AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1215080

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 24 sgRNAs with CRISPR-Local

Find 132 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAACACTGAGAAGCGAAAA+TGG 0.300690 8_1:+76158301 Msa1215080:CDS
AAGAAGAAGCAAGGTGTAGA+TGG 0.344753 8_1:-76158370 None:intergenic
CATACGAGCTCATCCCTTCA+AGG 0.437361 8_1:-76159603 None:intergenic
AACGAGGTTCCTAACCTTGA+AGG 0.452298 8_1:+76159589 Msa1215080:three_prime_UTR
GAGCTCATCCCTTCAAGGTT+AGG 0.453636 8_1:-76159598 None:intergenic
ATAGGAATCATCTTAGAGAT+AGG 0.479459 8_1:+76159677 Msa1215080:three_prime_UTR
ATCATCTTAGAGATAGGATG+TGG 0.498557 8_1:+76159683 Msa1215080:three_prime_UTR
TTAACAAGGTTATCTGATGA+AGG 0.516699 8_1:+76159634 Msa1215080:three_prime_UTR
TTATTGTTACTTAGTATGAC+AGG 0.524867 8_1:+76159529 Msa1215080:intron
TGATGAAGGTGCAGCTGAGA+TGG 0.559464 8_1:+76159648 Msa1215080:three_prime_UTR
CAGCTGAGATGGCAATGGAT+AGG 0.572746 8_1:+76159659 Msa1215080:three_prime_UTR
CGTATGTTGAAAACTTAACA+AGG 0.583345 8_1:+76159620 Msa1215080:three_prime_UTR
AGCGAAAATGGCGATTTCGA+CGG 0.590473 8_1:+76158313 Msa1215080:CDS
ACGAGGTTCCTAACCTTGAA+GGG 0.611095 8_1:+76159590 Msa1215080:three_prime_UTR
AAAACTTGAGGCGGTGAACG+AGG 0.615754 8_1:+76159573 Msa1215080:three_prime_UTR
ACCGTGCTTCTTCTTCTCTG+CGG 0.616187 8_1:+76158413 Msa1215080:CDS
ACCGCAGAGAAGAAGAAGCA+CGG 0.624330 8_1:-76158414 None:intergenic
TAACTGATATTGAAAACTTG+AGG 0.627113 8_1:+76159561 Msa1215080:three_prime_UTR
AGGTGCAGCTGAGATGGCAA+TGG 0.647281 8_1:+76159654 Msa1215080:three_prime_UTR
CTGATATTGAAAACTTGAGG+CGG 0.649713 8_1:+76159564 Msa1215080:three_prime_UTR
TCATCTTAGAGATAGGATGT+GGG 0.679475 8_1:+76159684 Msa1215080:three_prime_UTR
GCGGTGGAGAAGAAGAAGCA+AGG 0.680210 8_1:-76158379 None:intergenic
ACGGTAGAGAAGAAACGCGG+TGG 0.741441 8_1:-76158395 None:intergenic
AGCACGGTAGAGAAGAAACG+CGG 0.793637 8_1:-76158398 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTAGATTTTCTTATATA+TGG + chr8_1:76159741-76159760 Msa1215080:three_prime_UTR 10.0%
!!! TTTTTAGATTTTCTTATATA+TGG + chr8_1:76159741-76159760 Msa1215080:three_prime_UTR 10.0%
!!! TAAGTTTTTTTTATCTAAAC+AGG - chr8_1:76158750-76158769 None:intergenic 15.0%
!!! CATTTTGAAACAAATTTTTT+TGG - chr8_1:76159086-76159105 None:intergenic 15.0%
!!! TAGTTTTAAAAGTAATACTT+TGG - chr8_1:76159189-76159208 None:intergenic 15.0%
!! AAATTATCCTTATTAACTAT+TGG - chr8_1:76159213-76159232 None:intergenic 15.0%
!! AATAGTTAATAAGGATAATT+TGG + chr8_1:76159212-76159231 Msa1215080:intron 15.0%
!!! TAAGTTTTTTTTATCTAAAC+AGG - chr8_1:76158750-76158769 None:intergenic 15.0%
!!! CATTTTGAAACAAATTTTTT+TGG - chr8_1:76159086-76159105 None:intergenic 15.0%
!!! TAGTTTTAAAAGTAATACTT+TGG - chr8_1:76159189-76159208 None:intergenic 15.0%
