AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0405550


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 66 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCACGCCTCCGTTACCTTT+TGG 0.196515 3_2:-40298322 Msa0405550:CDS
CAGCTCACGTACCGCTTTAA+TGG 0.245260 3_2:-40298616 Msa0405550:CDS
TCTCAGGTAGACAGTTTCTA+TGG 0.287253 3_2:+40298287 None:intergenic
GGCAAAGAAGGCCTCCTTCC+GGG 0.289862 3_2:+40298186 None:intergenic
TTTACCGTTGGCACGATAAC+TGG 0.336021 3_2:-40298748 Msa0405550:CDS
TCCTCGGGCCAGACGGAGAT+TGG 0.349112 3_2:+40298351 None:intergenic
TCCCGTCGATGTGAGCTCTT+GGG 0.355274 3_2:-40298523 Msa0405550:CDS
AGGCAAAGAAGGCCTCCTTC+CGG 0.382980 3_2:+40298185 None:intergenic
AAAGTTACTCTAGGGATAAC+AGG 0.383241 3_2:+40298491 None:intergenic
TTCCCGTCGATGTGAGCTCT+TGG 0.386490 3_2:-40298524 Msa0405550:CDS
AGCTCACGTACCGCTTTAAT+GGG 0.395506 3_2:-40298615 Msa0405550:CDS
CTGTAGTATGTTCAAGGGTT+GGG 0.408364 3_2:+40298585 None:intergenic
CCCTTCTGCCTTTGCACTCG+AGG 0.411231 3_2:-40298375 Msa0405550:CDS
CTCACATCGACGGGAAGGTT+TGG 0.420533 3_2:+40298531 None:intergenic
CTGGAGCTGTAGTATGTTCA+AGG 0.420619 3_2:+40298579 None:intergenic
GACTGTCCCTTGGTCTGTAT+TGG 0.425548 3_2:-40298266 Msa0405550:CDS
GCTGTAGTATGTTCAAGGGT+TGG 0.437554 3_2:+40298584 None:intergenic
CCTTCTGCCTTTGCACTCGA+GGG 0.461384 3_2:-40298374 Msa0405550:CDS
GCAGTTATCCGCTCCGCACT+TGG 0.463896 3_2:-40298781 Msa0405550:CDS
CCCCAAGAGCTCACATCGAC+GGG 0.472021 3_2:+40298522 None:intergenic
ACAGACCAAGGGACAGTCTC+AGG 0.474421 3_2:+40298271 None:intergenic
CTCGAGGGCCAATCTCCGTC+TGG 0.480699 3_2:-40298359 Msa0405550:CDS
GATGTCGGCTCTTCGCCACC+TGG 0.508239 3_2:+40298560 None:intergenic
TCCTGCGCAGCTTAGGTGGA+AGG 0.508478 3_2:+40298165 None:intergenic
CTCAGGTAGACAGTTTCTAT+GGG 0.510655 3_2:+40298288 None:intergenic
CCCTCGAGTGCAAAGGCAGA+AGG 0.511073 3_2:+40298374 None:intergenic
CCTTGGTCTGTATTGGCACA+AGG 0.514139 3_2:-40298259 Msa0405550:CDS
GCAAAGAAGGCCTCCTTCCG+GGG 0.515468 3_2:+40298187 None:intergenic
GAGGCGTGCAAAGGTTTCCT+CGG 0.526013 3_2:+40298335 None:intergenic
GGCTACCCAGCGTTTACCGT+TGG 0.526912 3_2:-40298760 Msa0405550:CDS
AGGCGTGCAAAGGTTTCCTC+GGG 0.527025 3_2:+40298336 None:intergenic
CCAGAGTGGTATCTCACTGA+TGG 0.527423 3_2:-40298219 Msa0405550:CDS
CCCGTCGATGTGAGCTCTTG+GGG 0.534121 3_2:-40298522 Msa0405550:CDS
