AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0161900


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0161900 MtrunA17_Chr1g0202341 63.359 131 46 1 4 132 12 142 1.67e-50 170
Msa0161900 MtrunA17_Chr3g0077241 70.652 92 21 2 6 94 1 89 1.55e-39 129
Msa0161900 MtrunA17_Chr4g0052331 57.895 95 38 1 1 93 1 95 3.29e-33 112
Msa0161900 MtrunA17_Chr2g0329361 38.947 95 57 1 39 132 59 153 3.37e-18 78.2
Msa0161900 MtrunA17_Chr2g0329421 33.333 117 66 4 23 132 5 116 7.27e-16 71.2
Msa0161900 MtrunA17_Chr4g0033611 32.000 125 70 4 19 133 47 166 2.99e-15 70.1
Msa0161900 MtrunA17_Chr5g0448761 45.918 98 48 3 39 132 58 154 2.04e-13 66.2
Msa0161900 MtrunA17_Chr3g0078041 35.789 95 57 3 40 132 49 141 2.89e-12 61.6
Msa0161900 MtrunA17_Chr2g0287061 31.068 103 55 2 31 132 173 260 3.70e-12 62.8
Msa0161900 MtrunA17_Chr6g0458391 36.111 108 51 3 36 140 86 178 2.03e-11 60.5
Msa0161900 MtrunA17_Chr7g0233911 36.458 96 55 3 40 132 33 125 2.62e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0161900 AT3G59470.3 36.170 94 56 2 40 132 69 159 2.88e-15 70.5
Msa0161900 AT3G59470.1 36.170 94 56 2 40 132 69 159 2.88e-15 70.5
Msa0161900 AT3G59470.2 36.170 94 56 2 40 132 81 171 3.21e-15 70.5
Msa0161900 AT4G38180.1 36.242 149 74 6 2 132 21 166 6.24e-14 68.2
Msa0161900 AT3G06250.2 35.789 95 45 3 39 132 26 105 7.08e-13 65.1
Msa0161900 AT3G06250.1 35.789 95 45 3 39 132 26 105 7.08e-13 65.1
Msa0161900 AT3G06250.3 35.789 95 45 3 39 132 26 105 7.08e-13 65.1
Msa0161900 AT3G07500.1 38.947 95 55 2 39 132 31 123 2.45e-12 62.0
Msa0161900 AT5G18960.2 33.684 95 47 3 39 132 41 120 3.89e-12 62.8
Msa0161900 AT5G18960.1 33.684 95 47 3 39 132 41 120 3.89e-12 62.8

Find 39 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTCCTTCAAAGGGCTCTA+AGG 0.261818 1_4:-38015929 None:intergenic
GAAGAAGATTATGGAAGTTT+TGG 0.293650 1_4:+38015516 Msa0161900:five_prime_UTR
AGAACGGATGGTAGAGTAAT+TGG 0.359499 1_4:+38016045 Msa0161900:CDS
ACAAGGTACGCGAGGAATAA+AGG 0.387113 1_4:+38015988 Msa0161900:CDS
CTTCTTCGAAGACGGTTCTC+AGG 0.416570 1_4:-38015500 None:intergenic
CATGAACATACCAACATGAT+TGG 0.442395 1_4:+38015844 Msa0161900:CDS
ACCGTCTTCGAAGAAGATTA+TGG 0.460480 1_4:+38015507 Msa0161900:five_prime_UTR
CTTAGAGCCCTTTGAAGGAA+TGG 0.476103 1_4:+38015930 Msa0161900:CDS
ATTCCTTCAAAGGGCTCTAA+GGG 0.488264 1_4:-38015928 None:intergenic
CTCCCCTTAGAGCCCTTTGA+AGG 0.489876 1_4:+38015925 Msa0161900:CDS
CGTAAACTCCATTCCTTCAA+AGG 0.494092 1_4:-38015938 None:intergenic
TCAATACAACAAAACTCAAT+CGG 0.502319 1_4:+38015370 Msa0161900:five_prime_UTR
ATATCAAGAAAAGTGAAGAT+AGG 0.503755 1_4:+38016181 Msa0161900:CDS
TCAAGAGATTCTTTGTTCAA+AGG 0.507548 1_4:+38016068 Msa0161900:CDS
GGCTCTAAGGGGAGCTCCAA+TGG 0.508044 1_4:-38015916 None:intergenic
TCCATAATCTTCTTCGAAGA+CGG 0.517402 1_4:-38015508 None:intergenic
AGATTCTTTGTTCAAAGGAG+GGG 0.523644 1_4:+38016073 Msa0161900:CDS
TCTCAATGATAGACTACCAT+TGG 0.530176 1_4:+38015900 Msa0161900:CDS
TCAAACGAACAAAAGAAAGT+AGG 0.536997 1_4:-38015436 None:intergenic
