AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1178660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1178660 MtrunA17_Chr8g0343661 61.538 65 25 0 1 65 88 152 6.24e-23 90.1
Msa1178660 MtrunA17_Chr4g0005331 64.615 65 23 0 1 65 445 509 1.05e-22 89.4
Msa1178660 MtrunA17_Chr4g0005401 52.113 71 34 0 1 71 386 456 1.72e-19 80.5
Msa1178660 MtrunA17_Chr4g0005291 58.462 65 27 0 1 65 431 495 2.67e-19 79.7
Msa1178660 MtrunA17_Chr4g0005391 58.462 65 27 0 1 65 421 485 7.59e-19 78.6
Msa1178660 MtrunA17_Chr4g0005371 55.385 65 29 0 1 65 161 225 2.71e-18 75.9
Msa1178660 MtrunA17_Chr4g0005101 53.846 65 30 0 1 65 415 479 3.02e-18 76.6
Msa1178660 MtrunA17_Chr2g0330121 52.857 70 33 0 1 70 197 266 3.93e-18 76.6
Msa1178660 MtrunA17_Chr4g0005261 49.296 71 36 0 1 71 371 441 2.34e-17 74.3
Msa1178660 MtrunA17_Chr3g0118981 50.000 64 32 0 2 65 385 448 2.71e-17 73.9
Msa1178660 MtrunA17_Chr4g0018431 46.269 67 36 0 2 68 383 449 6.59e-16 70.1
Msa1178660 MtrunA17_Chr8g0342131 46.377 69 37 0 2 70 385 453 8.67e-16 69.7
Msa1178660 MtrunA17_Chr3g0102121 44.286 70 39 0 1 70 382 451 8.99e-16 69.7
Msa1178660 MtrunA17_Chr3g0102171 46.154 65 35 0 1 65 382 446 1.19e-15 69.3
Msa1178660 MtrunA17_Chr3g0102261 42.857 70 40 0 1 70 382 451 1.98e-15 68.9
Msa1178660 MtrunA17_Chr3g0102271 44.615 65 36 0 1 65 383 447 2.02e-15 68.9
Msa1178660 MtrunA17_Chr2g0298291 46.875 64 34 0 2 65 377 440 2.14e-15 68.6
Msa1178660 MtrunA17_Chr4g0005731 50.000 72 35 1 1 71 368 439 4.95e-15 67.8
Msa1178660 MtrunA17_Chr3g0102281 44.615 65 36 0 1 65 382 446 5.11e-15 67.8
Msa1178660 MtrunA17_Chr7g0248121 47.887 71 37 0 1 71 382 452 6.03e-15 67.4
Msa1178660 MtrunA17_Chr4g0020591 47.692 65 34 0 1 65 379 443 6.66e-15 67.4
Msa1178660 MtrunA17_Chr3g0119001 46.032 63 34 0 2 64 385 447 8.16e-15 67.0
Msa1178660 MtrunA17_Chr3g0102131 42.857 70 40 0 1 70 382 451 9.54e-15 67.0
Msa1178660 MtrunA17_Chr7g0248511 40.845 71 42 0 1 71 388 458 2.90e-14 65.5
Msa1178660 MtrunA17_Chr2g0299921 46.875 64 34 0 2 65 380 443 2.93e-14 65.5
Msa1178660 MtrunA17_Chr8g0348541 42.254 71 41 0 1 71 387 457 3.02e-14 65.5
Msa1178660 MtrunA17_Chr8g0350071 45.714 70 38 0 1 70 160 229 3.22e-14 65.1
Msa1178660 MtrunA17_Chr2g0299851 46.875 64 34 0 2 65 381 444 3.72e-14 65.1
Msa1178660 MtrunA17_Chr8g0343611 53.846 65 30 0 1 65 211 275 3.73e-14 65.1
Msa1178660 MtrunA17_Chr7g0248521 42.254 71 41 0 1 71 381 451 4.68e-14 65.1
Msa1178660 MtrunA17_Chr6g0481011 42.029 69 40 0 2 70 392 460 1.00e-13 63.9
