AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1466170


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCCGAAAGACTTTGATTT+TGG 0.140280 tig0046126:-2812 Msa1466170:five_prime_UTR
GGGTTGTAGTGAATGATTTC+TGG 0.176419 tig0046126:+2830 Msa1466170:intergenic
TTGGTTTATTTGGTCATTTC+AGG 0.180401 tig0046126:-2870 Msa1466170:five_prime_UTR
TTCCAAAATCAAAGTCTTTC+GGG 0.201270 tig0046126:+2810 Msa1466170:intergenic
TCAACAGATGATATAATTCT+TGG 0.237761 tig0046126:-2373 Msa1466170:five_prime_UTR
TTTCCAAAATCAAAGTCTTT+CGG 0.284158 tig0046126:+2809 Msa1466170:intergenic
AAAAGTTGTGAAATGTTCAT+TGG 0.344253 tig0046126:-2270 Msa1466170:CDS
TAGTGAATGATTTCTGGTTC+AGG 0.353491 tig0046126:+2836 Msa1466170:intergenic
TATATCATCTGTTGAGAAAT+CGG 0.357749 tig0046126:+2381 Msa1466170:intergenic
GTCATTTCCATTTCGCGATC+AGG 0.363246 tig0046126:-2780 Msa1466170:intron
CTTGGGTTAGAACCTGACTA+TGG 0.370130 tig0046126:-2469 Msa1466170:five_prime_UTR
CCTGACTATGGGCTTGTAGA+AGG 0.391456 tig0046126:-2457 Msa1466170:five_prime_UTR
AGTGAATGATTTCTGGTTCA+GGG 0.441741 tig0046126:+2837 Msa1466170:intergenic
TACTTCACCTGATCGCGAAA+TGG 0.443929 tig0046126:+2773 Msa1466170:intergenic
ATTTGGTCATTTCAGGCTGG+TGG 0.456524 tig0046126:-2863 Msa1466170:five_prime_UTR
TTGAGAAATCGGCCTCTTTG+CGG 0.457734 tig0046126:+2392 Msa1466170:intergenic
GAGAAGGCAAAGAGTGTGCT+TGG 0.468611 tig0046126:-2487 Msa1466170:five_prime_UTR
GATTCGTACAACCTGGACTT+TGG 0.476902 tig0046126:-2427 Msa1466170:five_prime_UTR
TTTATTTGGTCATTTCAGGC+TGG 0.485753 tig0046126:-2866 Msa1466170:five_prime_UTR
TTTGGTCATTTCAGGCTGGT+GGG 0.488489 tig0046126:-2862 Msa1466170:five_prime_UTR
CCTTCTACAAGCCCATAGTC+AGG 0.501301 tig0046126:+2457 Msa1466170:intergenic
TTTCTTTGCATCAGTGGAGA+AGG 0.513847 tig0046126:-2503 Msa1466170:five_prime_UTR
GCAGCATTTCTTTGCATCAG+TGG 0.519599 tig0046126:-2509 Msa1466170:intron
TACAACCTGGACTTTGGTAG+AGG 0.545552 tig0046126:-2421 Msa1466170:five_prime_UTR
TTGGGTTAGAACCTGACTAT+GGG 0.553185 tig0046126:-2468 Msa1466170:five_prime_UTR
AAGTTCCTCTACCAAAGTCC+AGG 0.565993 tig0046126:+2416 Msa1466170:intergenic
AGAAGGCAAAGAGTGTGCTT+GGG 0.585599 tig0046126:-2486 Msa1466170:five_prime_UTR
TAGAGGAACTTTCCGCAAAG+AGG 0.588443 tig0046126:-2404 Msa1466170:five_prime_UTR
GTGAAATGTTCATTGGATTG+CGG 0.623412 tig0046126:-2263 Msa1466170:CDS
TCTTACAGATTCGTACAACC+TGG 0.632752 tig0046126:-2434 Msa1466170:five_prime_UTR
TTCATTACATAAAACTAACA+TGG 0.657935 tig0046126:-2200 Msa1466170:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGTAAAAAAAAATCACT+TGG + tig0046126:2235-2254 None:intergenic 15.0%
!!! TTTTTTTACTAAAGTAGTTT+TGG - tig0046126:2242-2261 Msa1466170:CDS 15.0%