CTTGAACATACTACAGCTCC+AGG 0.534489 3_2:-40298578 Msa0405550:CDS
AAGGTTTGGCACCTCGATGT+CGG 0.545826 3_2:+40298545 None:intergenic
CAAAGAAGGCCTCCTTCCGG+GGG 0.550054 3_2:+40298188 None:intergenic
GCTTAGGTGGAAGGCAAAGA+AGG 0.550243 3_2:+40298174 None:intergenic
TCCCCAAGAGCTCACATCGA+CGG 0.555494 3_2:+40298521 None:intergenic
GCCAATCTCCGTCTGGCCCG+AGG 0.562208 3_2:-40298352 Msa0405550:CDS
GTCTACCTGAGACTGTCCCT+TGG 0.586612 3_2:-40298276 Msa0405550:CDS
AAGGTAACGGAGGCGTGCAA+AGG 0.595805 3_2:+40298326 None:intergenic
CCTCGAGTGCAAAGGCAGAA+GGG 0.595841 3_2:+40298375 None:intergenic
AAAGGTTTCCTCGGGCCAGA+CGG 0.597813 3_2:+40298344 None:intergenic
AAGAAGGCCTCCTTCCGGGG+GGG 0.600255 3_2:+40298190 None:intergenic
TGGGGCGTAGGCCTCCCAAA+AGG 0.606913 3_2:+40298307 None:intergenic
ATCGTGCCAACGGTAAACGC+TGG 0.607055 3_2:+40298754 None:intergenic
TCGTGCCAACGGTAAACGCT+GGG 0.607071 3_2:+40298755 None:intergenic
AAGAGCTCACATCGACGGGA+AGG 0.613365 3_2:+40298526 None:intergenic
CCTTGTGCCAATACAGACCA+AGG 0.618599 3_2:+40298259 None:intergenic
CACGATAACTGGCACACCAG+AGG 0.619554 3_2:-40298737 Msa0405550:intron
GGGCTGTTCGCCCATTAAAG+CGG 0.619701 3_2:+40298605 None:intergenic
TGGAGCTGTAGTATGTTCAA+GGG 0.621354 3_2:+40298580 None:intergenic
AGACAGTTTCTATGGGGCGT+AGG 0.622986 3_2:+40298295 None:intergenic
AAAGAAGGCCTCCTTCCGGG+GGG 0.627949 3_2:+40298189 None:intergenic
GTAGGCCTCCCAAAAGGTAA+CGG 0.632223 3_2:+40298313 None:intergenic
AAACGCTGGGTAGCCAAGTG+CGG 0.642570 3_2:+40298768 None:intergenic
TGTGCCAGTTATCGTGCCAA+CGG 0.646438 3_2:+40298744 None:intergenic
AGATTGGCCCTCGAGTGCAA+AGG 0.670375 3_2:+40298367 None:intergenic
CCATCAGTGAGATACCACTC+TGG 0.671241 3_2:+40298219 None:intergenic
GAATTCTAGCTCTTCCAGAG+TGG 0.675255 3_2:-40298233 Msa0405550:CDS
CTGGGTAGCCAAGTGCGGAG+CGG 0.679241 3_2:+40298773 None:intergenic
GGCCTCCCAAAAGGTAACGG+AGG 0.683463 3_2:+40298316 None:intergenic
CTTGTGCCAATACAGACCAA+GGG 0.693537 3_2:+40298260 None:intergenic
GTGGCGAAGAGCCGACATCG+AGG 0.704477 3_2:-40298556 Msa0405550:CDS
TCAGGTAGACAGTTTCTATG+GGG 0.720720 3_2:+40298289 None:intergenic
GAACATACTACAGCTCCAGG+TGG 0.771466 3_2:-40298575 Msa0405550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGGATAAAAGTTACTCTA+GGG + chr3_2:40298486-40298505 None:intergenic 30.0%
! AAAGTTACTCTAGGGATAAC+AGG + chr3_2:40298478-40298497 None:intergenic 35.0%