Msa1178660 MtrunA17_Chr6g0479631 41.429 70 41 0 2 71 384 453 1.11e-13 63.9
Msa1178660 MtrunA17_Chr1g0172811 49.275 69 35 0 2 70 381 449 1.31e-13 63.5
Msa1178660 MtrunA17_Chr8g0342201 42.029 69 40 0 2 70 418 486 1.39e-13 63.5
Msa1178660 MtrunA17_Chr8g0353001 44.928 69 38 0 2 70 381 449 1.46e-13 63.5
Msa1178660 MtrunA17_Chr8g0343671 52.308 65 31 0 1 65 419 483 1.52e-13 63.5
Msa1178660 MtrunA17_Chr8g0392051 47.143 70 37 0 1 70 156 225 1.86e-13 63.2
Msa1178660 MtrunA17_Chr2g0298531 43.750 64 36 0 2 65 382 445 2.51e-13 62.8
Msa1178660 MtrunA17_Chr2g0299791 45.312 64 35 0 2 65 382 445 2.75e-13 62.8
Msa1178660 MtrunA17_Chr6g0479641 40.000 70 42 0 2 71 386 455 2.90e-13 62.8
Msa1178660 MtrunA17_Chr6g0479761 38.571 70 43 0 2 71 241 310 3.05e-13 62.8
Msa1178660 MtrunA17_Chr6g0481001 40.580 69 41 0 2 70 389 457 3.20e-13 62.4
Msa1178660 MtrunA17_Chr6g0479621 38.571 70 43 0 2 71 387 456 3.27e-13 62.4
Msa1178660 MtrunA17_Chr8g0343581 49.231 65 33 0 1 65 426 490 3.30e-13 62.4
Msa1178660 MtrunA17_Chr8g0343631 50.769 65 32 0 1 65 396 460 3.93e-13 62.4
Msa1178660 MtrunA17_Chr6g0480311 40.000 70 42 0 2 71 373 442 4.48e-13 62.0
Msa1178660 MtrunA17_Chr6g0486221 47.692 65 34 0 1 65 386 450 5.55e-13 62.0
Msa1178660 MtrunA17_Chr2g0299811 43.750 64 36 0 2 65 229 292 5.83e-13 61.6
Msa1178660 MtrunA17_Chr2g0299881 45.312 64 35 0 2 65 386 449 6.26e-13 61.6
Msa1178660 MtrunA17_Chr3g0084841 44.615 65 36 0 1 65 386 450 6.79e-13 61.6
Msa1178660 MtrunA17_Chr8g0368251 40.000 70 42 0 2 71 385 454 7.20e-13 61.6
Msa1178660 MtrunA17_Chr3g0084731 46.875 64 34 0 2 65 384 447 7.55e-13 61.6
Msa1178660 MtrunA17_Chr2g0299841 46.875 64 34 0 2 65 423 486 7.94e-13 61.2
Msa1178660 MtrunA17_Chr6g0481251 38.571 70 43 0 2 71 242 311 8.90e-13 61.2
Msa1178660 MtrunA17_Chr8g0372681 41.429 70 41 0 1 70 379 448 9.61e-13 61.2
Msa1178660 MtrunA17_Chr6g0482111 44.286 70 39 0 1 70 382 451 9.71e-13 61.2
Msa1178660 MtrunA17_Chr6g0481221 38.571 70 43 0 2 71 385 454 1.08e-12 60.8
Msa1178660 MtrunA17_Chr6g0479591 40.000 70 42 0 2 71 411 480 1.29e-12 60.8
Msa1178660 MtrunA17_Chr8g0342911 44.928 69 38 0 2 70 394 462 1.38e-12 60.8
Msa1178660 MtrunA17_Chr6g0481141 38.571 70 43 0 2 71 436 505 1.56e-12 60.5
Msa1178660 MtrunA17_Chr6g0480461 40.580 69 41 0 2 70 436 504 1.60e-12 60.5
Msa1178660 MtrunA17_Chr4g0041241 43.478 69 39 0 2 70 387 455 1.70e-12 60.5