!! TTTAAAAAAAAATGATGTTC+TGG - tig0046126:2818-2837 Msa1466170:five_prime_UTR 15.0%
!! TTTAGTAAAAAAAAATCACT+TGG + tig0046126:2235-2254 Msa1466170:intergenic 15.0%
!!! TTTTTTTACTAAAGTAGTTT+TGG - tig0046126:2242-2261 Msa1466170:CDS 15.0%
!! TTTAAAAAAAAATGATGTTC+TGG - tig0046126:2818-2837 Msa1466170:five_prime_UTR 15.0%
!!! TAAAGTAGTTTTGGTTTATT+TGG - tig0046126:2251-2270 Msa1466170:CDS 20.0%
!! TTCATTACATAAAACTAACA+TGG - tig0046126:2931-2950 Msa1466170:five_prime_UTR 20.0%
!!! TAAAGTAGTTTTGGTTTATT+TGG - tig0046126:2251-2270 Msa1466170:CDS 20.0%
!! TTCATTACATAAAACTAACA+TGG - tig0046126:2931-2950 Msa1466170:five_prime_UTR 20.0%
! TTTCCAAAATCAAAGTCTTT+CGG + tig0046126:2325-2344 Msa1466170:intergenic 25.0%
!!! GTAGTTTTACTTTTAGTCAT+TGG + tig0046126:2406-2425 Msa1466170:intergenic 25.0%
!!! TATCACACGTGTTTTAATAT+TGG + tig0046126:2482-2501 Msa1466170:intergenic 25.0%
!! TTGATTTTTCTATGTAGTAG+GGG + tig0046126:2517-2536 Msa1466170:intergenic 25.0%
!!! GTTGATTTTTCTATGTAGTA+GGG + tig0046126:2518-2537 Msa1466170:intergenic 25.0%
!!! TGTTGATTTTTCTATGTAGT+AGG + tig0046126:2519-2538 Msa1466170:intergenic 25.0%
! ATGATTTCACTAATGAAAGA+AGG + tig0046126:2564-2583 Msa1466170:intergenic 25.0%
! TATATCATCTGTTGAGAAAT+CGG + tig0046126:2753-2772 Msa1466170:intergenic 25.0%
! TCAACAGATGATATAATTCT+TGG - tig0046126:2758-2777 Msa1466170:intron 25.0%
! AAAAGTTGTGAAATGTTCAT+TGG - tig0046126:2861-2880 Msa1466170:five_prime_UTR 25.0%
!! CACGAGAATTATATTTTCTT+TGG - tig0046126:2902-2921 Msa1466170:five_prime_UTR 25.0%
! TTTCCAAAATCAAAGTCTTT+CGG + tig0046126:2325-2344 Msa1466170:intergenic 25.0%
!!! GTAGTTTTACTTTTAGTCAT+TGG + tig0046126:2406-2425 Msa1466170:intergenic 25.0%
!!! TATCACACGTGTTTTAATAT+TGG + tig0046126:2482-2501 Msa1466170:intergenic 25.0%
!! TTGATTTTTCTATGTAGTAG+GGG + tig0046126:2517-2536 Msa1466170:intergenic 25.0%
!!! GTTGATTTTTCTATGTAGTA+GGG + tig0046126:2518-2537 Msa1466170:intergenic 25.0%
!!! TGTTGATTTTTCTATGTAGT+AGG + tig0046126:2519-2538 Msa1466170:intergenic 25.0%
! ATGATTTCACTAATGAAAGA+AGG + tig0046126:2564-2583 Msa1466170:intergenic 25.0%
! TATATCATCTGTTGAGAAAT+CGG + tig0046126:2753-2772 Msa1466170:intergenic 25.0%
! TCAACAGATGATATAATTCT+TGG - tig0046126:2758-2777 Msa1466170:intron 25.0%
! AAAAGTTGTGAAATGTTCAT+TGG - tig0046126:2861-2880 Msa1466170:five_prime_UTR 25.0%
!! CACGAGAATTATATTTTCTT+TGG - tig0046126:2902-2921 Msa1466170:five_prime_UTR 25.0%
TTGGTTTATTTGGTCATTTC+AGG - tig0046126:2261-2280 Msa1466170:CDS 30.0%
TTCCAAAATCAAAGTCTTTC+GGG + tig0046126:2324-2343 Msa1466170:intergenic 30.0%
CTACATGAACTAAAAGCAAA+AGG - tig0046126:2422-2441 Msa1466170:five_prime_UTR 30.0%
