AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0418590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0418590 MtrunA17_Chr5g0394361 75.000 216 30 2 1 199 1 209 5.99e-112 318
Msa0418590 MtrunA17_Chr1g0205591 96.629 89 3 0 111 199 1 89 2.49e-58 178
Msa0418590 MtrunA17_Chr1g0205601 64.948 97 20 2 1 90 1 90 9.07e-34 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0418590 AT4G02770.1 87.919 149 18 0 51 199 60 208 1.60e-96 279
Msa0418590 AT1G03130.1 89.041 146 16 0 54 199 59 204 2.16e-96 279

Find 77 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGTGCTGCCACTGAAAAT+TGG 0.193952 3_2:-66365352 None:intergenic
CGACCAGGGTTCACTTTCTC+TGG 0.220355 3_2:-66365631 None:intergenic
CAACTTGGGCCTTACATAAA+AGG 0.267884 3_2:-66365378 None:intergenic
AAAATTGGGGAGGGAGTGTC+TGG 0.303697 3_2:-66365337 None:intergenic
CCTTGCTAACTTGAGAAGAT+TGG 0.306141 3_2:-66365488 None:intergenic
ATTTCAAAGATTTGTTCTTT+TGG 0.309811 3_2:-66365430 None:intergenic
CAGTGCTGCCACTGAAAATT+GGG 0.315756 3_2:-66365351 None:intergenic
GGTCAGAACTTTAGAACTAT+TGG 0.337450 3_2:+66365664 Msa0418590:CDS
ATTGTGAGCTTGAGAGGGTT+TGG 0.372107 3_2:-66365243 None:intergenic
AGAGATACGGTCATTAGGTT+TGG 0.376453 3_2:-66365181 None:intergenic
CTCTTCACCCCTCCTCTCTC+TGG 0.385923 3_2:+66365156 Msa0418590:CDS
AAAGAACAATGTTTGGCTCT+TGG 0.389124 3_2:+66365511 Msa0418590:CDS
GGTACAGAGATACGGTCATT+AGG 0.394276 3_2:-66365186 None:intergenic
AGCAAGGAAAGAACAATGTT+TGG 0.394375 3_2:+66365504 Msa0418590:CDS
CTTGCTAACTTGAGAAGATT+GGG 0.409133 3_2:-66365487 None:intergenic
TGGGAAACACTCTATAGAAT+TGG 0.417334 3_2:-66365567 None:intergenic
CCACTGAACTTAACCTCTAT+AGG 0.417689 3_2:-66365700 None:intergenic
GAGATACGGTCATTAGGTTT+GGG 0.426468 3_2:-66365180 None:intergenic
TCTGGGTACACACCATCCTT+AGG 0.434810 3_2:-66365613 None:intergenic
TGGCTCTTGGAACTAGGTTG+AGG 0.435951 3_2:+66365524 Msa0418590:CDS
TCTATAGAGTGTTTCCCAAT+GGG 0.441504 3_2:+66365572 Msa0418590:CDS
AGAGAGAGGAGGGGTGAAGA+GGG 0.442080 3_2:-66365154 None:intergenic
AAGTATTGAACTTCCCCATT+GGG 0.462594 3_2:-66365586 None:intergenic
AATGTTTGGCTCTTGGAACT+AGG 0.466499 3_2:+66365518 Msa0418590:CDS
TGACCAACCCCTTGGCGACC+AGG 0.470301 3_2:-66365646 None:intergenic
TAAGAATGTTAGTCCTATAG+AGG 0.473752 3_2:+66365687 Msa0418590:CDS
TTGCTGAGGAAGGCACCAAT+TGG 0.475146 3_2:+66365292 Msa0418590:intron
GTTTGGGACCAGAGAGAGGA+GGG 0.477785 3_2:-66365164 None:intergenic
CAGAGAGAGGAGGGGTGAAG+AGG 0.479426 3_2:-66365155 None:intergenic
CTTGAAATTGTGAGCTTGAG+AGG 0.480961 3_2:-66365249 None:intergenic
CAAATCTTTGAAATGCCTAC+TGG 0.482126 3_2:+66365439 Msa0418590:CDS
GAGAGGAGGGGTGAAGAGGG+AGG 0.499448 3_2:-66365151 None:intergenic
AACCCTGGTCGCCAAGGGGT+TGG 0.500962 3_2:+66365643 Msa0418590:CDS