Msa1178660 MtrunA17_Chr3g0081531 42.857 70 40 0 1 70 373 442 1.73e-12 60.5
Msa1178660 MtrunA17_Chr8g0353371 45.455 66 36 0 5 70 397 462 2.01e-12 60.5
Msa1178660 MtrunA17_Chr6g0479671 37.500 64 40 0 2 65 385 448 2.01e-12 60.5
Msa1178660 MtrunA17_Chr4g0009401 42.424 66 38 0 1 66 370 435 2.25e-12 60.1
Msa1178660 MtrunA17_Chr3g0084851 44.615 65 36 0 1 65 385 449 2.59e-12 60.1
Msa1178660 MtrunA17_Chr6g0481191 39.130 69 42 0 2 70 75 143 2.84e-12 59.7
Msa1178660 MtrunA17_Chr6g0479731 39.130 69 42 0 2 70 383 451 3.24e-12 59.7
Msa1178660 MtrunA17_Chr6g0484161 40.000 70 42 0 2 71 409 478 3.50e-12 59.7
Msa1178660 MtrunA17_Chr8g0342641 47.692 65 34 0 2 66 361 425 3.51e-12 59.7
Msa1178660 MtrunA17_Chr1g0146421 40.580 69 41 0 2 70 385 453 4.01e-12 59.3
Msa1178660 MtrunA17_Chr6g0480321 39.130 69 42 0 2 70 243 311 4.68e-12 59.3
Msa1178660 MtrunA17_Chr6g0480911 42.188 64 37 0 2 65 387 450 9.97e-12 58.2
Msa1178660 MtrunA17_Chr6g0482511 39.130 69 42 0 2 70 400 468 1.38e-11 57.8
Msa1178660 MtrunA17_Chr4g0041441 43.077 65 37 0 1 65 369 433 1.40e-11 57.8
Msa1178660 MtrunA17_Chr6g0479651 37.143 70 44 0 2 71 389 458 1.58e-11 57.8
Msa1178660 MtrunA17_Chr3g0114401 41.791 67 38 1 1 66 256 322 1.95e-11 57.4
Msa1178660 MtrunA17_Chr4g0006771 38.571 70 43 0 1 70 390 459 3.18e-11 57.0
Msa1178660 MtrunA17_Chr8g0354721 39.062 64 39 0 2 65 378 441 4.57e-11 56.6
Msa1178660 MtrunA17_Chr2g0296461 43.284 67 37 1 1 66 162 228 4.57e-11 55.8
Msa1178660 MtrunA17_Chr6g0480521 37.500 64 40 0 2 65 386 449 4.62e-11 56.2
Msa1178660 MtrunA17_Chr6g0486271 42.647 68 39 0 1 68 386 453 4.94e-11 56.2
Msa1178660 MtrunA17_Chr8g0371711 40.625 64 38 0 2 65 385 448 4.95e-11 56.2
Msa1178660 MtrunA17_Chr6g0480151 36.620 71 45 0 1 71 384 454 5.70e-11 56.2
Msa1178660 MtrunA17_Chr6g0485991 43.077 65 37 0 1 65 386 450 6.57e-11 55.8
Msa1178660 MtrunA17_Chr6g0480421 40.580 69 41 0 2 70 243 311 6.68e-11 55.8
Msa1178660 MtrunA17_Chr6g0480451 36.232 69 44 0 2 70 450 518 7.05e-11 55.8
Msa1178660 MtrunA17_Chr6g0486311 43.077 65 37 0 1 65 386 450 7.56e-11 55.8
Msa1178660 MtrunA17_Chr8g0338981 41.538 65 37 1 1 64 373 437 8.16e-11 55.8
Msa1178660 MtrunA17_Chr5g0417071 35.211 71 46 0 1 71 125 195 9.52e-11 55.5
Msa1178660 MtrunA17_Chr6g0486481 43.077 65 37 0 1 65 386 450 9.93e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1178660 AT5G45060.2 43.056 72 40 1 1 71 405 476 2.85e-13 63.2
Msa1178660 AT5G45060.1 43.056 72 40 1 1 71 405 476 2.85e-13 63.2