CAACGGATAAAAGTTACTCT+AGG + chr3_2:40298487-40298506 None:intergenic 35.0%
CTGTAGTATGTTCAAGGGTT+GGG + chr3_2:40298384-40298403 None:intergenic 40.0%
TGGAGCTGTAGTATGTTCAA+GGG + chr3_2:40298389-40298408 None:intergenic 40.0%
! AACTTTTATCCGTTGAGCGA+CGG - chr3_2:40298492-40298511 Msa0405550:intron 40.0%
TCAGGTAGACAGTTTCTATG+GGG + chr3_2:40298680-40298699 None:intergenic 40.0%
CTCAGGTAGACAGTTTCTAT+GGG + chr3_2:40298681-40298700 None:intergenic 40.0%
TCTCAGGTAGACAGTTTCTA+TGG + chr3_2:40298682-40298701 None:intergenic 40.0%
TTTACCGTTGGCACGATAAC+TGG - chr3_2:40298218-40298237 Msa0405550:CDS 45.0%
ATTAAAGCGGTACGTGAGCT+GGG + chr3_2:40298351-40298370 None:intergenic 45.0%
AGCTCACGTACCGCTTTAAT+GGG - chr3_2:40298351-40298370 Msa0405550:CDS 45.0%
GCTGTAGTATGTTCAAGGGT+TGG + chr3_2:40298385-40298404 None:intergenic 45.0%
CTGGAGCTGTAGTATGTTCA+AGG + chr3_2:40298390-40298409 None:intergenic 45.0%
CTTGAACATACTACAGCTCC+AGG - chr3_2:40298388-40298407 Msa0405550:intron 45.0%
CTTGTGCCAATACAGACCAA+GGG + chr3_2:40298709-40298728 None:intergenic 45.0%
!! GAATTCTAGCTCTTCCAGAG+TGG - chr3_2:40298733-40298752 Msa0405550:intron 45.0%
TGTGCCAGTTATCGTGCCAA+CGG + chr3_2:40298225-40298244 None:intergenic 50.0%
TTTCCCTAGTACGAGAGGAC+CGG + chr3_2:40298265-40298284 None:intergenic 50.0%
!! GTGGGCATTAGAGCATTGAG+AGG + chr3_2:40298291-40298310 None:intergenic 50.0%
CAATGCTCTAATGCCCACAC+CGG - chr3_2:40298293-40298312 Msa0405550:CDS 50.0%
TCTAATGCCCACACCGGATA+TGG - chr3_2:40298299-40298318 Msa0405550:CDS 50.0%
GAGACAGTTCGGTCCATATC+CGG + chr3_2:40298315-40298334 None:intergenic 50.0%
CAGAACGTCGTGAGACAGTT+CGG + chr3_2:40298326-40298345 None:intergenic 50.0%
CATTAAAGCGGTACGTGAGC+TGG + chr3_2:40298352-40298371 None:intergenic 50.0%
CAGCTCACGTACCGCTTTAA+TGG - chr3_2:40298350-40298369 Msa0405550:CDS 50.0%
GAACATACTACAGCTCCAGG+TGG - chr3_2:40298391-40298410 Msa0405550:intron 50.0%
AAGGTTTGGCACCTCGATGT+CGG + chr3_2:40298424-40298443 None:intergenic 50.0%
GTAGGCCTCCCAAAAGGTAA+CGG + chr3_2:40298656-40298675 None:intergenic 50.0%
AGACAGTTTCTATGGGGCGT+AGG + chr3_2:40298674-40298693 None:intergenic 50.0%
GACTGTCCCTTGGTCTGTAT+TGG - chr3_2:40298700-40298719 Msa0405550:intron 50.0%
CCTTGTGCCAATACAGACCA+AGG + chr3_2:40298710-40298729 None:intergenic 50.0%
! CCTTGGTCTGTATTGGCACA+AGG - chr3_2:40298707-40298726 Msa0405550:intron 50.0%
