AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680034064.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680034064.01.T01 MTR_0050s0180 93.220 118 7 1 1 118 57 173 8.81e-76 222
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680034064.01.T01 AT5G51720 75.610 82 18 1 37 118 28 107 5.61e-42 134

Find 33 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCACTCTTCCTTATATC+TGG 0.212325 6:+79901423 None:intergenic
ATTTCTTATTTATTGAATTA+AGG 0.257072 6:-79900045 MsG0680034064.01.T01:three_prime_UTR
GAACTTTGCAATAAGGTAGA+TGG 0.326744 6:+79901668 None:intergenic
AAAGGAACTAGTGTTGAAAT+TGG 0.341338 6:+79901515 None:intergenic
AATTTCAACACTAGTTCCTT+TGG 0.378332 6:-79901513 MsG0680034064.01.T01:CDS
ACTGAACCATACCTGCAATA+AGG 0.381259 6:+79901351 None:intergenic
TGGCTTTGTTGTGCTTTACA+TGG 0.398604 6:+79900238 None:intergenic
TCTCACTTAAACATGGCTTT+TGG 0.402198 6:+79901559 None:intergenic
TATAAGGAAGAGTGAAGAAA+AGG 0.402584 6:-79901418 MsG0680034064.01.T01:CDS
AACACTAGTTCCTTTGGTAT+TGG 0.404546 6:-79901507 MsG0680034064.01.T01:CDS
AGGCTGTTACACCTTATTGC+AGG 0.425079 6:-79901362 MsG0680034064.01.T01:intron
GTAGCATAAATCCAGATATA+AGG 0.427754 6:-79901434 MsG0680034064.01.T01:CDS
TGATACAGATGCTGGAGATC+AGG 0.452783 6:-79900285 MsG0680034064.01.T01:intron
CAGACATAACATTTCAATGT+TGG 0.459795 6:-79900115 MsG0680034064.01.T01:three_prime_UTR
GGCACAAAACTACACCAACT+TGG 0.466620 6:+79901580 None:intergenic
GTGGTGGTGAAAGCAGAGAC+AGG 0.472527 6:-79901465 MsG0680034064.01.T01:CDS
AAGCCACTGGAGATAATGTT+GGG 0.514803 6:-79900221 MsG0680034064.01.T01:CDS
GCAATAAGGTGTAACAGCCT+TGG 0.525200 6:+79901365 None:intergenic
AAAGCCACTGGAGATAATGT+TGG 0.533290 6:-79900222 MsG0680034064.01.T01:CDS
CTAGTTCCTTTGGTATTGGT+AGG 0.550489 6:-79901503 MsG0680034064.01.T01:CDS
GAAAGCAAGAAGTGTGGTGG+TGG 0.552869 6:-79901481 MsG0680034064.01.T01:CDS
GGAACCTTTCCTCTGTGTGA+TGG 0.562888 6:-79900264 MsG0680034064.01.T01:CDS
GTAAAGCACAACAAAGCCAC+TGG 0.579483 6:-79900234 MsG0680034064.01.T01:CDS
TGCTTTCCTACCAATACCAA+AGG 0.582424 6:+79901497 None:intergenic
TGTGCTCAGTGAAGTCTCCA+AGG 0.596449 6:-79901382 MsG0680034064.01.T01:CDS
TGGTGGTGAAAGCAGAGACA+GGG 0.597940 6:-79901464 MsG0680034064.01.T01:CDS
GCTTCCATCACACAGAGGAA+AGG 0.616730 6:+79900260 None:intergenic
AGGCCCAACATTATCTCCAG+TGG 0.629442 6:+79900218 None:intergenic
TGGTAGGAAAGCAAGAAGTG+TGG 0.633825 6:-79901487 MsG0680034064.01.T01:CDS
GGTGGTGAAAGCAGAGACAG+GGG 0.666105 6:-79901463 MsG0680034064.01.T01:CDS
TAGGAAAGCAAGAAGTGTGG+TGG 0.698142 6:-79901484 MsG0680034064.01.T01:CDS
GTGGTGAAAGCAGAGACAGG+GGG 0.706898 6:-79901462 MsG0680034064.01.T01:CDS
ACATGGCTTCCATCACACAG+AGG 0.761842 6:+79900255 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTCTTATTTATTGAATTA+AGG - Chr6:79901669-79901688 MsG0680034064.01.T01:five_prime_UTR 10.0%
!!! TTATGTTTTTCATTTATTTA+TGG - Chr6:79900389-79900408 MsG0680034064.01.T01:intron 10.0%
