AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1446920

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1446920 MtrunA17_Chr1g0171881 83.929 168 23 2 1 168 1 164 4.20e-96 275
Msa1446920 MtrunA17_Chr4g0030371 79.518 83 11 1 86 168 1 77 2.44e-31 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1446920 AT5G40690.1 38.462 208 83 6 1 165 1 206 3.66e-36 125
Msa1446920 AT2G41730.1 50.000 84 36 2 1 81 1 81 3.51e-15 68.2
Msa1446920 AT5G24640.1 45.238 84 39 2 1 81 1 80 1.58e-12 61.2

Find 55 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCGCATTTGCCGGTGAATT+TGG 0.205363 tig0031537:+2580 None:intergenic
CAACCGGACTCGAATCTTAC+TGG 0.325031 tig0031537:-2467 Msa1446920:CDS
AAAATGCTTGTGATTACCTT+TGG 0.335803 tig0031537:+2502 None:intergenic
CGAGTACCGGGTGTCGGGTT+AGG 0.347158 tig0031537:+2677 None:intergenic
GTAACTTGTTCTACTGTCAT+TGG 0.359658 tig0031537:+2293 None:intergenic
CTGTGGCGTGCCGCATTTGC+CGG 0.362824 tig0031537:+2571 None:intergenic
TTTGGAATGATTGGTGGGCT+TGG 0.381078 tig0031537:+2598 None:intergenic
GCCGGTGAATTTGGAATGAT+TGG 0.385978 tig0031537:+2589 None:intergenic
TTCGATTCCCCTCCAACTGC+TGG 0.391701 tig0031537:-2641 Msa1446920:CDS
CTCCGGCTGCCGCCTCCATC+CGG 0.414148 tig0031537:-2546 Msa1446920:CDS
CAATCTTTCTGATTTCTACA+TGG 0.421569 tig0031537:-2420 Msa1446920:CDS
GAATGATTGGTGGGCTTGGA+AGG 0.425912 tig0031537:+2602 None:intergenic
CAGTTGGAGGGGAATCGAAC+CGG 0.429973 tig0031537:+2645 None:intergenic
TTTGGATTTGTTCTTTGACT+TGG 0.437582 tig0031537:+2520 None:intergenic
TGAATCGAGTACCGGGTGTC+GGG 0.444419 tig0031537:+2672 None:intergenic
GACCGGATGGAGGCGGCAGC+CGG 0.457432 tig0031537:+2544 None:intergenic
CTTACTGGGTTGTCCGCGAC+CGG 0.458599 tig0031537:-2452 Msa1446920:CDS
TGCGGCACGCCACAGTGCTC+CGG 0.463907 tig0031537:-2563 Msa1446920:CDS
AGAAAGATTGTTTAAAGTCC+CGG 0.477317 tig0031537:+2433 None:intergenic
TTGTTCTTTGACTTGGAGAC+CGG 0.480998 tig0031537:+2527 None:intergenic
ATATGAAGATGATTGGTGTT+TGG 0.490876 tig0031537:-2261 Msa1446920:CDS
ATGAATCGAGTACCGGGTGT+CGG 0.510454 tig0031537:+2671 None:intergenic
TCCAAATTCACCGGCAAATG+CGG 0.527550 tig0031537:-2581 Msa1446920:CDS
ATTGTTTAAAGTCCCGGTCG+CGG 0.529848 tig0031537:+2439 None:intergenic
ATGGTATGGTGAGGACATAT+CGG 0.534382 tig0031537:-2706 Msa1446920:CDS
ACTTGGAGACCGGATGGAGG+CGG 0.537276 tig0031537:+2537 None:intergenic
TACCGGGTGTCGGGTTAGGA+AGG 0.539780 tig0031537:+2681 None:intergenic
TGAAGAGTCCAGCAGTTGGA+GGG 0.540070 tig0031537:+2633 None:intergenic