TCACATAAAATTCCTCAACT+TGG 0.507482 3_2:-66365393 None:intergenic
TCAGGTGGGGTGAAGCCAAT+TGG 0.510396 3_2:-66365307 None:intergenic
GACCAGGGTTCACTTTCTCT+GGG 0.517976 3_2:-66365630 None:intergenic
AATGTGGGTGATTGTTTCCA+TGG 0.524862 3_2:-66365207 None:intergenic
GAGCTTGAGAGGGTTTGGAT+TGG 0.531093 3_2:-66365238 None:intergenic
TAAAGTTCTGACCAACCCCT+TGG 0.532779 3_2:-66365654 None:intergenic
TTCTATAGAGTGTTTCCCAA+TGG 0.534519 3_2:+66365571 Msa0418590:CDS
GAGAGGGTTTGGATTGGTGA+AGG 0.539245 3_2:-66365232 None:intergenic
CAAGTATTGAACTTCCCCAT+TGG 0.539423 3_2:-66365587 None:intergenic
GAGGGAGGTTTGAGTTGTCA+TGG 0.540329 3_2:-66365136 None:intergenic
TGGATTGGTGAAGGACAATG+TGG 0.545639 3_2:-66365223 None:intergenic
AAAGTGAACCCTGGTCGCCA+AGG 0.548177 3_2:+66365637 Msa0418590:CDS
GTTTCCATGGTACAGAGATA+CGG 0.551001 3_2:-66365194 None:intergenic
CACATAAAATTCCTCAACTT+GGG 0.551301 3_2:-66365392 None:intergenic
GGAGTGTCTGGGACTAACTC+AGG 0.553809 3_2:-66365325 None:intergenic
TGTCTGGGACTAACTCAGGT+GGG 0.554597 3_2:-66365321 None:intergenic
TTGAAATTGTGAGCTTGAGA+GGG 0.558382 3_2:-66365248 None:intergenic
GGTTTGGGACCAGAGAGAGG+AGG 0.559759 3_2:-66365165 None:intergenic
AAGTGAACCCTGGTCGCCAA+GGG 0.562644 3_2:+66365638 Msa0418590:CDS
ATTGGGACCTTCCCTCATGA+TGG 0.564788 3_2:-66365470 None:intergenic
GTGTCTGGGACTAACTCAGG+TGG 0.570065 3_2:-66365322 None:intergenic
TTTATGTAAGGCCCAAGTTG+AGG 0.578463 3_2:+66365381 Msa0418590:CDS
AGTTCAATACTTGCATCCTA+AGG 0.578655 3_2:+66365597 Msa0418590:CDS
GACCAACCCCTTGGCGACCA+GGG 0.583738 3_2:-66365645 None:intergenic
CCAATCTTCTCAAGTTAGCA+AGG 0.583877 3_2:+66365488 Msa0418590:CDS
CAATACTTGCATCCTAAGGA+TGG 0.585635 3_2:+66365601 Msa0418590:CDS
CTGGTGGTGCAGCCATCATG+AGG 0.591206 3_2:+66365458 Msa0418590:CDS
CCTATAGAGGTTAAGTTCAG+TGG 0.595489 3_2:+66365700 Msa0418590:CDS
TTAGGTTTGGGACCAGAGAG+AGG 0.606251 3_2:-66365168 None:intergenic
CTGCCACTGAAAATTGGGGA+GGG 0.607497 3_2:-66365346 None:intergenic
GTCTGGGACTAACTCAGGTG+GGG 0.609250 3_2:-66365320 None:intergenic
TTTGGGACCAGAGAGAGGAG+GGG 0.614499 3_2:-66365163 None:intergenic
AGTGCTGCCACTGAAAATTG+GGG 0.629529 3_2:-66365350 None:intergenic
GGTGCAGCCATCATGAGGGA+AGG 0.635464 3_2:+66365463 Msa0418590:CDS
AAATTGGGGAGGGAGTGTCT+GGG 0.645471 3_2:-66365336 None:intergenic
ATGATGGCTGCACCACCAGT+AGG 0.647307 3_2:-66365454 None:intergenic
GCTGCCACTGAAAATTGGGG+AGG 0.656201 3_2:-66365347 None:intergenic
CTATAGAGTGTTTCCCAATG+GGG 0.656977 3_2:+66365573 Msa0418590:CDS
ATCTTTGAAATGCCTACTGG+TGG 0.664160 3_2:+66365442 Msa0418590:CDS
TGGTGGTGCAGCCATCATGA+GGG 0.675901 3_2:+66365459 Msa0418590:CDS
TACCCAGAGAAAGTGAACCC+TGG 0.676997 3_2:+66365628 Msa0418590:CDS