CCATCAGTGAGATACCACTC+TGG + chr3_2:40298750-40298769 None:intergenic 50.0%
CCAGAGTGGTATCTCACTGA+TGG - chr3_2:40298747-40298766 Msa0405550:CDS 50.0%
AAACGCTGGGTAGCCAAGTG+CGG + chr3_2:40298201-40298220 None:intergenic 55.0%
TCGTGCCAACGGTAAACGCT+GGG + chr3_2:40298214-40298233 None:intergenic 55.0%
ATCGTGCCAACGGTAAACGC+TGG + chr3_2:40298215-40298234 None:intergenic 55.0%
CACGATAACTGGCACACCAG+AGG - chr3_2:40298229-40298248 Msa0405550:CDS 55.0%
TTCCCGGTCCTCTCGTACTA+GGG - chr3_2:40298259-40298278 Msa0405550:CDS 55.0%
TTCCCTAGTACGAGAGGACC+GGG + chr3_2:40298264-40298283 None:intergenic 55.0%
GGTCCTCTCGTACTAGGGAA+AGG - chr3_2:40298264-40298283 Msa0405550:CDS 55.0%
GGACCTTTCCCTAGTACGAG+AGG + chr3_2:40298270-40298289 None:intergenic 55.0%
GTTCGGTCCATATCCGGTGT+GGG + chr3_2:40298309-40298328 None:intergenic 55.0%
AGTTCGGTCCATATCCGGTG+TGG + chr3_2:40298310-40298329 None:intergenic 55.0%
GGGCTGTTCGCCCATTAAAG+CGG + chr3_2:40298364-40298383 None:intergenic 55.0%
CTCACATCGACGGGAAGGTT+TGG + chr3_2:40298438-40298457 None:intergenic 55.0%
AAGAGCTCACATCGACGGGA+AGG + chr3_2:40298443-40298462 None:intergenic 55.0%
TTCCCGTCGATGTGAGCTCT+TGG - chr3_2:40298442-40298461 Msa0405550:intron 55.0%
TCCCGTCGATGTGAGCTCTT+GGG - chr3_2:40298443-40298462 Msa0405550:intron 55.0%
TCCCCAAGAGCTCACATCGA+CGG + chr3_2:40298448-40298467 None:intergenic 55.0%
AGTCGGCCTTAGTGATCCGA+CGG + chr3_2:40298533-40298552 None:intergenic 55.0%
CCTCGAGTGCAAAGGCAGAA+GGG + chr3_2:40298594-40298613 None:intergenic 55.0%
CCTTCTGCCTTTGCACTCGA+GGG - chr3_2:40298592-40298611 Msa0405550:CDS 55.0%
! AGATTGGCCCTCGAGTGCAA+AGG + chr3_2:40298602-40298621 None:intergenic 55.0%
AAAGGTTTCCTCGGGCCAGA+CGG + chr3_2:40298625-40298644 None:intergenic 55.0%
AGGCGTGCAAAGGTTTCCTC+GGG + chr3_2:40298633-40298652 None:intergenic 55.0%
GAGGCGTGCAAAGGTTTCCT+CGG + chr3_2:40298634-40298653 None:intergenic 55.0%
!! AAGGTAACGGAGGCGTGCAA+AGG + chr3_2:40298643-40298662 None:intergenic 55.0%
! TGCACGCCTCCGTTACCTTT+TGG - chr3_2:40298644-40298663 Msa0405550:intron 55.0%
! GCACGCCTCCGTTACCTTTT+GGG - chr3_2:40298645-40298664 Msa0405550:intron 55.0%
GTCTACCTGAGACTGTCCCT+TGG - chr3_2:40298690-40298709 Msa0405550:intron 55.0%
ACAGACCAAGGGACAGTCTC+AGG + chr3_2:40298698-40298717 None:intergenic 55.0%
AGGCAAAGAAGGCCTCCTTC+CGG + chr3_2:40298784-40298803 None:intergenic 55.0%