!! AAAAGGTGCTATATTTGCAA+GGG - tig0046126:2439-2458 Msa1466170:five_prime_UTR 30.0%
TTGGTTTATTTGGTCATTTC+AGG - tig0046126:2261-2280 Msa1466170:CDS 30.0%
TTCCAAAATCAAAGTCTTTC+GGG + tig0046126:2324-2343 Msa1466170:intergenic 30.0%
CTACATGAACTAAAAGCAAA+AGG - tig0046126:2422-2441 Msa1466170:five_prime_UTR 30.0%
!! AAAAGGTGCTATATTTGCAA+GGG - tig0046126:2439-2458 Msa1466170:five_prime_UTR 30.0%
TTTATTTGGTCATTTCAGGC+TGG - tig0046126:2265-2284 Msa1466170:CDS 35.0%
!! AGTGAATGATTTCTGGTTCA+GGG + tig0046126:2297-2316 Msa1466170:intergenic 35.0%
!! TAGTGAATGATTTCTGGTTC+AGG + tig0046126:2298-2317 Msa1466170:intergenic 35.0%
!! AACCCGAAAGACTTTGATTT+TGG - tig0046126:2319-2338 Msa1466170:exon 35.0%
!! CAAAAGGTGCTATATTTGCA+AGG - tig0046126:2438-2457 Msa1466170:five_prime_UTR 35.0%
GTGAAATGTTCATTGGATTG+CGG - tig0046126:2868-2887 Msa1466170:five_prime_UTR 35.0%
TTTATTTGGTCATTTCAGGC+TGG - tig0046126:2265-2284 Msa1466170:CDS 35.0%
!! AGTGAATGATTTCTGGTTCA+GGG + tig0046126:2297-2316 Msa1466170:intergenic 35.0%
!! TAGTGAATGATTTCTGGTTC+AGG + tig0046126:2298-2317 Msa1466170:intergenic 35.0%
!! AACCCGAAAGACTTTGATTT+TGG - tig0046126:2319-2338 Msa1466170:exon 35.0%
!! CAAAAGGTGCTATATTTGCA+AGG - tig0046126:2438-2457 Msa1466170:five_prime_UTR 35.0%
GTGAAATGTTCATTGGATTG+CGG - tig0046126:2868-2887 Msa1466170:five_prime_UTR 35.0%
GGGTTGTAGTGAATGATTTC+TGG + tig0046126:2304-2323 Msa1466170:intergenic 40.0%
TTTCTTTGCATCAGTGGAGA+AGG - tig0046126:2628-2647 Msa1466170:intron 40.0%
! TTGGGTTAGAACCTGACTAT+GGG - tig0046126:2663-2682 Msa1466170:intron 40.0%
TCTTACAGATTCGTACAACC+TGG - tig0046126:2697-2716 Msa1466170:intron 40.0%
GGGTTGTAGTGAATGATTTC+TGG + tig0046126:2304-2323 Msa1466170:intergenic 40.0%
TTTCTTTGCATCAGTGGAGA+AGG - tig0046126:2628-2647 Msa1466170:intron 40.0%
! TTGGGTTAGAACCTGACTAT+GGG - tig0046126:2663-2682 Msa1466170:intron 40.0%
TCTTACAGATTCGTACAACC+TGG - tig0046126:2697-2716 Msa1466170:intron 40.0%
ATTTGGTCATTTCAGGCTGG+TGG - tig0046126:2268-2287 Msa1466170:CDS 45.0%
TTTGGTCATTTCAGGCTGGT+GGG - tig0046126:2269-2288 Msa1466170:CDS 45.0%
GTCATTTCCATTTCGCGATC+AGG - tig0046126:2351-2370 Msa1466170:five_prime_UTR 45.0%
TACTTCACCTGATCGCGAAA+TGG + tig0046126:2361-2380 Msa1466170:intergenic 45.0%
GCAGCATTTCTTTGCATCAG+TGG - tig0046126:2622-2641 Msa1466170:intron 45.0%
! AGAAGGCAAAGAGTGTGCTT+GGG - tig0046126:2645-2664 Msa1466170:intron 45.0%
! CTTGGGTTAGAACCTGACTA+TGG - tig0046126:2662-2681 Msa1466170:intron 45.0%
GATTCGTACAACCTGGACTT+TGG - tig0046126:2704-2723 Msa1466170:intron 45.0%
TACAACCTGGACTTTGGTAG+AGG - tig0046126:2710-2729 Msa1466170:intron 45.0%