!! CAATAATCAAATTTCAATAA+TGG + Chr6:79900480-79900499 None:intergenic 15.0%
!! CATTATTGAAATTTGATTAT+TGG - Chr6:79900478-79900497 MsG0680034064.01.T01:intron 15.0%
!! AAAACAAATCTTAATCTTTC+TGG - Chr6:79901394-79901413 MsG0680034064.01.T01:CDS 20.0%
!! CTAAATTCAATAAACTATGT+AGG + Chr6:79900538-79900557 None:intergenic 20.0%
!! TATCACAAATTAACAATGTT+TGG - Chr6:79900881-79900900 MsG0680034064.01.T01:intron 20.0%
!! TATGCTTCTATAATATATGT+TGG - Chr6:79901204-79901223 MsG0680034064.01.T01:intron 20.0%
!!! AGAAAGATTAAGATTTGTTT+TGG + Chr6:79901395-79901414 None:intergenic 20.0%
!!! GAAAAAAAATCAATTTTCAG+AGG - Chr6:79901564-79901583 MsG0680034064.01.T01:CDS 20.0%
!!! TGATTATTGGTTAATTTATG+TGG - Chr6:79900491-79900510 MsG0680034064.01.T01:intron 20.0%
! ATGTTTAAGTGAGAGAAAAA+AGG - Chr6:79900164-79900183 MsG0680034064.01.T01:three_prime_UTR 25.0%
! CACAAAAAATTCATACTCAA+TGG - Chr6:79900098-79900117 MsG0680034064.01.T01:three_prime_UTR 25.0%
! CCACATAAAGAACTTATTAA+TGG - Chr6:79901166-79901185 MsG0680034064.01.T01:intron 25.0%
! CCATTAATAAGTTCTTTATG+TGG + Chr6:79901169-79901188 None:intergenic 25.0%
! TGATATTAGATGAATGATTC+TGG - Chr6:79900728-79900747 MsG0680034064.01.T01:intron 25.0%
! TGTTTAAGTGAGAGAAAAAA+GGG - Chr6:79900165-79900184 MsG0680034064.01.T01:three_prime_UTR 25.0%
!! ATGATAATCTGGAATAATGT+CGG - Chr6:79900935-79900954 MsG0680034064.01.T01:intron 25.0%
!! GCATTTTGTATATGATAATC+TGG - Chr6:79900924-79900943 MsG0680034064.01.T01:intron 25.0%
!! TTTTGTGTTTATCTTCTCTT+TGG + Chr6:79900085-79900104 None:intergenic 25.0%
!!! AAGTTTTGAACTTTGCAATA+AGG + Chr6:79900056-79900075 None:intergenic 25.0%
!!! AATCTTAATCTTTCTGGTTT+TGG - Chr6:79901400-79901419 MsG0680034064.01.T01:CDS 25.0%
!!! ATCTTAATCTTTCTGGTTTT+GGG - Chr6:79901401-79901420 MsG0680034064.01.T01:CDS 25.0%
!!! CTCTATTTTTTCAAAAGAAG+AGG + Chr6:79901519-79901538 None:intergenic 25.0%
!!! TTTTTTCTCTCACTTAAACA+TGG + Chr6:79900165-79900184 None:intergenic 25.0%
AATTTCAACACTAGTTCCTT+TGG - Chr6:79900201-79900220 MsG0680034064.01.T01:CDS 30.0%
CAGACATAACATTTCAATGT+TGG - Chr6:79901599-79901618 MsG0680034064.01.T01:CDS 30.0%
GAATCTCTTGTTGAGAAATT+AGG - Chr6:79900978-79900997 MsG0680034064.01.T01:intron 30.0%
GAGAGAAAAAAGGGAATTAT+AGG - Chr6:79900174-79900193 MsG0680034064.01.T01:three_prime_UTR 30.0%
GCTTCTATAATATATGTTGG+TGG - Chr6:79901207-79901226 MsG0680034064.01.T01:intron 30.0%
GTAGCATAAATCCAGATATA+AGG - Chr6:79900280-79900299 MsG0680034064.01.T01:CDS 30.0%
TATAAGGAAGAGTGAAGAAA+AGG - Chr6:79900296-79900315 MsG0680034064.01.T01:intron 30.0%
TATGGTTAAGTGTATCATTG+TGG - Chr6:79900407-79900426 MsG0680034064.01.T01:intron 30.0%
TGAGAAATTAGGATGTTGAT+AGG - Chr6:79900989-79901008 MsG0680034064.01.T01:intron 30.0%
TGATTGATTACATCTGTTTC+TGG - Chr6:79900806-79900825 MsG0680034064.01.T01:intron 30.0%