GTGAAGAGTCCAGCAGTTGG+AGG 0.542067 tig0031537:+2632 None:intergenic
GGTGAATTTGGAATGATTGG+TGG 0.542800 tig0031537:+2592 None:intergenic
AGAGGGTAAGCAACATGGTA+TGG 0.544442 tig0031537:-2720 Msa1446920:CDS
ACCAATCATTCCAAATTCAC+CGG 0.547455 tig0031537:-2590 Msa1446920:CDS
GTGAATTTGGAATGATTGGT+GGG 0.548712 tig0031537:+2593 None:intergenic
AATGATTGGTGGGCTTGGAA+GGG 0.549805 tig0031537:+2603 None:intergenic
CCGGGTGATGAATCGAGTAC+CGG 0.558963 tig0031537:+2664 None:intergenic
AACCGGACTCGAATCTTACT+GGG 0.569785 tig0031537:-2466 Msa1446920:CDS
TTACTGGGTTGTCCGCGACC+GGG 0.572711 tig0031537:-2451 Msa1446920:CDS
TGCACTCTAGATGAAGAAGT+GGG 0.574866 tig0031537:-2320 Msa1446920:CDS
CCGGTACTCGATTCATCACC+CGG 0.575989 tig0031537:-2664 Msa1446920:CDS
ATCCTTCCTAACCCGACACC+CGG 0.577836 tig0031537:-2683 Msa1446920:CDS
AGTTGGAGGGGAATCGAACC+GGG 0.578688 tig0031537:+2646 None:intergenic
TTTGTGAAGAGTCCAGCAGT+TGG 0.579848 tig0031537:+2629 None:intergenic
TCTTTGACTTGGAGACCGGA+TGG 0.580250 tig0031537:+2531 None:intergenic
CGGGTGATGAATCGAGTACC+GGG 0.588075 tig0031537:+2665 None:intergenic
AACCCAGTAAGATTCGAGTC+CGG 0.603480 tig0031537:+2464 None:intergenic
GAAGAGTCCAGCAGTTGGAG+GGG 0.603678 tig0031537:+2634 None:intergenic
TTGACTTGGAGACCGGATGG+AGG 0.611016 tig0031537:+2534 None:intergenic
AAGAGAGAGGGTAAGCAACA+TGG 0.611292 tig0031537:-2725 Msa1446920:CDS
GTGCACTCTAGATGAAGAAG+TGG 0.617109 tig0031537:-2321 Msa1446920:CDS
AGGCGGCAGCCGGAGCACTG+TGG 0.644535 tig0031537:+2554 None:intergenic
GATGAACGTGTTGACCATGT+TGG 0.655419 tig0031537:-2362 Msa1446920:CDS
AAGTCAAAGAACAAATCCAA+AGG 0.656581 tig0031537:-2518 Msa1446920:CDS
AATTTACATTAAAACCAACA+TGG 0.665222 tig0031537:+2348 None:intergenic
GTAAGCAACATGGTATGGTG+AGG 0.672721 tig0031537:-2715 Msa1446920:CDS
GCACTCTAGATGAAGAAGTG+GGG 0.714162 tig0031537:-2319 Msa1446920:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTACATTAAAACCAACA+TGG + tig0031537:2627-2646 None:intergenic 20.0%
!! AAGAAAAATATGAAGATGAT+TGG - tig0031537:2704-2723 Msa1446920:CDS 20.0%
! TTTGGATTTGTTCTTTGACT+TGG + tig0031537:2455-2474 None:intergenic 30.0%
AAGTCAAAGAACAAATCCAA+AGG - tig0031537:2454-2473 Msa1446920:CDS 30.0%
AAAATGCTTGTGATTACCTT+TGG + tig0031537:2473-2492 None:intergenic 30.0%
! AAGGTAATCACAAGCATTTT+AGG - tig0031537:2473-2492 Msa1446920:CDS 30.0%
! AGGTAATCACAAGCATTTTA+GGG - tig0031537:2474-2493 Msa1446920:CDS 30.0%
! AGAAAGATTGTTTAAAGTCC+CGG + tig0031537:2542-2561 None:intergenic 30.0%