GCAGTTATCCGCTCCGCACT+TGG - chr3_2:40298185-40298204 Msa0405550:CDS 60.0%
GGCTACCCAGCGTTTACCGT+TGG - chr3_2:40298206-40298225 Msa0405550:CDS 60.0%
CTAGTACGAGAGGACCGGGA+AGG + chr3_2:40298260-40298279 None:intergenic 60.0%
CTTCCCGGTCCTCTCGTACT+AGG - chr3_2:40298258-40298277 Msa0405550:CDS 60.0%
CCCCAAGAGCTCACATCGAC+GGG + chr3_2:40298447-40298466 None:intergenic 60.0%
CCCGTCGATGTGAGCTCTTG+GGG - chr3_2:40298444-40298463 Msa0405550:intron 60.0%
TCGGCACCGTCGGATCACTA+AGG - chr3_2:40298524-40298543 Msa0405550:CDS 60.0%
CGTCGAGCAGGGACGAAAGT+CGG + chr3_2:40298550-40298569 None:intergenic 60.0%
CGACTTTCGTCCCTGCTCGA+CGG - chr3_2:40298548-40298567 Msa0405550:CDS 60.0%
GACTTTCGTCCCTGCTCGAC+GGG - chr3_2:40298549-40298568 Msa0405550:CDS 60.0%
CCCTTCTGCCTTTGCACTCG+AGG - chr3_2:40298591-40298610 Msa0405550:CDS 60.0%
CCCTCGAGTGCAAAGGCAGA+AGG + chr3_2:40298595-40298614 None:intergenic 60.0%
! CGCCTCCGTTACCTTTTGGG+AGG - chr3_2:40298648-40298667 Msa0405550:intron 60.0%
! GGCCTCCCAAAAGGTAACGG+AGG + chr3_2:40298653-40298672 None:intergenic 60.0%
AAAGAAGGCCTCCTTCCGGG+GGG + chr3_2:40298780-40298799 None:intergenic 60.0%
CAAAGAAGGCCTCCTTCCGG+GGG + chr3_2:40298781-40298800 None:intergenic 60.0%
GCAAAGAAGGCCTCCTTCCG+GGG + chr3_2:40298782-40298801 None:intergenic 60.0%
GGCAAAGAAGGCCTCCTTCC+GGG + chr3_2:40298783-40298802 None:intergenic 60.0%
CTGGGTAGCCAAGTGCGGAG+CGG + chr3_2:40298196-40298215 None:intergenic 65.0%
! CACCAGAGGTGCGTCCTTCC+CGG - chr3_2:40298243-40298262 Msa0405550:CDS 65.0%
!! GATGTCGGCTCTTCGCCACC+TGG + chr3_2:40298409-40298428 None:intergenic 65.0%
GTGGCGAAGAGCCGACATCG+AGG - chr3_2:40298410-40298429 Msa0405550:intron 65.0%
GTGGAAGGGCCGTCGCTCAA+CGG + chr3_2:40298504-40298523 None:intergenic 65.0%
TGAGCGACGGCCCTTCCACT+CGG - chr3_2:40298505-40298524 Msa0405550:CDS 65.0%
! TCCGACGGTGCCGAGTGGAA+GGG + chr3_2:40298518-40298537 None:intergenic 65.0%
! ATCCGACGGTGCCGAGTGGA+AGG + chr3_2:40298519-40298538 None:intergenic 65.0%
! AGTGATCCGACGGTGCCGAG+TGG + chr3_2:40298523-40298542 None:intergenic 65.0%
TTTCGTCCCTGCTCGACGGG+TGG - chr3_2:40298552-40298571 Msa0405550:CDS 65.0%
TTCGTCCCTGCTCGACGGGT+GGG - chr3_2:40298553-40298572 Msa0405550:CDS 65.0%
CAAGACCCACCCGTCGAGCA+GGG + chr3_2:40298561-40298580 None:intergenic 65.0%
