AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480020850.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020850.01.T01 MTR_4g061050 94.574 129 7 0 3 131 930 1058 1.01e-82 262
MsG0480020850.01.T01 MTR_4g036760 85.271 129 19 0 3 131 931 1059 4.19e-71 230
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020850.01.T01 AT5G61460 70.543 129 38 0 3 131 929 1057 5.16e-60 199
MsG0480020850.01.T01 AT5G07660 69.767 129 39 0 3 131 930 1058 1.09e-55 186

Find 41 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTCATCCATTGCTCTAAA+TGG 0.155010 4:+49637516 None:intergenic
GGATGAATTTGATGTCTTTA+TGG 0.190524 4:-49637502 MsG0480020850.01.T01:intron
TCGAGACACAGGGGACTTTC+AGG 0.220544 4:-49638184 MsG0480020850.01.T01:intron
ATCCTCATGATCAGATTTAA+TGG 0.238416 4:-49638476 None:intergenic
TTTAAAATCTGTGATGTGTT+AGG 0.288975 4:-49636580 MsG0480020850.01.T01:three_prime_UTR
CAGCTCTGTTTGATGTATCT+TGG 0.325637 4:+49638208 None:intergenic
ATTGTGATTTCCTTTATTTA+TGG 0.326107 4:-49636698 MsG0480020850.01.T01:three_prime_UTR
AGCTCTGTTTGATGTATCTT+GGG 0.341882 4:+49638209 None:intergenic
CAATATACCTAGTATCATTC+GGG 0.359556 4:+49637193 None:intergenic
CTTCAAGCTGCCATAAATAA+AGG 0.364431 4:+49636688 None:intergenic
GCTTGGTGAAGGGAGGGAAC+AGG 0.377631 4:-49636760 MsG0480020850.01.T01:CDS
ATTCATCCATTGCTCTAAAT+GGG 0.390531 4:+49637517 None:intergenic
CCAATATACCTAGTATCATT+CGG 0.408883 4:+49637192 None:intergenic
TAAATAAAGGAAATCACAAT+TGG 0.455083 4:+49636701 None:intergenic
TGATCACCCCGAATGATACT+AGG 0.480437 4:-49637200 MsG0480020850.01.T01:intron
CAAATTTACCTCAATCGATA+AGG 0.486609 4:+49638397 None:intergenic
ACTTATCAAAGTTGATTATG+AGG 0.494408 4:-49638426 MsG0480020850.01.T01:CDS
AACAGAGCTGTTCGAGACAC+AGG 0.499601 4:-49638195 MsG0480020850.01.T01:CDS
TCGGGGTGATCAATATCCAC+TGG 0.514310 4:+49637211 None:intergenic
TTGAATGTGCAGCTTGGTGA+AGG 0.546479 4:-49636771 MsG0480020850.01.T01:intron
AATCACAATTGGTCAAGCAC+GGG 0.546782 4:+49636712 None:intergenic
CTTGGTGAAGGGAGGGAACA+GGG 0.567012 4:-49636759 MsG0480020850.01.T01:CDS
GGAGGCCCCATTTAGAGCAA+TGG 0.569434 4:-49637523 MsG0480020850.01.T01:CDS
AAATCACAATTGGTCAAGCA+CGG 0.573228 4:+49636711 None:intergenic
CAGGGTTAAGAAGATGCAAA+TGG 0.576301 4:-49636741 MsG0480020850.01.T01:CDS
GGGCCTCCGTCATTTCATGA+AGG 0.578750 4:+49637538 None:intergenic
CGGGGTGATCAATATCCACT+GGG 0.591640 4:+49637212 None:intergenic
GGAAACGACCTTATCGATTG+AGG 0.596487 4:-49638405 MsG0480020850.01.T01:intron
ACAGAGCTGTTCGAGACACA+GGG 0.599630 4:-49638194 MsG0480020850.01.T01:CDS