Msa1178660 AT4G36150.1 41.538 65 38 0 1 65 402 466 3.64e-13 62.8
Msa1178660 AT5G44870.1 42.857 70 38 1 2 69 443 512 7.38e-12 58.9
Msa1178660 AT2G17060.1 38.462 65 40 0 2 66 408 472 8.80e-12 58.9
Msa1178660 AT2G17060.2 38.462 65 40 0 2 66 408 472 9.59e-12 58.9
Msa1178660 AT5G44870.2 42.254 71 39 1 1 69 178 248 1.03e-11 58.5
Msa1178660 AT5G17890.1 42.857 70 39 1 1 70 356 424 1.59e-11 58.2

Find 7 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACTAGTTCTTGAAGTTT+TGG 0.201475 8_1:+11557640 Msa1178660:CDS
TAACAAAAGTACCAATTAAA+AGG 0.220459 8_1:+11557717 Msa1178660:CDS
AACAAAAGTACCAATTAAAA+GGG 0.494203 8_1:+11557718 Msa1178660:CDS
ATCTTGATCGTCACGAGAAG+AGG 0.499108 8_1:+11557771 Msa1178660:CDS
CCCAAAACTTCAAGAACTAG+TGG 0.546860 8_1:-11557641 None:intergenic
AAGATGGTCAATTATGCTGA+TGG 0.591798 8_1:+11557614 None:intergenic
AGATATGCAGTTAAATCCAA+AGG 0.612078 8_1:+11558313 Msa1178660:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATATCAATTATTTTTTGT+AGG + chr8_1:11558191-11558210 Msa1178660:intron 10.0%
!! ATGGAAAAAACAAAAAGATA+TGG + chr8_1:11557675-11557694 Msa1178660:CDS 20.0%
!! TGGAAAAAACAAAAAGATAT+GGG + chr8_1:11557676-11557695 Msa1178660:CDS 20.0%
!!! TAACAAAAGTACCAATTAAA+AGG + chr8_1:11557717-11557736 Msa1178660:CDS 20.0%
!!! AACAAAAGTACCAATTAAAA+GGG + chr8_1:11557718-11557737 Msa1178660:CDS 20.0%
!! AGTTGACATAATAAAATTGT+TGG + chr8_1:11557838-11557857 Msa1178660:intron 20.0%
!!! GCTTTTTAAAATCAGTTAAT+AGG - chr8_1:11558083-11558102 None:intergenic 20.0%
!!! ATTTTAAAAAGCAAATTGAG+TGG + chr8_1:11558091-11558110 Msa1178660:intron 20.0%
!! TTGATATATTCATCAATGAT+TGG - chr8_1:11558125-11558144 None:intergenic 20.0%
!! TGAATAAGAAATCATATAGA+TGG + chr8_1:11558165-11558184 Msa1178660:intron 20.0%
!!! TTTTTTTTTTACGACTTTGT+TGG + chr8_1:11558240-11558259 Msa1178660:intron 20.0%
! AGTACTCGATAAATATCATT+AGG - chr8_1:11558040-11558059 None:intergenic 25.0%
! TTGATGAATATATCAACGAT+CGG + chr8_1:11558129-11558148 Msa1178660:intron 25.0%
! ACATCATTGACCCTTTTAAT+TGG - chr8_1:11557731-11557750 None:intergenic 30.0%
!!! GACATTGCATGTTTTTTAGA+TGG + chr8_1:11557803-11557822 Msa1178660:intron 30.0%
! AAATTGTTGGTGAAAGATCA+TGG + chr8_1:11557851-11557870 Msa1178660:intron 30.0%
TTCTTGTATAATGCTATGCA+TGG - chr8_1:11557951-11557970 None:intergenic 30.0%
CATTATACAAGAAACAGCTT+GGG + chr8_1:11557958-11557977 Msa1178660:intron 30.0%
!! TCGAGTACTGAAAAATAACA+AGG + chr8_1:11558051-11558070 Msa1178660:intron 30.0%