ATGACCGTATCTCTGTACCA+TGG 0.695290 3_2:+66365190 Msa0418590:CDS
AGTGAACCCTGGTCGCCAAG+GGG 0.697482 3_2:+66365639 Msa0418590:CDS
GGATTGGTGAAGGACAATGT+GGG 0.717553 3_2:-66365222 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTCAAAGATTTGTTCTTT+TGG - chr3_2:66365433-66365452 None:intergenic 20.0%
CACATAAAATTCCTCAACTT+GGG - chr3_2:66365395-66365414 None:intergenic 30.0%
TCACATAAAATTCCTCAACT+TGG - chr3_2:66365396-66365415 None:intergenic 30.0%
! AGGAATTTTATGTGATCACA+TGG + chr3_2:66365401-66365420 Msa0418590:CDS 30.0%
! GGAATTTTATGTGATCACAT+GGG + chr3_2:66365402-66365421 Msa0418590:CDS 30.0%
TAAGAATGTTAGTCCTATAG+AGG + chr3_2:66365687-66365706 Msa0418590:CDS 30.0%
TTGAAATTGTGAGCTTGAGA+GGG - chr3_2:66365251-66365270 None:intergenic 35.0%
!! CAAATCTTTGAAATGCCTAC+TGG + chr3_2:66365439-66365458 Msa0418590:CDS 35.0%
CTTGCTAACTTGAGAAGATT+GGG - chr3_2:66365490-66365509 None:intergenic 35.0%
AGCAAGGAAAGAACAATGTT+TGG + chr3_2:66365504-66365523 Msa0418590:CDS 35.0%
!! AAAGAACAATGTTTGGCTCT+TGG + chr3_2:66365511-66365530 Msa0418590:CDS 35.0%
TGGGAAACACTCTATAGAAT+TGG - chr3_2:66365570-66365589 None:intergenic 35.0%
! TTCTATAGAGTGTTTCCCAA+TGG + chr3_2:66365571-66365590 Msa0418590:CDS 35.0%
! TCTATAGAGTGTTTCCCAAT+GGG + chr3_2:66365572-66365591 Msa0418590:CDS 35.0%
!! AAGTATTGAACTTCCCCATT+GGG - chr3_2:66365589-66365608 None:intergenic 35.0%
AGTTCAATACTTGCATCCTA+AGG + chr3_2:66365597-66365616 Msa0418590:CDS 35.0%
!! GGTCAGAACTTTAGAACTAT+TGG + chr3_2:66365664-66365683 Msa0418590:CDS 35.0%
GAGATACGGTCATTAGGTTT+GGG - chr3_2:66365183-66365202 None:intergenic 40.0%
AGAGATACGGTCATTAGGTT+TGG - chr3_2:66365184-66365203 None:intergenic 40.0%
GTTTCCATGGTACAGAGATA+CGG - chr3_2:66365197-66365216 None:intergenic 40.0%
AATGTGGGTGATTGTTTCCA+TGG - chr3_2:66365210-66365229 None:intergenic 40.0%
CTTGAAATTGTGAGCTTGAG+AGG - chr3_2:66365252-66365271 None:intergenic 40.0%
CAACTTGGGCCTTACATAAA+AGG - chr3_2:66365381-66365400 None:intergenic 40.0%
TTTATGTAAGGCCCAAGTTG+AGG + chr3_2:66365381-66365400 Msa0418590:CDS 40.0%
!! ATCTTTGAAATGCCTACTGG+TGG + chr3_2:66365442-66365461 Msa0418590:CDS 40.0%
CCTTGCTAACTTGAGAAGAT+TGG - chr3_2:66365491-66365510 None:intergenic 40.0%
CCAATCTTCTCAAGTTAGCA+AGG + chr3_2:66365488-66365507 Msa0418590:CDS 40.0%
!! AATGTTTGGCTCTTGGAACT+AGG + chr3_2:66365518-66365537 Msa0418590:CDS 40.0%
! CTATAGAGTGTTTCCCAATG+GGG + chr3_2:66365573-66365592 Msa0418590:CDS 40.0%
!! CAAGTATTGAACTTCCCCAT+TGG - chr3_2:66365590-66365609 None:intergenic 40.0%
CAATACTTGCATCCTAAGGA+TGG + chr3_2:66365601-66365620 Msa0418590:CDS 40.0%
CCACTGAACTTAACCTCTAT+AGG - chr3_2:66365703-66365722 None:intergenic 40.0%
CCTATAGAGGTTAAGTTCAG+TGG + chr3_2:66365700-66365719 Msa0418590:CDS 40.0%