GGCCTCCGTCATTTCATGAA+GGG 0.610350 4:+49637539 None:intergenic
ATTAGCCCTTCATGAAATGA+CGG 0.611197 4:-49637544 MsG0480020850.01.T01:CDS
GCTCTGTTTGATGTATCTTG+GGG 0.619473 4:+49638210 None:intergenic
TGAATGTGCAGCTTGGTGAA+GGG 0.630847 4:-49636770 MsG0480020850.01.T01:intron
TTCATCCATTGCTCTAAATG+GGG 0.635651 4:+49637518 None:intergenic
ATCACAATTGGTCAAGCACG+GGG 0.646023 4:+49636713 None:intergenic
TGTGCAGCTTGGTGAAGGGA+GGG 0.668613 4:-49636766 MsG0480020850.01.T01:intron
ATGTGCAGCTTGGTGAAGGG+AGG 0.676851 4:-49636767 MsG0480020850.01.T01:intron
CTGAGGCACAAGGATCCCAG+TGG 0.705015 4:-49637227 MsG0480020850.01.T01:CDS
AGCCCTTCATGAAATGACGG+AGG 0.719050 4:-49637541 MsG0480020850.01.T01:CDS
AATATACCTAGTATCATTCG+GGG 0.733090 4:+49637194 None:intergenic
CAGAGCTGTTCGAGACACAG+GGG 0.773484 4:-49638193 MsG0480020850.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATTGTATGTATAAATAA+TGG + Chr4:49636826-49636845 None:intergenic 10.0%
!!! TGAGTTTTAATTTATTTTTC+TGG - Chr4:49637151-49637170 MsG0480020850.01.T01:intron 15.0%
!!! TTAAAATAAGTAAACGTTTT+AGG + Chr4:49636695-49636714 None:intergenic 15.0%
!! ACCAATTAATTACCATAAAA+AGG + Chr4:49636638-49636657 None:intergenic 20.0%
!! AGGTAAATGAAAAGTAAAAA+AGG + Chr4:49636618-49636637 None:intergenic 20.0%
!! ATAGTTTATTTAGATTACAC+TGG + Chr4:49637522-49637541 None:intergenic 20.0%
!! TAAATAAAGGAAATCACAAT+TGG + Chr4:49638256-49638275 None:intergenic 20.0%
!!! AAAAAGATGATTTTCACAAA+TGG + Chr4:49638293-49638312 None:intergenic 20.0%
!!! AATTTGCTTCTTTTGTTTTT+AGG - Chr4:49636713-49636732 MsG0480020850.01.T01:exon 20.0%
!!! ACCTTTTTATGGTAATTAAT+TGG - Chr4:49636634-49636653 MsG0480020850.01.T01:three_prime_UTR 20.0%
!!! ACTTTTCATTTACCTTTTTA+TGG - Chr4:49636623-49636642 MsG0480020850.01.T01:three_prime_UTR 20.0%
!!! ATTGTGATTTCCTTTATTTA+TGG - Chr4:49638256-49638275 MsG0480020850.01.T01:intron 20.0%
!!! ATTTTATTATTGAAGTGACA+TGG - Chr4:49638083-49638102 MsG0480020850.01.T01:intron 20.0%
! AACCTACTTAAGTATAATAC+AGG + Chr4:49637858-49637877 None:intergenic 25.0%
! AATTTGATGTCTTTATGGTA+TGG - Chr4:49637457-49637476 MsG0480020850.01.T01:intron 25.0%
! AGAGCACATAGAATTAATTT+AGG - Chr4:49637009-49637028 MsG0480020850.01.T01:intron 25.0%
! ATGGACATTATTATTTGTTC+TGG - Chr4:49637793-49637812 MsG0480020850.01.T01:intron 25.0%
! CCAAATAAAACTACTTGATT+TGG - Chr4:49637964-49637983 MsG0480020850.01.T01:intron 25.0%
! GTAAAAAAGGAAACTGAAAA+TGG + Chr4:49636605-49636624 None:intergenic 25.0%
! TAATTGACTACTATGTAACT+GGG - Chr4:49637646-49637665 MsG0480020850.01.T01:intron 25.0%