TTATGTGGAATCTACTAACT+GGG + Chr6:79901154-79901173 None:intergenic 30.0%
TTTATGTGGAATCTACTAAC+TGG + Chr6:79901155-79901174 None:intergenic 30.0%
! AAAGGAACTAGTGTTGAAAT+TGG + Chr6:79900202-79900221 None:intergenic 30.0%
! TGATAATCTGGAATAATGTC+GGG - Chr6:79900936-79900955 MsG0680034064.01.T01:intron 30.0%
AACACTAGTTCCTTTGGTAT+TGG - Chr6:79900207-79900226 MsG0680034064.01.T01:CDS 35.0%
CTCTCAAATAGTTTCACAAG+TGG - Chr6:79900601-79900620 MsG0680034064.01.T01:intron 35.0%
GAACTTTGCAATAAGGTAGA+TGG + Chr6:79900049-79900068 None:intergenic 35.0%
TCTTCACTCTTCCTTATATC+TGG + Chr6:79900294-79900313 None:intergenic 35.0%
TTTGTCGAATCTCTATAACG+TGG - Chr6:79901111-79901130 MsG0680034064.01.T01:intron 35.0%
! ACATAAGCAGGATTTTTACG+TGG + Chr6:79901017-79901036 None:intergenic 35.0%
! GATAATCTGGAATAATGTCG+GGG - Chr6:79900937-79900956 MsG0680034064.01.T01:intron 35.0%
! TCTCACTTAAACATGGCTTT+TGG + Chr6:79900158-79900177 None:intergenic 35.0%
!! ATTACATCTGTTTCTGGAAG+TGG - Chr6:79900812-79900831 MsG0680034064.01.T01:intron 35.0%
AAAGCCACTGGAGATAATGT+TGG - Chr6:79901492-79901511 MsG0680034064.01.T01:CDS 40.0%
AAGCCACTGGAGATAATGTT+GGG - Chr6:79901493-79901512 MsG0680034064.01.T01:CDS 40.0%
ACTGAACCATACCTGCAATA+AGG + Chr6:79900366-79900385 None:intergenic 40.0%
GTTACACCTTATTGCAGGTA+TGG - Chr6:79900357-79900376 MsG0680034064.01.T01:intron 40.0%
TAAAAGGAGAGGGTTGTGTT+AGG - Chr6:79901067-79901086 MsG0680034064.01.T01:intron 40.0%
TAACGAGGCTTAACATAAGC+AGG + Chr6:79901029-79901048 None:intergenic 40.0%
TAAGCCTCGTTATACATTGC+CGG - Chr6:79901037-79901056 MsG0680034064.01.T01:intron 40.0%
TGCTTTCCTACCAATACCAA+AGG + Chr6:79900220-79900239 None:intergenic 40.0%
TGGAATCTACTAACTGGGAT+CGG + Chr6:79901149-79901168 None:intergenic 40.0%
! ACAACCCTCTCCTTTTACTT+GGG + Chr6:79901064-79901083 None:intergenic 40.0%
!! AAGTTTTACGTTGACTGTCG+AGG + Chr6:79901093-79901112 None:intergenic 40.0%
!! CTAGTTCCTTTGGTATTGGT+AGG - Chr6:79900211-79900230 MsG0680034064.01.T01:CDS 40.0%
!! GCATCTGTTTTAAGCCAAGT+TGG - Chr6:79900120-79900139 MsG0680034064.01.T01:three_prime_UTR 40.0%
!! TGGCTTTGTTGTGCTTTACA+TGG + Chr6:79901479-79901498 None:intergenic 40.0%
AGGCTGTTACACCTTATTGC+AGG - Chr6:79900352-79900371 MsG0680034064.01.T01:intron 45.0%
GCAATAAGGTGTAACAGCCT+TGG + Chr6:79900352-79900371 None:intergenic 45.0%
GGCACAAAACTACACCAACT+TGG + Chr6:79900137-79900156 None:intergenic 45.0%
GTAAAGCACAACAAAGCCAC+TGG - Chr6:79901480-79901499 MsG0680034064.01.T01:CDS 45.0%
TGATACAGATGCTGGAGATC+AGG - Chr6:79901429-79901448 MsG0680034064.01.T01:CDS 45.0%
TGGTAGGAAAGCAAGAAGTG+TGG - Chr6:79900227-79900246 MsG0680034064.01.T01:CDS 45.0%
! CACAACCCTCTCCTTTTACT+TGG + Chr6:79901065-79901084 None:intergenic 45.0%
! TAGGAAAGCAAGAAGTGTGG+TGG - Chr6:79900230-79900249 MsG0680034064.01.T01:CDS 45.0%
ACATGGCTTCCATCACACAG+AGG + Chr6:79901462-79901481 None:intergenic 50.0%
