e-28 111
Msa1244460 AT2G27110.2 34.597 211 126 6 1 209 379 579 1.27e-27 110
Msa1244460 AT2G27110.1 34.597 211 126 6 1 209 379 579 1.27e-27 110
Msa1244460 AT5G18960.2 31.905 210 132 5 1 209 529 728 7.60e-24 99.8
Msa1244460 AT5G18960.1 31.905 210 132 5 1 209 529 728 7.60e-24 99.8
Msa1244460 AT3G06250.2 30.144 209 137 3 1 209 505 704 2.61e-23 98.2
Msa1244460 AT3G06250.1 30.144 209 137 3 1 209 505 704 2.61e-23 98.2
Msa1244460 AT3G06250.3 30.144 209 137 3 1 209 505 704 2.61e-23 98.2
Msa1244460 AT1G10240.2 30.516 213 123 8 1 206 410 604 1.03e-20 90.9
Msa1244460 AT1G10240.1 30.516 213 123 8 1 206 410 604 1.03e-20 90.9

Find 36 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCTTGTTTGAATTTAA+AGG 0.112904 8_2:+32881580 Msa1244460:CDS
CATATGTAAGGGACACATTT+TGG 0.131035 8_2:+32881152 Msa1244460:CDS
ATTTACCAATGCAAAGTTTA+AGG 0.141446 8_2:+32881387 Msa1244460:CDS
TGTGCCATCTAATTATATTT+TGG 0.166070 8_2:+32881657 Msa1244460:CDS
TTAAACTTTGCATTGGTAAA+TGG 0.204335 8_2:-32881385 None:intergenic
TAAATGTGGTGTTGATAATT+TGG 0.259658 8_2:+32881720 Msa1244460:CDS
TTTCAACAGATTGGAGGATT+TGG 0.276962 8_2:+32881453 Msa1244460:CDS
CTTTGTGTGCTTAAGCTCAT+AGG 0.292164 8_2:+32881622 Msa1244460:CDS
GATGAAAGATATTGTGTTCA+TGG 0.400462 8_2:+32881519 Msa1244460:CDS
TCATGCATGTTTCAACAGAT+TGG 0.428105 8_2:+32881444 Msa1244460:CDS
ATTTGTTGAGCGACATCGTT+GGG 0.428935 8_2:+32881123 Msa1244460:CDS
CGTGCCAAAATATAATTAGA+TGG 0.452638 8_2:-32881661 None:intergenic
ATTTCTTGTATTAGTCACTT+TGG 0.452992 8_2:+32881340 Msa1244460:CDS
GTTGGGTCCCTGCATATGTA+AGG 0.456247 8_2:+32881140 Msa1244460:CDS
AAAGTTTAAGGAATTCCAAT+TGG 0.460527 8_2:+32881399 Msa1244460:CDS
TCATAGAAGCTATTTCCAAT+TGG 0.475525 8_2:-32881414 None:intergenic
AATGTGTCCCTTACATATGC+AGG 0.477892 8_2:-32881148 None:intergenic
TTTGTGTGCTTAAGCTCATA+GGG 0.489887 8_2:+32881623 Msa1244460:CDS
TTTAAATTCAAACAAGCAGC+AGG 0.496973 8_2:-32881578 None:intergenic
ATTGAAAGATAAAATTGAAA+AGG 0.501824 8_2:+32881282 Msa1244460:CDS
GAATTCCTTAAACTTTGCAT+TGG 0.503666 8_2:-32881392 None:intergenic
AGGATAGCGAATGGCTGAAA+GGG 0.505592 8_2:+32881098 Msa1244460:CDS
TGCATGTTTCAACAGATTGG+AGG 0.514840 8_2:+32881447 Msa1244460:CDS
CAGGATAGCGAATGGCTGAA+AGG 0.529566 8_2:+32881097 Msa1244460:CDS
GATTGAGTGTTACAAACTAC+AGG 0.556519 8_2:+32881078 Msa1244460:CDS
TATCAACACCACATTTAACA+AGG 0.590139 8_2:-32881714 None:intergenic
TATTTGTTGAGCGACATCGT+TGG 0.591607 8_2:+32881122 Msa1244460:CDS
TTGGGTCCCTGCATATGTAA+GGG 0.619298 8_2:+32881141 Msa1244460:CDS
ATGTGTCCCTTACATATGCA+GGG 0.621051 8_2:-32881147 None:intergenic
AGGTATACCCTTGTTAAATG+TGG 0.622387 8_2:+32881706 Msa1244460:CDS
ATCAACACCACATTTAACAA+GGG 0.638905 8_2:-32881713 None:intergenic
ACAAACTACAGGATAGCGAA+TGG 0.662045 8_2:+32881089 Msa1244460:CDS
CTATGAGCTTAAGCACACAA+AGG 0.703144 8_2:-32881621 None:intergenic
GGTGGAGGAAGGATATAAAG+CGG 0.707303 8_2:+32881683 Msa1244460:CDS
GGAGGAAGGATATAAAGCGG+AGG 0.711941 8_2:+32881686 Msa1244460:CDS
TTTATGAATTTGCTTCAACG+AGG 0.719121 8_2:+32881745 Msa1244460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGAAAGATAAAATTGAAA+AGG + chr8_2:32881282-32881301 Msa1244460:CDS 15.0%
!!! AATTTAAAGGCATTTTATGT+AGG + chr8_2:32881593-32881612 Msa1244460:CDS 20.0%
!!! AGTATGAACTCATTTTTTGA+TGG + chr8_2:32881205-32881224 Msa1244460:CDS 25.0%
! ATTTCTTGTATTAGTCACTT+TGG + chr8_2:32881340-32881359 Msa1244460:CDS 25.0%
!! TTAAACTTTGCATTGGTAAA+TGG - chr8_2:32881388-32881407 None:intergenic 25.0%
! ATTTACCAATGCAAAGTTTA+AGG + chr8_2:32881387-32881406 Msa1244460:CDS 25.0%