! TGCAAACATATTGTATCATA+TGG - Chr4:49636894-49636913 MsG0480020850.01.T01:intron 25.0%
! TTAATTGACTACTATGTAAC+TGG - Chr4:49637645-49637664 MsG0480020850.01.T01:intron 25.0%
! TTACACTGGTAAAATACTAA+TGG + Chr4:49637508-49637527 None:intergenic 25.0%
!! AACTAATTCTAAAGATTACG+AGG - Chr4:49636969-49636988 MsG0480020850.01.T01:intron 25.0%
!! ACTTATCAAAGTTGATTATG+AGG - Chr4:49636528-49636547 MsG0480020850.01.T01:intron 25.0%
!! TTTAAAATCTGTGATGTGTT+AGG - Chr4:49638374-49638393 MsG0480020850.01.T01:intron 25.0%
!!! AGGTATATTGGTTTCAAATA+TGG - Chr4:49637774-49637793 MsG0480020850.01.T01:intron 25.0%
!!! ATATCAGACATTACTTTTCT+TGG + Chr4:49637908-49637927 None:intergenic 25.0%
!!! CCAAATCAAGTAGTTTTATT+TGG + Chr4:49637967-49637986 None:intergenic 25.0%
AATATACCTAGTATCATTCG+GGG + Chr4:49637763-49637782 None:intergenic 30.0%
AGTAAGCAGAAAAATTAGCA+TGG - Chr4:49637686-49637705 MsG0480020850.01.T01:intron 30.0%
ATACATATTGAACAGCAAAG+TGG - Chr4:49638128-49638147 MsG0480020850.01.T01:intron 30.0%
CAAATTTACCTCAATCGATA+AGG + Chr4:49636560-49636579 None:intergenic 30.0%
CAATATACCTAGTATCATTC+GGG + Chr4:49637764-49637783 None:intergenic 30.0%
CCAATATACCTAGTATCATT+CGG + Chr4:49637765-49637784 None:intergenic 30.0%
GGATGAATTTGATGTCTTTA+TGG - Chr4:49637452-49637471 MsG0480020850.01.T01:intron 30.0%
TGCCTGTATTATACTTAAGT+AGG - Chr4:49637853-49637872 MsG0480020850.01.T01:intron 30.0%
TGTTGTGTGTGCATTTAATT+AGG - Chr4:49637354-49637373 MsG0480020850.01.T01:intron 30.0%
! AATTCATCCATTGCTCTAAA+TGG + Chr4:49637441-49637460 None:intergenic 30.0%
! ATGCTAATTTTTCTGCTTAC+TGG + Chr4:49637687-49637706 None:intergenic 30.0%
! ATTCATCCATTGCTCTAAAT+GGG + Chr4:49637440-49637459 None:intergenic 30.0%
! CTTATCGATTGAGGTAAATT+TGG - Chr4:49636558-49636577 MsG0480020850.01.T01:intron 30.0%
! TAAGCATCTAGTTTACACTT+TGG - Chr4:49637604-49637623 MsG0480020850.01.T01:intron 30.0%
!! TTGTTGCAAAATGATGGATA+TGG - Chr4:49636798-49636817 MsG0480020850.01.T01:intron 30.0%
!!! TTTCATTTGTCCTAGTTTTG+TGG - Chr4:49637186-49637205 MsG0480020850.01.T01:intron 30.0%
AAATCACAATTGGTCAAGCA+CGG + Chr4:49638246-49638265 None:intergenic 35.0%
AAGAACCAGAAAAGCAAACA+AGG - Chr4:49637881-49637900 MsG0480020850.01.T01:intron 35.0%
AATCTTATACCTTTCGAGCA+TGG - Chr4:49637255-49637274 MsG0480020850.01.T01:CDS 35.0%
AGAACCAGAAAAGCAAACAA+GGG - Chr4:49637882-49637901 MsG0480020850.01.T01:intron 35.0%
AGCTCTGTTTGATGTATCTT+GGG + Chr4:49636748-49636767 None:intergenic 35.0%