TTTAATTATCGACAAGTCGA+TGG - chr8_1:11558294-11558313 None:intergenic 30.0%
AGATATGCAGTTAAATCCAA+AGG + chr8_1:11558313-11558332 Msa1178660:intron 30.0%
!! TCCACTAGTTCTTGAAGTTT+TGG + chr8_1:11557640-11557659 Msa1178660:CDS 35.0%
!! CCACTAGTTCTTGAAGTTTT+GGG + chr8_1:11557641-11557660 Msa1178660:CDS 35.0%
! TTGGTACTTTTGTTAGCATC+TGG - chr8_1:11557712-11557731 None:intergenic 35.0%
GCATTATACAAGAAACAGCT+TGG + chr8_1:11557957-11557976 Msa1178660:intron 35.0%
!!! TTTTTTACGACTTTGTTGGC+AGG + chr8_1:11558244-11558263 Msa1178660:intron 35.0%
! TTTTTACGACTTTGTTGGCA+GGG + chr8_1:11558245-11558264 Msa1178660:intron 35.0%
CCCAAAACTTCAAGAACTAG+TGG - chr8_1:11557644-11557663 None:intergenic 40.0%
!! CTTTTGTTAGCATCTGGAAC+TGG - chr8_1:11557706-11557725 None:intergenic 40.0%
! TTTTACGACTTTGTTGGCAG+GGG + chr8_1:11558246-11558265 Msa1178660:intron 40.0%
!! GTTTTGGGTCGTCATCTTCA+TGG + chr8_1:11557656-11557675 Msa1178660:CDS 45.0%
ATCTTGATCGTCACGAGAAG+AGG + chr8_1:11557771-11557790 Msa1178660:CDS 45.0%
AAAGAATCCATCGACGACCC+TGG + chr8_1:11557992-11558011 Msa1178660:intron 50.0%
! GTAGTCGACTTCGCTTTCCA+GGG - chr8_1:11558012-11558031 None:intergenic 50.0%
! AGTAGTCGACTTCGCTTTCC+AGG - chr8_1:11558013-11558032 None:intergenic 50.0%
TGGAAAGCGAAGTCGACTAC+TGG + chr8_1:11558012-11558031 Msa1178660:intron 50.0%
ACTTTGTTGGCAGGGGAGTA+AGG + chr8_1:11558253-11558272 Msa1178660:intron 50.0%
TCGCTTTCCAGGGTCGTCGA+TGG - chr8_1:11558002-11558021 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 11557617 11558345 11557617 ID=Msa1178660;Name=Msa1178660
chr8_1 mRNA 11557617 11558345 11557617 ID=Msa1178660-mRNA-1;Parent=Msa1178660;Name=Msa1178660-mRNA-1;_AED=0.49;_eAED=0.54;_QI=0|0|0|1|0|0.5|2|0|72
chr8_1 exon 11557617 11557812 11557617 ID=Msa1178660-mRNA-1:exon:4081;Parent=Msa1178660-mRNA-1
chr8_1 exon 11558323 11558345 11558323 ID=Msa1178660-mRNA-1:exon:4082;Parent=Msa1178660-mRNA-1
chr8_1 CDS 11557617 11557812 11557617 ID=Msa1178660-mRNA-1:cds;Parent=Msa1178660-mRNA-1
chr8_1 CDS 11558323 11558345 11558323 ID=Msa1178660-mRNA-1:cds;Parent=Msa1178660-mRNA-1
Gene Sequence

>Msa1178660

ATGGTCAATTATGCTGATGGCAATCCACTAGTTCTTGAAGTTTTGGGTCGTCATCTTCATGGAAAAAACAAAAAGATATGGGAAAGCCAGTTCCAGATGCTAACAAAAGTACCAATTAAAAGGGTCAATGATGTTGTTAAATTGAGCTACAATGATCTTGATCGTCACGAGAAGAGGATACTTTTAGACATTGCATTTAAATCCAAAGGTGTTTTCTAA
Protein sequence

>Msa1178660

MVNYADGNPLVLEVLGRHLHGKNKKIWESQFQMLTKVPIKRVNDVVKLSYNDLDRHEKRILLDIAFKSKGVF*