! AAAGTTTAAGGAATTCCAAT+TGG + chr8_2:32881399-32881418 Msa1244460:CDS 25.0%
!! TGTGCCATCTAATTATATTT+TGG + chr8_2:32881657-32881676 Msa1244460:CDS 25.0%
!!! CATCTAATTATATTTTGGCA+CGG + chr8_2:32881662-32881681 Msa1244460:CDS 25.0%
!!! TAAATGTGGTGTTGATAATT+TGG + chr8_2:32881720-32881739 Msa1244460:CDS 25.0%
! ATATGTAAGGGACACATTTT+GGG + chr8_2:32881153-32881172 Msa1244460:CDS 30.0%
!!! TGGTAAATGGTTTTTGGAAT+TGG - chr8_2:32881375-32881394 None:intergenic 30.0%
!! TTGCATTGGTAAATGGTTTT+TGG - chr8_2:32881381-32881400 None:intergenic 30.0%
GAATTCCTTAAACTTTGCAT+TGG - chr8_2:32881395-32881414 None:intergenic 30.0%
! TCATAGAAGCTATTTCCAAT+TGG - chr8_2:32881417-32881436 None:intergenic 30.0%
GATGAAAGATATTGTGTTCA+TGG + chr8_2:32881519-32881538 Msa1244460:CDS 30.0%
TTTAAATTCAAACAAGCAGC+AGG - chr8_2:32881581-32881600 None:intergenic 30.0%
! TGCTGCTTGTTTGAATTTAA+AGG + chr8_2:32881580-32881599 Msa1244460:CDS 30.0%
CGTGCCAAAATATAATTAGA+TGG - chr8_2:32881664-32881683 None:intergenic 30.0%
ATCAACACCACATTTAACAA+GGG - chr8_2:32881716-32881735 None:intergenic 30.0%
TATCAACACCACATTTAACA+AGG - chr8_2:32881717-32881736 None:intergenic 30.0%
! TTTATGAATTTGCTTCAACG+AGG + chr8_2:32881745-32881764 Msa1244460:CDS 30.0%
GATTGAGTGTTACAAACTAC+AGG + chr8_2:32881078-32881097 Msa1244460:CDS 35.0%
! CATATGTAAGGGACACATTT+TGG + chr8_2:32881152-32881171 Msa1244460:CDS 35.0%
TCATGCATGTTTCAACAGAT+TGG + chr8_2:32881444-32881463 Msa1244460:CDS 35.0%
TTTCAACAGATTGGAGGATT+TGG + chr8_2:32881453-32881472 Msa1244460:CDS 35.0%
TTTGTGTGCTTAAGCTCATA+GGG + chr8_2:32881623-32881642 Msa1244460:CDS 35.0%
!!! CTAATTATATTTTGGCACGG+TGG + chr8_2:32881665-32881684 Msa1244460:CDS 35.0%
AGGTATACCCTTGTTAAATG+TGG + chr8_2:32881706-32881725 Msa1244460:CDS 35.0%
ACAAACTACAGGATAGCGAA+TGG + chr8_2:32881089-32881108 Msa1244460:CDS 40.0%
! TATTTGTTGAGCGACATCGT+TGG + chr8_2:32881122-32881141 Msa1244460:CDS 40.0%
! ATTTGTTGAGCGACATCGTT+GGG + chr8_2:32881123-32881142 Msa1244460:CDS 40.0%
ATGTGTCCCTTACATATGCA+GGG - chr8_2:32881150-32881169 None:intergenic 40.0%
AATGTGTCCCTTACATATGC+AGG - chr8_2:32881151-32881170 None:intergenic 40.0%
TGCATGTTTCAACAGATTGG+AGG + chr8_2:32881447-32881466 Msa1244460:CDS 40.0%
CTATGAGCTTAAGCACACAA+AGG - chr8_2:32881624-32881643 None:intergenic 40.0%
CTTTGTGTGCTTAAGCTCAT+AGG + chr8_2:32881622-32881641 Msa1244460:CDS 40.0%
!!! ATTATATTTTGGCACGGTGG+AGG + chr8_2:32881668-32881687 Msa1244460:CDS 40.0%
AGGATAGCGAATGGCTGAAA+GGG + chr8_2:32881098-32881117 Msa1244460:CDS 45.0%
TTGGGTCCCTGCATATGTAA+GGG + chr8_2:32881141-32881160 Msa1244460:CDS 45.0%
GGTGGAGGAAGGATATAAAG+CGG + chr8_2:32881683-32881702 Msa1244460:CDS 45.0%
CAGGATAGCGAATGGCTGAA+AGG + chr8_2:32881097-32881116 Msa1244460:CDS 50.0%
GTTGGGTCCCTGCATATGTA+AGG + chr8_2:32881140-32881159 Msa1244460:CDS 50.0%
! GTAAGGGACACATTTTGGGC+TGG + chr8_2:32881157-32881176 Msa1244460:CDS 50.0%
!!! TATTTTGGCACGGTGGAGGA+AGG + chr8_2:32881672-32881691 Msa1244460:CDS 50.0%
GGAGGAAGGATATAAAGCGG+AGG + chr8_2:32881686-32881705 Msa1244460:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 32881076 32881771 32881076 ID=Msa1244460;Name=Msa1244460
chr8_2 mRNA 32881076 32881771 32881076 ID=Msa1244460-mRNA-1;Parent=Msa1244460;Name=Msa1244460-mRNA-1;_AED=0.95;_eAED=0.95;_QI=0|-1|0|1|-1|1|1|0|231
chr8_2 exon 32881076 32881771 32881076 ID=Msa1244460-mRNA-1:exon:10691;Parent=Msa1244460-mRNA-1
chr8_2 CDS 32881076 32881771 32881076 ID=Msa1244460-mRNA-1:cds;Parent=Msa1244460-mRNA-1
Gene Sequence