GGTACAGAGATACGGTCATT+AGG - chr3_2:66365189-66365208 None:intergenic 45.0%
ATGACCGTATCTCTGTACCA+TGG + chr3_2:66365190-66365209 Msa0418590:CDS 45.0%
! GGATTGGTGAAGGACAATGT+GGG - chr3_2:66365225-66365244 None:intergenic 45.0%
!! TGGATTGGTGAAGGACAATG+TGG - chr3_2:66365226-66365245 None:intergenic 45.0%
ATTGTGAGCTTGAGAGGGTT+TGG - chr3_2:66365246-66365265 None:intergenic 45.0%
AGTGCTGCCACTGAAAATTG+GGG - chr3_2:66365353-66365372 None:intergenic 45.0%
CAGTGCTGCCACTGAAAATT+GGG - chr3_2:66365354-66365373 None:intergenic 45.0%
! CACTGGAGGCCTTTTATGTA+AGG + chr3_2:66365369-66365388 Msa0418590:CDS 45.0%
! TAAAGTTCTGACCAACCCCT+TGG - chr3_2:66365657-66365676 None:intergenic 45.0%
!! GAGGGAGGTTTGAGTTGTCA+TGG - chr3_2:66365139-66365158 None:intergenic 50.0%
! TTAGGTTTGGGACCAGAGAG+AGG - chr3_2:66365171-66365190 None:intergenic 50.0%
!! GAGAGGGTTTGGATTGGTGA+AGG - chr3_2:66365235-66365254 None:intergenic 50.0%
GAGCTTGAGAGGGTTTGGAT+TGG - chr3_2:66365241-66365260 None:intergenic 50.0%
CATAACAGCAGCTGTTGCTG+AGG + chr3_2:66365278-66365297 Msa0418590:intron 50.0%
!! TTGCTGAGGAAGGCACCAAT+TGG + chr3_2:66365292-66365311 Msa0418590:intron 50.0%
! TGTCTGGGACTAACTCAGGT+GGG - chr3_2:66365324-66365343 None:intergenic 50.0%
!! AAATTGGGGAGGGAGTGTCT+GGG - chr3_2:66365339-66365358 None:intergenic 50.0%
!! AAAATTGGGGAGGGAGTGTC+TGG - chr3_2:66365340-66365359 None:intergenic 50.0%
! ACTCCCTCCCCAATTTTCAG+TGG + chr3_2:66365343-66365362 Msa0418590:CDS 50.0%
CTGCCACTGAAAATTGGGGA+GGG - chr3_2:66365349-66365368 None:intergenic 50.0%
CCAGTGCTGCCACTGAAAAT+TGG - chr3_2:66365355-66365374 None:intergenic 50.0%
! CCAATTTTCAGTGGCAGCAC+TGG + chr3_2:66365352-66365371 Msa0418590:CDS 50.0%
!! ATTTTCAGTGGCAGCACTGG+AGG + chr3_2:66365355-66365374 Msa0418590:CDS 50.0%
ATTGGGACCTTCCCTCATGA+TGG - chr3_2:66365473-66365492 None:intergenic 50.0%
TGGCTCTTGGAACTAGGTTG+AGG + chr3_2:66365524-66365543 Msa0418590:CDS 50.0%
TCTGGGTACACACCATCCTT+AGG - chr3_2:66365616-66365635 None:intergenic 50.0%
TACCCAGAGAAAGTGAACCC+TGG + chr3_2:66365628-66365647 Msa0418590:CDS 50.0%
GACCAGGGTTCACTTTCTCT+GGG - chr3_2:66365633-66365652 None:intergenic 50.0%
AGAGAGAGGAGGGGTGAAGA+GGG - chr3_2:66365157-66365176 None:intergenic 55.0%
! TTTGGGACCAGAGAGAGGAG+GGG - chr3_2:66365166-66365185 None:intergenic 55.0%
! GTTTGGGACCAGAGAGAGGA+GGG - chr3_2:66365167-66365186 None:intergenic 55.0%
ACAGCAGCTGTTGCTGAGGA+AGG + chr3_2:66365282-66365301 Msa0418590:intron 55.0%
TCAGGTGGGGTGAAGCCAAT+TGG - chr3_2:66365310-66365329 None:intergenic 55.0%
! GTCTGGGACTAACTCAGGTG+GGG - chr3_2:66365323-66365342 None:intergenic 55.0%
! GTGTCTGGGACTAACTCAGG+TGG - chr3_2:66365325-66365344 None:intergenic 55.0%