!! AAATTATCCTTATTAACTAT+TGG - chr8_1:76159213-76159232 None:intergenic 15.0%
!! AATAGTTAATAAGGATAATT+TGG + chr8_1:76159212-76159231 Msa1215080:intron 15.0%
!! AGTAAAAAAATCGCTATATT+AGG - chr8_1:76158516-76158535 None:intergenic 20.0%
!! AAAAACACAAAATCATAGAA+CGG - chr8_1:76158568-76158587 None:intergenic 20.0%
!!! TCTATGTAAATTTAAGATTG+CGG + chr8_1:76158592-76158611 Msa1215080:intron 20.0%
!! AGAAAAAGTTATTATTGCAT+TGG - chr8_1:76159126-76159145 None:intergenic 20.0%
!! AAACTAACCAATAGTTAATA+AGG + chr8_1:76159203-76159222 Msa1215080:intron 20.0%
!! AATGATTAAGAGAAAGAAAA+TGG - chr8_1:76159246-76159265 None:intergenic 20.0%
!! TATACAAATACTAGATAAGT+AGG - chr8_1:76159379-76159398 None:intergenic 20.0%
!! TACTTATCTAGTATTTGTAT+AGG + chr8_1:76159378-76159397 Msa1215080:intron 20.0%
!!! ATTTTCTTATATATGGAGTA+TGG + chr8_1:76159748-76159767 Msa1215080:three_prime_UTR 20.0%
!! AGTAAAAAAATCGCTATATT+AGG - chr8_1:76158516-76158535 None:intergenic 20.0%
!! AAAAACACAAAATCATAGAA+CGG - chr8_1:76158568-76158587 None:intergenic 20.0%
!!! TCTATGTAAATTTAAGATTG+CGG + chr8_1:76158592-76158611 Msa1215080:intron 20.0%
!! AGAAAAAGTTATTATTGCAT+TGG - chr8_1:76159126-76159145 None:intergenic 20.0%
!! AAACTAACCAATAGTTAATA+AGG + chr8_1:76159203-76159222 Msa1215080:intron 20.0%
!! AATGATTAAGAGAAAGAAAA+TGG - chr8_1:76159246-76159265 None:intergenic 20.0%
!! TATACAAATACTAGATAAGT+AGG - chr8_1:76159379-76159398 None:intergenic 20.0%
!! TACTTATCTAGTATTTGTAT+AGG + chr8_1:76159378-76159397 Msa1215080:intron 20.0%
!!! ATTTTCTTATATATGGAGTA+TGG + chr8_1:76159748-76159767 Msa1215080:three_prime_UTR 20.0%
! TGTATCTTTCAATATTCACA+CGG + chr8_1:76159007-76159026 Msa1215080:intron 25.0%
! TAGAGAAGTAAACAATCATA+AGG - chr8_1:76159406-76159425 None:intergenic 25.0%
!! TTATTGTTACTTAGTATGAC+AGG + chr8_1:76159529-76159548 Msa1215080:intron 25.0%
! TAACTGATATTGAAAACTTG+AGG + chr8_1:76159561-76159580 Msa1215080:three_prime_UTR 25.0%
!!! GAGTTTTGTTAGTTATTTTG+CGG + chr8_1:76159770-76159789 Msa1215080:three_prime_UTR 25.0%
! TGTATCTTTCAATATTCACA+CGG + chr8_1:76159007-76159026 Msa1215080:intron 25.0%
! TAGAGAAGTAAACAATCATA+AGG - chr8_1:76159406-76159425 None:intergenic 25.0%
!! TTATTGTTACTTAGTATGAC+AGG + chr8_1:76159529-76159548 Msa1215080:intron 25.0%
! TAACTGATATTGAAAACTTG+AGG + chr8_1:76159561-76159580 Msa1215080:three_prime_UTR 25.0%
!!! GAGTTTTGTTAGTTATTTTG+CGG + chr8_1:76159770-76159789 Msa1215080:three_prime_UTR 25.0%
!! TTAGTTTTTCTGCAGAATGA+GGG - chr8_1:76158277-76158296 None:intergenic 30.0%
TGTAGATGGAAGAAAAATCA+CGG - chr8_1:76158359-76158378 None:intergenic 30.0%
GATTGATATTTGCAGCTTAT+AGG + chr8_1:76158711-76158730 Msa1215080:intron 30.0%