AAGTTCCTCTACCAAAGTCC+AGG + tig0046126:2718-2737 Msa1466170:intergenic 45.0%
TAGAGGAACTTTCCGCAAAG+AGG - tig0046126:2727-2746 Msa1466170:intron 45.0%
TTGAGAAATCGGCCTCTTTG+CGG + tig0046126:2742-2761 Msa1466170:intergenic 45.0%
ATTTGGTCATTTCAGGCTGG+TGG - tig0046126:2268-2287 Msa1466170:CDS 45.0%
TTTGGTCATTTCAGGCTGGT+GGG - tig0046126:2269-2288 Msa1466170:CDS 45.0%
GTCATTTCCATTTCGCGATC+AGG - tig0046126:2351-2370 Msa1466170:five_prime_UTR 45.0%
TACTTCACCTGATCGCGAAA+TGG + tig0046126:2361-2380 Msa1466170:intergenic 45.0%
GCAGCATTTCTTTGCATCAG+TGG - tig0046126:2622-2641 Msa1466170:intron 45.0%
! AGAAGGCAAAGAGTGTGCTT+GGG - tig0046126:2645-2664 Msa1466170:intron 45.0%
! CTTGGGTTAGAACCTGACTA+TGG - tig0046126:2662-2681 Msa1466170:intron 45.0%
GATTCGTACAACCTGGACTT+TGG - tig0046126:2704-2723 Msa1466170:intron 45.0%
TACAACCTGGACTTTGGTAG+AGG - tig0046126:2710-2729 Msa1466170:intron 45.0%
AAGTTCCTCTACCAAAGTCC+AGG + tig0046126:2718-2737 Msa1466170:intergenic 45.0%
TAGAGGAACTTTCCGCAAAG+AGG - tig0046126:2727-2746 Msa1466170:intron 45.0%
TTGAGAAATCGGCCTCTTTG+CGG + tig0046126:2742-2761 Msa1466170:intergenic 45.0%
! GAGAAGGCAAAGAGTGTGCT+TGG - tig0046126:2644-2663 Msa1466170:intron 50.0%
CCTTCTACAAGCCCATAGTC+AGG + tig0046126:2677-2696 Msa1466170:intergenic 50.0%
CCTGACTATGGGCTTGTAGA+AGG - tig0046126:2674-2693 Msa1466170:intron 50.0%
! GAGAAGGCAAAGAGTGTGCT+TGG - tig0046126:2644-2663 Msa1466170:intron 50.0%
CCTTCTACAAGCCCATAGTC+AGG + tig0046126:2677-2696 Msa1466170:intergenic 50.0%
CCTGACTATGGGCTTGTAGA+AGG - tig0046126:2674-2693 Msa1466170:intron 50.0%
Chromosome Type Strat End Strand Name
tig0046126 gene 2185 2968 2185 ID=Msa1466170;Name=Msa1466170
tig0046126 mRNA 2185 2968 2185 ID=Msa1466170-mRNA-1;Parent=Msa1466170;Name=Msa1466170-mRNA-1;_AED=0.00;_eAED=0.00;_QI=391|1|1|1|1|1|2|26|37
tig0046126 exon 2185 2527 2185 ID=Msa1466170-mRNA-1:exon:25007;Parent=Msa1466170-mRNA-1
tig0046126 exon 2781 2968 2781 ID=Msa1466170-mRNA-1:exon:25006;Parent=Msa1466170-mRNA-1
tig0046126 five_prime_UTR 2781 2968 2781 ID=Msa1466170-mRNA-1:five_prime_utr;Parent=Msa1466170-mRNA-1
tig0046126 five_prime_UTR 2325 2527 2325 ID=Msa1466170-mRNA-1:five_prime_utr;Parent=Msa1466170-mRNA-1
tig0046126 CDS 2211 2324 2211 ID=Msa1466170-mRNA-1:cds;Parent=Msa1466170-mRNA-1
tig0046126 three_prime_UTR 2185 2210 2185 ID=Msa1466170-mRNA-1:three_prime_utr;Parent=Msa1466170-mRNA-1
Gene Sequence

>Msa1466170

ATGATGTTCTGGTTTGCTACAATATCATCAGAAAAAGTTGTGAAATGTTCATTGGATTGCGGATTCAAACTTGCACGAGAATTATATTTTCTTTGGAGCATGTTCATTACATAA

Protein sequence

>Msa1466170

MMFWFATISSEKVVKCSLDCGFKLARELYFLWSMFIT*