CTCGAGGGCCAATCTCCGTC+TGG - chr3_2:40298607-40298626 Msa0405550:CDS 65.0%
TCCTCGGGCCAGACGGAGAT+TGG + chr3_2:40298618-40298637 None:intergenic 65.0%
TGGGGCGTAGGCCTCCCAAA+AGG + chr3_2:40298662-40298681 None:intergenic 65.0%
AAGAAGGCCTCCTTCCGGGG+GGG + chr3_2:40298779-40298798 None:intergenic 65.0%
GACCGGGAAGGACGCACCTC+TGG + chr3_2:40298248-40298267 None:intergenic 70.0%
GCCCTTCCACTCGGCACCGT+CGG - chr3_2:40298514-40298533 Msa0405550:CDS 70.0%
GCAAGACCCACCCGTCGAGC+AGG + chr3_2:40298562-40298581 None:intergenic 70.0%
GCCAATCTCCGTCTGGCCCG+AGG - chr3_2:40298614-40298633 Msa0405550:CDS 70.0%
ACTGATGGCTCGAGCCCCCC+CGG - chr3_2:40298762-40298781 Msa0405550:CDS 70.0%
ATGGCTCGAGCCCCCCCGGA+AGG - chr3_2:40298766-40298785 Msa0405550:CDS 75.0%
! GCTCGAGCCCCCCCGGAAGG+AGG - chr3_2:40298769-40298788 Msa0405550:CDS 80.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 40298176 40298812 40298176 ID=Msa0405550;Name=Msa0405550
chr3_2 mRNA 40298176 40298812 40298176 ID=Msa0405550-mRNA-1;Parent=Msa0405550;Name=Msa0405550-mRNA-1;_AED=0.53;_eAED=0.61;_QI=0|0|0|0.66|1|1|3|0|146
chr3_2 exon 40298738 40298812 40298738 ID=Msa0405550-mRNA-1:exon:7827;Parent=Msa0405550-mRNA-1
chr3_2 exon 40298499 40298635 40298499 ID=Msa0405550-mRNA-1:exon:7826;Parent=Msa0405550-mRNA-1
chr3_2 exon 40298176 40298404 40298176 ID=Msa0405550-mRNA-1:exon:7825;Parent=Msa0405550-mRNA-1
chr3_2 CDS 40298738 40298812 40298738 ID=Msa0405550-mRNA-1:cds;Parent=Msa0405550-mRNA-1
chr3_2 CDS 40298499 40298635 40298499 ID=Msa0405550-mRNA-1:cds;Parent=Msa0405550-mRNA-1
chr3_2 CDS 40298176 40298404 40298176 ID=Msa0405550-mRNA-1:cds;Parent=Msa0405550-mRNA-1
Gene Sequence

>Msa0405550

ATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTACCCAGCGTTTACCGTTGGCACGATAACTGGCACACCAGAGCTCACGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGAACATACTACAGCTCCAGGTGGCGAAGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAGCTCTTGGGGAAGATCAGCCTGTTATCCCTAGATCAAGCTCCCTTCTGCCTTTGCACTCGAGGGCCAATCTCCGTCTGGCCCGAGGAAACCTTTGCACGCCTCCGTTACCTTTTGGGAGGCCTACGCCCCATAGAAACTGTCTACCTGAGACTGTCCCTTGGTCTGTATTGGCACAAGGTTAGAATTCTAGCTCTTCCAGAGTGGTATCTCACTGATGGCTCGAGCCCCCCCGGAAGGAGGCCTTCTTTGCCTTCCACCTAA

Protein sequence

>Msa0405550

MLSAVIRSALGYPAFTVGTITGTPELTYRFNGRTAQPLNILQLQVAKSRHRGAKPSRRCELLGKISLLSLDQAPFCLCTRGPISVWPEETFARLRYLLGGLRPIETVYLRLSLGLYWHKVRILALPEWYLTDGSSPPGRRPSLPST*