!!! TTCAAAATGAGTGTCGTTTT+AGG - chr8_1:76159097-76159116 None:intergenic 30.0%
!! AAACGACACTCATTTTGAAA+CGG + chr8_1:76159295-76159314 Msa1215080:intron 30.0%
CTCGATAAGAGGAAAATAAA+AGG - chr8_1:76159492-76159511 None:intergenic 30.0%
CGTATGTTGAAAACTTAACA+AGG + chr8_1:76159620-76159639 Msa1215080:three_prime_UTR 30.0%
TTAACAAGGTTATCTGATGA+AGG + chr8_1:76159634-76159653 Msa1215080:three_prime_UTR 30.0%
ATAGGAATCATCTTAGAGAT+AGG + chr8_1:76159677-76159696 Msa1215080:three_prime_UTR 30.0%
!! TTAGTTTTTCTGCAGAATGA+GGG - chr8_1:76158277-76158296 None:intergenic 30.0%
TGTAGATGGAAGAAAAATCA+CGG - chr8_1:76158359-76158378 None:intergenic 30.0%
GATTGATATTTGCAGCTTAT+AGG + chr8_1:76158711-76158730 Msa1215080:intron 30.0%
!!! TTCAAAATGAGTGTCGTTTT+AGG - chr8_1:76159097-76159116 None:intergenic 30.0%
!! AAACGACACTCATTTTGAAA+CGG + chr8_1:76159295-76159314 Msa1215080:intron 30.0%
CTCGATAAGAGGAAAATAAA+AGG - chr8_1:76159492-76159511 None:intergenic 30.0%
CGTATGTTGAAAACTTAACA+AGG + chr8_1:76159620-76159639 Msa1215080:three_prime_UTR 30.0%
TTAACAAGGTTATCTGATGA+AGG + chr8_1:76159634-76159653 Msa1215080:three_prime_UTR 30.0%
ATAGGAATCATCTTAGAGAT+AGG + chr8_1:76159677-76159696 Msa1215080:three_prime_UTR 30.0%
!!! GTTAGTTTTTCTGCAGAATG+AGG - chr8_1:76158278-76158297 None:intergenic 35.0%
ATATTTGCAGCTTATAGGTC+TGG + chr8_1:76158716-76158735 Msa1215080:intron 35.0%
TTCAATATTCACACGGATAC+CGG + chr8_1:76159014-76159033 Msa1215080:intron 35.0%
!! AAGCGACACTCATTTTGAAA+CGG - chr8_1:76159060-76159079 None:intergenic 35.0%
! TGTGCAGAGTATTAATTGGA+GGG - chr8_1:76159160-76159179 None:intergenic 35.0%
! GTAGTGTGCAGAGTATTAAT+TGG - chr8_1:76159164-76159183 None:intergenic 35.0%
AAAACACGATACTCGATAAG+AGG - chr8_1:76159503-76159522 None:intergenic 35.0%
CTGATATTGAAAACTTGAGG+CGG + chr8_1:76159564-76159583 Msa1215080:three_prime_UTR 35.0%
ATCATCTTAGAGATAGGATG+TGG + chr8_1:76159683-76159702 Msa1215080:three_prime_UTR 35.0%
TCATCTTAGAGATAGGATGT+GGG + chr8_1:76159684-76159703 Msa1215080:three_prime_UTR 35.0%
!!! GTTAGTTTTTCTGCAGAATG+AGG - chr8_1:76158278-76158297 None:intergenic 35.0%
ATATTTGCAGCTTATAGGTC+TGG + chr8_1:76158716-76158735 Msa1215080:intron 35.0%
TTCAATATTCACACGGATAC+CGG + chr8_1:76159014-76159033 Msa1215080:intron 35.0%
!! AAGCGACACTCATTTTGAAA+CGG - chr8_1:76159060-76159079 None:intergenic 35.0%
! TGTGCAGAGTATTAATTGGA+GGG - chr8_1:76159160-76159179 None:intergenic 35.0%
! GTAGTGTGCAGAGTATTAAT+TGG - chr8_1:76159164-76159183 None:intergenic 35.0%
AAAACACGATACTCGATAAG+AGG - chr8_1:76159503-76159522 None:intergenic 35.0%
CTGATATTGAAAACTTGAGG+CGG + chr8_1:76159564-76159583 Msa1215080:three_prime_UTR 35.0%
ATCATCTTAGAGATAGGATG+TGG + chr8_1:76159683-76159702 Msa1215080:three_prime_UTR 35.0%