CAATCTTTCTGATTTCTACA+TGG - tig0031537:2552-2571 Msa1446920:CDS 30.0%
! ATATGAAGATGATTGGTGTT+TGG - tig0031537:2711-2730 Msa1446920:CDS 30.0%
! GTGAATTTGGAATGATTGGT+GGG + tig0031537:2382-2401 None:intergenic 35.0%
ACCAATCATTCCAAATTCAC+CGG - tig0031537:2382-2401 Msa1446920:CDS 35.0%
!! GTAACTTGTTCTACTGTCAT+TGG + tig0031537:2682-2701 None:intergenic 35.0%
ATGGTATGGTGAGGACATAT+CGG - tig0031537:2266-2285 Msa1446920:CDS 40.0%
! GGTGAATTTGGAATGATTGG+TGG + tig0031537:2383-2402 None:intergenic 40.0%
!! TTGTTCTTTGACTTGGAGAC+CGG + tig0031537:2448-2467 None:intergenic 40.0%
!!! TCACAAGCATTTTAGGGTCA+TGG - tig0031537:2480-2499 Msa1446920:CDS 40.0%
!!! TTTTAGGGTCATGGAACAAC+CGG - tig0031537:2489-2508 Msa1446920:CDS 40.0%
! TGACGATGATGATGATGATG+TGG - tig0031537:2585-2604 Msa1446920:CDS 40.0%
TGCACTCTAGATGAAGAAGT+GGG - tig0031537:2652-2671 Msa1446920:CDS 40.0%
AAGAGAGAGGGTAAGCAACA+TGG - tig0031537:2247-2266 Msa1446920:CDS 45.0%
AGAGGGTAAGCAACATGGTA+TGG - tig0031537:2252-2271 Msa1446920:CDS 45.0%
GTAAGCAACATGGTATGGTG+AGG - tig0031537:2257-2276 Msa1446920:CDS 45.0%
TTTGTGAAGAGTCCAGCAGT+TGG + tig0031537:2346-2365 None:intergenic 45.0%
!! AATGATTGGTGGGCTTGGAA+GGG + tig0031537:2372-2391 None:intergenic 45.0%
!! TTTGGAATGATTGGTGGGCT+TGG + tig0031537:2377-2396 None:intergenic 45.0%
! GCCGGTGAATTTGGAATGAT+TGG + tig0031537:2386-2405 None:intergenic 45.0%
TCCAAATTCACCGGCAAATG+CGG - tig0031537:2391-2410 Msa1446920:CDS 45.0%
AACCGGACTCGAATCTTACT+GGG - tig0031537:2506-2525 Msa1446920:CDS 45.0%
AACCCAGTAAGATTCGAGTC+CGG + tig0031537:2511-2530 None:intergenic 45.0%
! ATTGTTTAAAGTCCCGGTCG+CGG + tig0031537:2536-2555 None:intergenic 45.0%
! GATGAACGTGTTGACCATGT+TGG - tig0031537:2610-2629 Msa1446920:CDS 45.0%
GTGCACTCTAGATGAAGAAG+TGG - tig0031537:2651-2670 Msa1446920:CDS 45.0%
GCACTCTAGATGAAGAAGTG+GGG - tig0031537:2653-2672 Msa1446920:CDS 45.0%
!! ATGAATCGAGTACCGGGTGT+CGG + tig0031537:2304-2323 None:intergenic 50.0%
TGAAGAGTCCAGCAGTTGGA+GGG + tig0031537:2342-2361 None:intergenic 50.0%
!! GAATGATTGGTGGGCTTGGA+AGG + tig0031537:2373-2392 None:intergenic 50.0%
!! TCTTTGACTTGGAGACCGGA+TGG + tig0031537:2444-2463 None:intergenic 50.0%
CAACCGGACTCGAATCTTAC+TGG - tig0031537:2505-2524 Msa1446920:CDS 50.0%
ATCCTTCCTAACCCGACACC+CGG - tig0031537:2289-2308 Msa1446920:CDS 55.0%
!! TGAATCGAGTACCGGGTGTC+GGG + tig0031537:2303-2322 None:intergenic 55.0%
CGGGTGATGAATCGAGTACC+GGG + tig0031537:2310-2329 None:intergenic 55.0%
CCGGGTGATGAATCGAGTAC+CGG + tig0031537:2311-2330 None:intergenic 55.0%