ATAAGTGTAGTGATCACTAG+AGG + Chr4:49637304-49637323 None:intergenic 35.0%
ATCTTATACCTTTCGAGCAT+GGG - Chr4:49637256-49637275 MsG0480020850.01.T01:CDS 35.0%
ATTAGCCCTTCATGAAATGA+CGG - Chr4:49637410-49637429 MsG0480020850.01.T01:intron 35.0%
ATTTAGCTAGCAATCTCATG+AGG - Chr4:49638057-49638076 MsG0480020850.01.T01:intron 35.0%
CCGAATGATACTAGGTATAT+TGG - Chr4:49637762-49637781 MsG0480020850.01.T01:intron 35.0%
CTTCAAGCTGCCATAAATAA+AGG + Chr4:49638269-49638288 None:intergenic 35.0%
TGACTCTTGCATTTCATTTC+AGG - Chr4:49636662-49636681 MsG0480020850.01.T01:three_prime_UTR 35.0%
TGTGTGTGCATTTAATTAGG+CGG - Chr4:49637357-49637376 MsG0480020850.01.T01:intron 35.0%
TTGTTTCAAAGCAGATGCAA+TGG - Chr4:49636868-49636887 MsG0480020850.01.T01:intron 35.0%
! GTTCGTTTGTTGCAAAATGA+TGG - Chr4:49636792-49636811 MsG0480020850.01.T01:intron 35.0%
! TGTAGCTTTTGAATAAGACG+CGG - Chr4:49636922-49636941 MsG0480020850.01.T01:intron 35.0%
! TTCATCCATTGCTCTAAATG+GGG + Chr4:49637439-49637458 None:intergenic 35.0%
!! GATTTAATGGCCTTTTGAAG+AGG - Chr4:49636491-49636510 MsG0480020850.01.T01:three_prime_UTR 35.0%
!!! GTAGTTTTATTTGGAAGTGC+AGG + Chr4:49637958-49637977 None:intergenic 35.0%
!!! GTGTGTTTTGTTTGCTCATT+TGG - Chr4:49637543-49637562 MsG0480020850.01.T01:CDS 35.0%
AATACAGGCACCACTTAACA+AGG + Chr4:49637843-49637862 None:intergenic 40.0%
AATCACAATTGGTCAAGCAC+GGG + Chr4:49638245-49638264 None:intergenic 40.0%
CAGCTCTGTTTGATGTATCT+TGG + Chr4:49636749-49636768 None:intergenic 40.0%
CAGGGTTAAGAAGATGCAAA+TGG - Chr4:49638213-49638232 MsG0480020850.01.T01:CDS 40.0%
CGGAACAACTGTACAATACA+GGG - Chr4:49636942-49636961 MsG0480020850.01.T01:intron 40.0%
GCGACCGCTACAATAATATT+GGG - Chr4:49637815-49637834 MsG0480020850.01.T01:intron 40.0%
GCTCTGTTTGATGTATCTTG+GGG + Chr4:49636747-49636766 None:intergenic 40.0%
GGCACCCAATATTATTGTAG+CGG + Chr4:49637822-49637841 None:intergenic 40.0%
GTGTGTGCATTTAATTAGGC+GGG - Chr4:49637358-49637377 MsG0480020850.01.T01:intron 40.0%
TGATCACTAGAGGTCTCTAA+TGG + Chr4:49637294-49637313 None:intergenic 40.0%
TGTGTGCATTTAATTAGGCG+GGG - Chr4:49637359-49637378 MsG0480020850.01.T01:intron 40.0%
TTAATTCACCCATGCTCGAA+AGG + Chr4:49637267-49637286 None:intergenic 40.0%
TTGTGTTTGAATGTGCAGCT+TGG - Chr4:49638177-49638196 MsG0480020850.01.T01:intron 40.0%
! ATATTGGGTGCCTTGTTAAG+TGG - Chr4:49637830-49637849 MsG0480020850.01.T01:intron 40.0%
! TAGCGAAGTACCACAAAACT+AGG + Chr4:49637199-49637218 None:intergenic 40.0%
! TATTTGGAAGTGCAGGAGTT+TGG + Chr4:49637951-49637970 None:intergenic 40.0%