TCATCTTAGAGATAGGATGT+GGG + chr8_1:76159684-76159703 Msa1215080:three_prime_UTR 35.0%
AGAACACTGAGAAGCGAAAA+TGG + chr8_1:76158301-76158320 Msa1215080:CDS 40.0%
AGATGGAAGAAAAATCACGG+CGG - chr8_1:76158356-76158375 None:intergenic 40.0%
AAGAAGAAGCAAGGTGTAGA+TGG - chr8_1:76158373-76158392 None:intergenic 40.0%
!!! TTCTTCTCTGCGGTTTTTTC+AGG + chr8_1:76158423-76158442 Msa1215080:CDS 40.0%
!!! GACACTCATTTTGAAACGGA+GGG - chr8_1:76159299-76159318 None:intergenic 40.0%
! GTGTGCAGAGTATTAATTGG+AGG - chr8_1:76159161-76159180 None:intergenic 40.0%
!!! GACACTCATTTTGAAACGGA+GGG + chr8_1:76159299-76159318 Msa1215080:intron 40.0%
!! AACGGAGGGAGTATTTGTTT+AGG + chr8_1:76159313-76159332 Msa1215080:intron 40.0%
AGAACACTGAGAAGCGAAAA+TGG + chr8_1:76158301-76158320 Msa1215080:CDS 40.0%
AGATGGAAGAAAAATCACGG+CGG - chr8_1:76158356-76158375 None:intergenic 40.0%
AAGAAGAAGCAAGGTGTAGA+TGG - chr8_1:76158373-76158392 None:intergenic 40.0%
!!! TTCTTCTCTGCGGTTTTTTC+AGG + chr8_1:76158423-76158442 Msa1215080:CDS 40.0%
!!! GACACTCATTTTGAAACGGA+GGG - chr8_1:76159299-76159318 None:intergenic 40.0%
! GTGTGCAGAGTATTAATTGG+AGG - chr8_1:76159161-76159180 None:intergenic 40.0%
!!! GACACTCATTTTGAAACGGA+GGG + chr8_1:76159299-76159318 Msa1215080:intron 40.0%
!! AACGGAGGGAGTATTTGTTT+AGG + chr8_1:76159313-76159332 Msa1215080:intron 40.0%
AGCGAAAATGGCGATTTCGA+CGG + chr8_1:76158313-76158332 Msa1215080:CDS 45.0%
AGAAAAATCACGGCGGAGAT+CGG - chr8_1:76158349-76158368 None:intergenic 45.0%
!! GGGAGTACAGGTTTTGTATC+CGG - chr8_1:76159036-76159055 None:intergenic 45.0%
!!! TTTTGAAACGGAGGGAGTAC+AGG - chr8_1:76159048-76159067 None:intergenic 45.0%
!!! CGACACTCATTTTGAAACGG+AGG - chr8_1:76159298-76159317 None:intergenic 45.0%
!!! CGACACTCATTTTGAAACGG+AGG + chr8_1:76159298-76159317 Msa1215080:intron 45.0%
AACGAGGTTCCTAACCTTGA+AGG + chr8_1:76159589-76159608 Msa1215080:three_prime_UTR 45.0%
ACGAGGTTCCTAACCTTGAA+GGG + chr8_1:76159590-76159609 Msa1215080:three_prime_UTR 45.0%
AGCGAAAATGGCGATTTCGA+CGG + chr8_1:76158313-76158332 Msa1215080:CDS 45.0%
AGAAAAATCACGGCGGAGAT+CGG - chr8_1:76158349-76158368 None:intergenic 45.0%
!! GGGAGTACAGGTTTTGTATC+CGG - chr8_1:76159036-76159055 None:intergenic 45.0%
!!! TTTTGAAACGGAGGGAGTAC+AGG - chr8_1:76159048-76159067 None:intergenic 45.0%
!!! CGACACTCATTTTGAAACGG+AGG - chr8_1:76159298-76159317 None:intergenic 45.0%
!!! CGACACTCATTTTGAAACGG+AGG + chr8_1:76159298-76159317 Msa1215080:intron 45.0%
AACGAGGTTCCTAACCTTGA+AGG + chr8_1:76159589-76159608 Msa1215080:three_prime_UTR 45.0%
ACGAGGTTCCTAACCTTGAA+GGG + chr8_1:76159590-76159609 Msa1215080:three_prime_UTR 45.0%
AGCACGGTAGAGAAGAAACG+CGG - chr8_1:76158401-76158420 None:intergenic 50.0%