>Msa1244460

ATGATTGAGTGTTACAAACTACAGGATAGCGAATGGCTGAAAGGGTTATTTGTTGAGCGACATCGTTGGGTCCCTGCATATGTAAGGGACACATTTTGGGCTGGAATGTCAACTACACAACGAAGTGAAAGTATGAACTCATTTTTTGATGGATATGTAAGCTCAAAGACAACATTGAAGCAATTTGTTGAGCAATATGATAATGCATTGAAAGATAAAATTGAAAAGGAAAACATTGCTGACTTTCGTTCTTTTAATACAGTCATTTCTTGTATTAGTCACTTTGGATTTGAGTTCCAATTCCAAAAACCATTTACCAATGCAAAGTTTAAGGAATTCCAATTGGAAATAGCTTCTATGATGTACTGTCATGCATGTTTCAACAGATTGGAGGATTTGGATTCAATATTTTATGTTACAGAAAGTAAGAAAGTATATGACAAGATGAAAGATATTGTGTTCATGGTGTTCTTCAATGAAAAAGACTTTGTGTTGAAATGCACCTGCTGCTTGTTTGAATTTAAAGGCATTTTATGTAGGCACATCCTTTGTGTGCTTAAGCTCATAGGGAAAACAGATTTTGTGCCATCTAATTATATTTTGGCACGGTGGAGGAAGGATATAAAGCGGAGGTATACCCTTGTTAAATGTGGTGTTGATAATTTGGCTTTTATGAATTTGCTTCAACGAGGATAA

Protein sequence

>Msa1244460

MIECYKLQDSEWLKGLFVERHRWVPAYVRDTFWAGMSTTQRSESMNSFFDGYVSSKTTLKQFVEQYDNALKDKIEKENIADFRSFNTVISCISHFGFEFQFQKPFTNAKFKEFQLEIASMMYCHACFNRLEDLDSIFYVTESKKVYDKMKDIVFMVFFNEKDFVLKCTCCLFEFKGILCRHILCVLKLIGKTDFVPSNYILARWRKDIKRRYTLVKCGVDNLAFMNLLQRG*