!! AATGGCCTTTTGAAGAGGAA+GGG - Chr4:49636496-49636515 MsG0480020850.01.T01:three_prime_UTR 40.0%
!! ATTGATTTTGCTGAGGCACA+AGG - Chr4:49637717-49637736 MsG0480020850.01.T01:intron 40.0%
!! CACTCTGATTGATTTTGCTG+AGG - Chr4:49637710-49637729 MsG0480020850.01.T01:intron 40.0%
!! TAATGGCCTTTTGAAGAGGA+AGG - Chr4:49636495-49636514 MsG0480020850.01.T01:three_prime_UTR 40.0%
!! TGCATCTGCTTTGAAACAAG+AGG + Chr4:49636867-49636886 None:intergenic 40.0%
ATCACAATTGGTCAAGCACG+GGG + Chr4:49638244-49638263 None:intergenic 45.0%
GCGGAACAACTGTACAATAC+AGG - Chr4:49636941-49636960 MsG0480020850.01.T01:intron 45.0%
GGCGACCGCTACAATAATAT+TGG - Chr4:49637814-49637833 MsG0480020850.01.T01:intron 45.0%
TGATCACCCCGAATGATACT+AGG - Chr4:49637754-49637773 MsG0480020850.01.T01:intron 45.0%
TGTAACTGGGTTTGACATGC+AGG - Chr4:49637659-49637678 MsG0480020850.01.T01:intron 45.0%
! GGAAACGACCTTATCGATTG+AGG - Chr4:49636549-49636568 MsG0480020850.01.T01:intron 45.0%
! TGAATGTGCAGCTTGGTGAA+GGG - Chr4:49638184-49638203 MsG0480020850.01.T01:intron 45.0%
! TTGAATGTGCAGCTTGGTGA+AGG - Chr4:49638183-49638202 MsG0480020850.01.T01:intron 45.0%
!! ATGGCCTTTTGAAGAGGAAG+GGG - Chr4:49636497-49636516 MsG0480020850.01.T01:three_prime_UTR 45.0%
!! TTGGCCCTTGTTTGCTTTTC+TGG + Chr4:49637889-49637908 None:intergenic 45.0%
AACAGAGCTGTTCGAGACAC+AGG - Chr4:49636759-49636778 MsG0480020850.01.T01:CDS 50.0%
ACAGAGCTGTTCGAGACACA+GGG - Chr4:49636760-49636779 MsG0480020850.01.T01:CDS 50.0%
AGCCCTTCATGAAATGACGG+AGG - Chr4:49637413-49637432 MsG0480020850.01.T01:intron 50.0%
CGGGGTGATCAATATCCACT+GGG + Chr4:49637745-49637764 None:intergenic 50.0%
GGCCTCCGTCATTTCATGAA+GGG + Chr4:49637418-49637437 None:intergenic 50.0%
GTGGACGAGCTCTTGAAACA+TGG - Chr4:49638147-49638166 MsG0480020850.01.T01:intron 50.0%
TCGGGGTGATCAATATCCAC+TGG + Chr4:49637746-49637765 None:intergenic 50.0%
TGACCCCCTTCCTCTTCAAA+AGG + Chr4:49636504-49636523 None:intergenic 50.0%
!! TGGCCTTTTGAAGAGGAAGG+GGG - Chr4:49636498-49636517 MsG0480020850.01.T01:three_prime_UTR 50.0%
CAGAGCTGTTCGAGACACAG+GGG - Chr4:49636761-49636780 MsG0480020850.01.T01:CDS 55.0%
CTTGGTGAAGGGAGGGAACA+GGG - Chr4:49638195-49638214 MsG0480020850.01.T01:CDS 55.0%
GGGCCTCCGTCATTTCATGA+AGG + Chr4:49637419-49637438 None:intergenic 55.0%
TCGAGACACAGGGGACTTTC+AGG - Chr4:49636770-49636789 MsG0480020850.01.T01:intron 55.0%
TTGAAGAGGAAGGGGGTCAG+TGG - Chr4:49636505-49636524 MsG0480020850.01.T01:three_prime_UTR 55.0%
! ATGTGCAGCTTGGTGAAGGG+AGG - Chr4:49638187-49638206 MsG0480020850.01.T01:CDS 55.0%