! GGAGTGTCTGGGACTAACTC+AGG - chr3_2:66365328-66365347 None:intergenic 55.0%
GCTGCCACTGAAAATTGGGG+AGG - chr3_2:66365350-66365369 None:intergenic 55.0%
ATGATGGCTGCACCACCAGT+AGG - chr3_2:66365457-66365476 None:intergenic 55.0%
! TGGTGGTGCAGCCATCATGA+GGG + chr3_2:66365459-66365478 Msa0418590:CDS 55.0%
CGACCAGGGTTCACTTTCTC+TGG - chr3_2:66365634-66365653 None:intergenic 55.0%
AAAGTGAACCCTGGTCGCCA+AGG + chr3_2:66365637-66365656 Msa0418590:CDS 55.0%
AAGTGAACCCTGGTCGCCAA+GGG + chr3_2:66365638-66365657 Msa0418590:CDS 55.0%
CAGAGAGAGGAGGGGTGAAG+AGG - chr3_2:66365158-66365177 None:intergenic 60.0%
CTCTTCACCCCTCCTCTCTC+TGG + chr3_2:66365156-66365175 Msa0418590:CDS 60.0%
! GGTTTGGGACCAGAGAGAGG+AGG - chr3_2:66365168-66365187 None:intergenic 60.0%
! CTGGTGGTGCAGCCATCATG+AGG + chr3_2:66365458-66365477 Msa0418590:CDS 60.0%
GGTGCAGCCATCATGAGGGA+AGG + chr3_2:66365463-66365482 Msa0418590:CDS 60.0%
AGTGAACCCTGGTCGCCAAG+GGG + chr3_2:66365639-66365658 Msa0418590:CDS 60.0%
GAGAGGAGGGGTGAAGAGGG+AGG - chr3_2:66365154-66365173 None:intergenic 65.0%
AACCCTGGTCGCCAAGGGGT+TGG + chr3_2:66365643-66365662 Msa0418590:CDS 65.0%
GACCAACCCCTTGGCGACCA+GGG - chr3_2:66365648-66365667 None:intergenic 65.0%
TGACCAACCCCTTGGCGACC+AGG - chr3_2:66365649-66365668 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 66365132 66365744 66365132 ID=Msa0418590;Name=Msa0418590
chr3_2 mRNA 66365132 66365744 66365132 ID=Msa0418590-mRNA-1;Parent=Msa0418590;Name=Msa0418590-mRNA-1;_AED=0.01;_eAED=0.04;_QI=0|0|0|1|0|0|2|0|199
chr3_2 exon 66365132 66365290 66365132 ID=Msa0418590-mRNA-1:exon:15172;Parent=Msa0418590-mRNA-1
chr3_2 exon 66365304 66365744 66365304 ID=Msa0418590-mRNA-1:exon:15173;Parent=Msa0418590-mRNA-1
chr3_2 CDS 66365132 66365290 66365132 ID=Msa0418590-mRNA-1:cds;Parent=Msa0418590-mRNA-1
chr3_2 CDS 66365304 66365744 66365304 ID=Msa0418590-mRNA-1:cds;Parent=Msa0418590-mRNA-1
Gene Sequence

>Msa0418590

ATGGCCATGACAACTCAAACCTCCCTCTTCACCCCTCCTCTCTCTGGTCCCAAACCTAATGACCGTATCTCTGTACCATGGAAACAATCACCCACATTGTCCTTCACCAATCCAAACCCTCTCAAGCTCACAATTTCAAGAAACATCATAACAGCAGCTGCACCAATTGGCTTCACCCCACCTGAGTTAGTCCCAGACACTCCCTCCCCAATTTTCAGTGGCAGCACTGGAGGCCTTTTATGTAAGGCCCAAGTTGAGGAATTTTATGTGATCACATGGGATTCTCCAAAAGAACAAATCTTTGAAATGCCTACTGGTGGTGCAGCCATCATGAGGGAAGGTCCCAATCTTCTCAAGTTAGCAAGGAAAGAACAATGTTTGGCTCTTGGAACTAGGTTGAGGTCAAAGTACAAGATCAAGTACCAATTCTATAGAGTGTTTCCCAATGGGGAAGTTCAATACTTGCATCCTAAGGATGGTGTGTACCCAGAGAAAGTGAACCCTGGTCGCCAAGGGGTTGGTCAGAACTTTAGAACTATTGGTAAGAATGTTAGTCCTATAGAGGTTAAGTTCAGTGGCAAGCAAGTGTATGAATTGTGA
Protein sequence

>Msa0418590

MAMTTQTSLFTPPLSGPKPNDRISVPWKQSPTLSFTNPNPLKLTISRNIITAAAPIGFTPPELVPDTPSPIFSGSTGGLLCKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGQNFRTIGKNVSPIEVKFSGKQVYEL*