CCGGTACTCGATTCATCACC+CGG - tig0031537:2308-2327 Msa1446920:CDS 55.0%
AGTTGGAGGGGAATCGAACC+GGG + tig0031537:2329-2348 None:intergenic 55.0%
CAGTTGGAGGGGAATCGAAC+CGG + tig0031537:2330-2349 None:intergenic 55.0%
TTCGATTCCCCTCCAACTGC+TGG - tig0031537:2331-2350 Msa1446920:CDS 55.0%
GAAGAGTCCAGCAGTTGGAG+GGG + tig0031537:2341-2360 None:intergenic 55.0%
GTGAAGAGTCCAGCAGTTGG+AGG + tig0031537:2343-2362 None:intergenic 55.0%
GCCGCATTTGCCGGTGAATT+TGG + tig0031537:2395-2414 None:intergenic 55.0%
!! TTGACTTGGAGACCGGATGG+AGG + tig0031537:2441-2460 None:intergenic 55.0%
!! TACCGGGTGTCGGGTTAGGA+AGG + tig0031537:2294-2313 None:intergenic 60.0%
ACTTGGAGACCGGATGGAGG+CGG + tig0031537:2438-2457 None:intergenic 60.0%
CTTACTGGGTTGTCCGCGAC+CGG - tig0031537:2520-2539 Msa1446920:CDS 60.0%
TTACTGGGTTGTCCGCGACC+GGG - tig0031537:2521-2540 Msa1446920:CDS 60.0%
!! CGAGTACCGGGTGTCGGGTT+AGG + tig0031537:2298-2317 None:intergenic 65.0%
CTGTGGCGTGCCGCATTTGC+CGG + tig0031537:2404-2423 None:intergenic 65.0%
TGCGGCACGCCACAGTGCTC+CGG - tig0031537:2409-2428 Msa1446920:CDS 70.0%
!! AGGCGGCAGCCGGAGCACTG+TGG + tig0031537:2421-2440 None:intergenic 75.0%
CTCCGGCTGCCGCCTCCATC+CGG - tig0031537:2426-2445 Msa1446920:CDS 75.0%
GACCGGATGGAGGCGGCAGC+CGG + tig0031537:2431-2450 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
tig0031537 gene 2244 2750 2244 ID=Msa1446920;Name=Msa1446920
tig0031537 mRNA 2244 2750 2244 ID=Msa1446920-mRNA-1;Parent=Msa1446920;Name=Msa1446920-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|168
tig0031537 exon 2244 2750 2244 ID=Msa1446920-mRNA-1:exon:15632;Parent=Msa1446920-mRNA-1
tig0031537 CDS 2244 2750 2244 ID=Msa1446920-mRNA-1:cds;Parent=Msa1446920-mRNA-1
Gene Sequence

>Msa1446920

ATGAAGAGAGAGGGTAAGCAACATGGTATGGTGAGGACATATCGGATCCTTCCTAACCCGACACCCGGTACTCGATTCATCACCCGGTTCGATTCCCCTCCAACTGCTGGACTCTTCACAAAAGTCCCTTCCAAGCCCACCAATCATTCCAAATTCACCGGCAAATGCGGCACGCCACAGTGCTCCGGCTGCCGCCTCCATCCGGTCTCCAAGTCAAAGAACAAATCCAAAGGTAATCACAAGCATTTTAGGGTCATGGAACAACCGGACTCGAATCTTACTGGGTTGTCCGCGACCGGGACTTTAAACAATCTTTCTGATTTCTACATGGATGATGATGATGACGATGATGATGATGATGTGGAAGATGAACGTGTTGACCATGTTGGTTTTAATGTAAATTATTCGTGCACTCTAGATGAAGAAGTGGGGATTCCAATGACAGTAGAACAAGTTACAGAAGAAAAATATGAAGATGATTGGTGTTTGGTAGAATGTTGTTCTTGA
Protein sequence

>Msa1446920

MKREGKQHGMVRTYRILPNPTPGTRFITRFDSPPTAGLFTKVPSKPTNHSKFTGKCGTPQCSGCRLHPVSKSKNKSKGNHKHFRVMEQPDSNLTGLSATGTLNNLSDFYMDDDDDDDDDDVEDERVDHVGFNVNYSCTLDEEVGIPMTVEQVTEEKYEDDWCLVECCS*