! GGAGGCCCCATTTAGAGCAA+TGG - Chr4:49637431-49637450 MsG0480020850.01.T01:intron 55.0%
! TGTGCAGCTTGGTGAAGGGA+GGG - Chr4:49638188-49638207 MsG0480020850.01.T01:CDS 55.0%
CTGAGGCACAAGGATCCCAG+TGG - Chr4:49637727-49637746 MsG0480020850.01.T01:intron 60.0%
! GCTTGGTGAAGGGAGGGAAC+AGG - Chr4:49638194-49638213 MsG0480020850.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr4 gene 49636484 49638492 49636484 ID=MsG0480020850.01;Name=MsG0480020850.01
Chr4 mRNA 49636484 49638492 49636484 ID=MsG0480020850.01.T01;Parent=MsG0480020850.01;Name=MsG0480020850.01.T01;_AED=0.46;_eAED=0.46;_QI=0|0.8|0.66|1|0.4|0.16|6|206|131
Chr4 exon 49636484 49636532 49636484 ID=MsG0480020850.01.T01:exon:166;Parent=MsG0480020850.01.T01
Chr4 exon 49636567 49636781 49636567 ID=MsG0480020850.01.T01:exon:165;Parent=MsG0480020850.01.T01
Chr4 exon 49637201 49637295 49637201 ID=MsG0480020850.01.T01:exon:164;Parent=MsG0480020850.01.T01
Chr4 exon 49637503 49637601 49637503 ID=MsG0480020850.01.T01:exon:163;Parent=MsG0480020850.01.T01
Chr4 exon 49638185 49638241 49638185 ID=MsG0480020850.01.T01:exon:162;Parent=MsG0480020850.01.T01
Chr4 exon 49638406 49638492 49638406 ID=MsG0480020850.01.T01:exon:161;Parent=MsG0480020850.01.T01
Chr4 CDS 49638406 49638492 49638406 ID=MsG0480020850.01.T01:cds;Parent=MsG0480020850.01.T01
Chr4 CDS 49638185 49638241 49638185 ID=MsG0480020850.01.T01:cds;Parent=MsG0480020850.01.T01
Chr4 CDS 49637503 49637601 49637503 ID=MsG0480020850.01.T01:cds;Parent=MsG0480020850.01.T01
Chr4 CDS 49637201 49637295 49637201 ID=MsG0480020850.01.T01:cds;Parent=MsG0480020850.01.T01
Chr4 CDS 49636724 49636781 49636724 ID=MsG0480020850.01.T01:cds;Parent=MsG0480020850.01.T01
Chr4 three_prime_UTR 49636567 49636723 49636567 ID=MsG0480020850.01.T01:three_prime_utr;Parent=MsG0480020850.01.T01
Chr4 three_prime_UTR 49636484 49636532 49636484 ID=MsG0480020850.01.T01:three_prime_utr;Parent=MsG0480020850.01.T01
Gene Sequence

>MsG0480020850.01.T01

ATGATCAGATTTAATGGCCTTTTGAAGAGGAAGGGGGTCAGTGGACTTATCAAAGTTGATTATGAGGAAACGACCTTATCGATTGAGGTACAAATGCCCCAAGATACATCAAACAGAGCTGTTCGAGACACAGGGGACTTTCAGGGCGGGGAGCGCTCTTTTTCAACTTTGTGCTTTGCATTAGCCCTTCATGAAATGACGGAGGCCCCATTTAGAGCAATGGATGAATTTGATGTCTTTATGGATCCAGTAAGCAGAAAAATTAGCATGGACACTCTGATTGATTTTGCTGAGGCACAAGGATCCCAGTGGATATTGATCACCCCGAATGATACTAGCTTGGTGAAGGGAGGGAACAGGGTTAAGAAGATGCAAATGGCAGCTCCCCGTGCTTGA
Protein sequence

>MsG0480020850.01.T01

MIRFNGLLKRKGVSGLIKVDYEETTLSIEVQMPQDTSNRAVRDTGDFQGGERSFSTLCFALALHEMTEAPFRAMDEFDVFMDPVSRKISMDTLIDFAEAQGSQWILITPNDTSLVKGGNRVKKMQMAAPRA*