ACCGTGCTTCTTCTTCTCTG+CGG + chr8_1:76158413-76158432 Msa1215080:CDS 50.0%
ACCGCAGAGAAGAAGAAGCA+CGG - chr8_1:76158417-76158436 None:intergenic 50.0%
AAAACTTGAGGCGGTGAACG+AGG + chr8_1:76159573-76159592 Msa1215080:three_prime_UTR 50.0%
GAGCTCATCCCTTCAAGGTT+AGG - chr8_1:76159601-76159620 None:intergenic 50.0%
CATACGAGCTCATCCCTTCA+AGG - chr8_1:76159606-76159625 None:intergenic 50.0%
! TGATGAAGGTGCAGCTGAGA+TGG + chr8_1:76159648-76159667 Msa1215080:three_prime_UTR 50.0%
CAGCTGAGATGGCAATGGAT+AGG + chr8_1:76159659-76159678 Msa1215080:three_prime_UTR 50.0%
AGCACGGTAGAGAAGAAACG+CGG - chr8_1:76158401-76158420 None:intergenic 50.0%
ACCGTGCTTCTTCTTCTCTG+CGG + chr8_1:76158413-76158432 Msa1215080:CDS 50.0%
ACCGCAGAGAAGAAGAAGCA+CGG - chr8_1:76158417-76158436 None:intergenic 50.0%
AAAACTTGAGGCGGTGAACG+AGG + chr8_1:76159573-76159592 Msa1215080:three_prime_UTR 50.0%
GAGCTCATCCCTTCAAGGTT+AGG - chr8_1:76159601-76159620 None:intergenic 50.0%
CATACGAGCTCATCCCTTCA+AGG - chr8_1:76159606-76159625 None:intergenic 50.0%
! TGATGAAGGTGCAGCTGAGA+TGG + chr8_1:76159648-76159667 Msa1215080:three_prime_UTR 50.0%
CAGCTGAGATGGCAATGGAT+AGG + chr8_1:76159659-76159678 Msa1215080:three_prime_UTR 50.0%
GCGGTGGAGAAGAAGAAGCA+AGG - chr8_1:76158382-76158401 None:intergenic 55.0%
ACGGTAGAGAAGAAACGCGG+TGG - chr8_1:76158398-76158417 None:intergenic 55.0%
AGGTGCAGCTGAGATGGCAA+TGG + chr8_1:76159654-76159673 Msa1215080:three_prime_UTR 55.0%
GCGGTGGAGAAGAAGAAGCA+AGG - chr8_1:76158382-76158401 None:intergenic 55.0%
ACGGTAGAGAAGAAACGCGG+TGG - chr8_1:76158398-76158417 None:intergenic 55.0%
AGGTGCAGCTGAGATGGCAA+TGG + chr8_1:76159654-76159673 Msa1215080:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 76158253 76159844 76158253 ID=Msa1215080;Name=Msa1215080
chr8_1 mRNA 76158253 76159844 76158253 ID=Msa1215080-mRNA-1;Parent=Msa1215080;Name=Msa1215080-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|0|1|2|287|68
chr8_1 exon 76158253 76158444 76158253 ID=Msa1215080-mRNA-1:exon:26142;Parent=Msa1215080-mRNA-1
chr8_1 exon 76159543 76159844 76159543 ID=Msa1215080-mRNA-1:exon:26143;Parent=Msa1215080-mRNA-1
chr8_1 CDS 76158253 76158444 76158253 ID=Msa1215080-mRNA-1:cds;Parent=Msa1215080-mRNA-1
chr8_1 CDS 76159543 76159557 76159543 ID=Msa1215080-mRNA-1:cds;Parent=Msa1215080-mRNA-1
chr8_1 three_prime_UTR 76159558 76159844 76159558 ID=Msa1215080-mRNA-1:three_prime_utr;Parent=Msa1215080-mRNA-1
Gene Sequence

>Msa1215080

AAAATTTGGATCAAAAATTATCCCTCATTCTGCAGAAAAACTAACGTGAGAACACTGAGAAGCGAAAATGGCGATTTCGACGGCGATTCTTCTCCGATCTCCGCCGTGATTTTTCTTCCATCTACACCTTGCTTCTTCTTCTCCACCGCGTTTCTTCTCTACCGTGCTTCTTCTTCTCTGCGGTTTTTTCAGTATGACAGGTTATAA
Protein sequence

>Msa1215080

KIWIKNYPSFCRKTNVRTLRSENGDFDGDSSPISAVIFLPSTPCFFFSTAFLLYRASSSLRFFQYDRL*