AGGCCCAACATTATCTCCAG+TGG + Chr6:79901499-79901518 None:intergenic 50.0%
CATTGCCGGTCCCAAGTAAA+AGG - Chr6:79901051-79901070 MsG0680034064.01.T01:intron 50.0%
CGGTCCCAAGTAAAAGGAGA+GGG - Chr6:79901057-79901076 MsG0680034064.01.T01:intron 50.0%
GCTTCCATCACACAGAGGAA+AGG + Chr6:79901457-79901476 None:intergenic 50.0%
GGAACCTTTCCTCTGTGTGA+TGG - Chr6:79901450-79901469 MsG0680034064.01.T01:CDS 50.0%
GGGTGCTTTGATACAGATGC+TGG - Chr6:79901421-79901440 MsG0680034064.01.T01:CDS 50.0%
TGTGCTCAGTGAAGTCTCCA+AGG - Chr6:79900332-79900351 MsG0680034064.01.T01:intron 50.0%
! CCTCTCCTTTTACTTGGGAC+CGG + Chr6:79901059-79901078 None:intergenic 50.0%
! GAAAGCAAGAAGTGTGGTGG+TGG - Chr6:79900233-79900252 MsG0680034064.01.T01:CDS 50.0%
! TGGTGGTGAAAGCAGAGACA+GGG - Chr6:79900250-79900269 MsG0680034064.01.T01:CDS 50.0%
CCGGTCCCAAGTAAAAGGAG+AGG - Chr6:79901056-79901075 MsG0680034064.01.T01:intron 55.0%
GGGACCGGCAATGTATAACG+AGG + Chr6:79901044-79901063 None:intergenic 55.0%
GGTGGTGAAAGCAGAGACAG+GGG - Chr6:79900251-79900270 MsG0680034064.01.T01:CDS 55.0%
GTGGTGAAAGCAGAGACAGG+GGG - Chr6:79900252-79900271 MsG0680034064.01.T01:CDS 55.0%
! AAAGCAGAGACAGGGGGTGT+GGG - Chr6:79900258-79900277 MsG0680034064.01.T01:CDS 55.0%
! GTGGTGGTGAAAGCAGAGAC+AGG - Chr6:79900249-79900268 MsG0680034064.01.T01:CDS 55.0%
GAAAGCAGAGACAGGGGGTG+TGG - Chr6:79900257-79900276 MsG0680034064.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr6 gene 79900016 79901720 79900016 ID=MsG0680034064.01;Name=MsG0680034064.01
Chr6 mRNA 79900016 79901720 79900016 ID=MsG0680034064.01.T01;Parent=MsG0680034064.01;Name=MsG0680034064.01.T01;_AED=0.45;_eAED=0.45;_QI=101|1|1|1|0|0|2|184|118
Chr6 exon 79901363 79901720 79901363 ID=MsG0680034064.01.T01:exon:9705;Parent=MsG0680034064.01.T01
Chr6 exon 79900016 79900299 79900016 ID=MsG0680034064.01.T01:exon:9706;Parent=MsG0680034064.01.T01
Chr6 five_prime_UTR 79901620 79901720 79901620 ID=MsG0680034064.01.T01:five_prime_utr;Parent=MsG0680034064.01.T01
Chr6 CDS 79901363 79901619 79901363 ID=MsG0680034064.01.T01:cds;Parent=MsG0680034064.01.T01
Chr6 CDS 79900200 79900299 79900200 ID=MsG0680034064.01.T01:cds;Parent=MsG0680034064.01.T01
Chr6 three_prime_UTR 79900016 79900199 79900016 ID=MsG0680034064.01.T01:three_prime_utr;Parent=MsG0680034064.01.T01
Gene Sequence

>MsG0680034064.01.T01

ATGGCATCTGTTTTAAGCCAAGTTGGTGTAGTTTTGTGCCAAAAGCCATGTTTAAGTGAGAGAAAAAAGGGAATTATAGGTACCAATTTCAACACTAGTTCCTTTGGTATTGGTAGGAAAGCAAGAAGTGTGGTGGTGGTGAAAGCAGAGACAGGGGGTGTGGGTAGCATAAATCCAGATATAAGGAAGAGTGAAGAAAAGGTTGTTGATGCTGTTGTGCTCAGTGAAGTCTCCAAGGCTGTTACACCTTATTGCAGATGCTGGAGATCAGGAACCTTTCCTCTGTGTGATGGAAGCCATGTAAAGCACAACAAAGCCACTGGAGATAATGTTGGGCCTCTTCTTTTGAAAAAATAG

Protein sequence

>MsG0680034064.01.T01

MASVLSQVGVVLCQKPCLSERKKGIIGTNFNTSSFGIGRKARSVVVVKAETGGVGSINPDIRKSEEKVVDAVVLSEVSKAVTPYCRCWRSGTFPLCDGSHVKHNKATGDNVGPLLLKK*