GAGATTCTTTGTTCAAAGGA+GGG 0.539548 1_4:+38016072 Msa0161900:CDS
ACTGTTTGTGTTGAAGCTGC+AGG 0.548752 1_4:+38016207 Msa0161900:CDS
AGAGATTCTTTGTTCAAAGG+AGG 0.550163 1_4:+38016071 Msa0161900:CDS
GTAAACTCCATTCCTTCAAA+GGG 0.551143 1_4:-38015937 None:intergenic
TTTGTGTTGAAGCTGCAGGC+AGG 0.559406 1_4:+38016211 Msa0161900:CDS
TCAAACAAGGGTAGGATGCA+AGG 0.583329 1_4:+38016149 Msa0161900:CDS
AATGGTAGTCTTATTGTACA+TGG 0.595875 1_4:+38016126 Msa0161900:CDS
TCAAGAAAAGTGAAGATAGG+TGG 0.599813 1_4:+38016184 Msa0161900:CDS
TTATTGTACATGGTCAAACA+AGG 0.601311 1_4:+38016136 Msa0161900:CDS
ATCATCTGAGCCAATCATGT+TGG 0.609119 1_4:-38015854 None:intergenic
GTTACTAAATCAAGAACGGA+TGG 0.614185 1_4:+38016033 Msa0161900:CDS
AATGGTAGTCTATCATTGAG+AGG 0.621900 1_4:-38015898 None:intergenic
TGGTCTGAGACATTATAACC+AGG 0.630311 1_4:+38015536 Msa0161900:five_prime_UTR
AGACGGTTCTCAGGTCGTAA+CGG 0.630551 1_4:-38015491 None:intergenic
GTACATGGTCAAACAAGGGT+AGG 0.635603 1_4:+38016141 Msa0161900:CDS
TCGTGTTACTAAATCAAGAA+CGG 0.641576 1_4:+38016029 Msa0161900:CDS
AATACTACACAAGGTACGCG+AGG 0.651596 1_4:+38015980 Msa0161900:CDS
TTCCTTCAAAGGGCTCTAAG+GGG 0.687755 1_4:-38015927 None:intergenic
TATTGTACATGGTCAAACAA+GGG 0.709401 1_4:+38016137 Msa0161900:CDS
CGGTTCTCAGGTCGTAACGG+CGG 0.719840 1_4:-38015488 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTTTTTTCAAATTTTTTT+GGG - chr1_4:38016106-38016125 None:intergenic 10.0%
!!! TTTCTTTTTTCAAATTTTTT+TGG - chr1_4:38016107-38016126 None:intergenic 10.0%
!! AAAAATTTGAAAAAAGAAAA+TGG + chr1_4:38016108-38016127 Msa0161900:CDS 10.0%
!!! TTCTTTTTTCAAATTTTTTT+GGG - chr1_4:38016106-38016125 None:intergenic 10.0%
!!! TTTCTTTTTTCAAATTTTTT+TGG - chr1_4:38016107-38016126 None:intergenic 10.0%
!! AAAAATTTGAAAAAAGAAAA+TGG + chr1_4:38016108-38016127 Msa0161900:CDS 10.0%
!! TTCATATTTAAACATGTTTG+TGG + chr1_4:38015674-38015693 Msa0161900:intron 20.0%
!!! TTAACTTGCTTTTCTAAATA+TGG + chr1_4:38015747-38015766 Msa0161900:intron 20.0%
!! ATGTAAAAAAATACTACACA+AGG + chr1_4:38015971-38015990 Msa0161900:CDS 20.0%
!! TTCATATTTAAACATGTTTG+TGG + chr1_4:38015674-38015693 Msa0161900:intron 20.0%
!!! TTAACTTGCTTTTCTAAATA+TGG + chr1_4:38015747-38015766 Msa0161900:intron 20.0%
!! ATGTAAAAAAATACTACACA+AGG + chr1_4:38015971-38015990 Msa0161900:CDS 20.0%
!!! ATTGAGTTTTGTTGTATTGA+CGG - chr1_4:38015370-38015389 None:intergenic 25.0%
! TCAATACAACAAAACTCAAT+CGG + chr1_4:38015370-38015389 Msa0161900:five_prime_UTR 25.0%
!! TGAATTTTATTCAGCATAAC+AGG + chr1_4:38015779-38015798 Msa0161900:intron 25.0%
! ATATCAAGAAAAGTGAAGAT+AGG + chr1_4:38016181-38016200 Msa0161900:CDS 25.0%
!!! ATTGAGTTTTGTTGTATTGA+CGG - chr1_4:38015370-38015389 None:intergenic 25.0%
! TCAATACAACAAAACTCAAT+CGG + chr1_4:38015370-38015389 Msa0161900:five_prime_UTR 25.0%
!! TGAATTTTATTCAGCATAAC+AGG + chr1_4:38015779-38015798 Msa0161900:intron 25.0%
! ATATCAAGAAAAGTGAAGAT+AGG + chr1_4:38016181-38016200 Msa0161900:CDS 25.0%
!!! TCTCTCTCTTTTTCAATTGA+AGG + chr1_4:38015394-38015413 Msa0161900:five_prime_UTR 30.0%
TCAAACGAACAAAAGAAAGT+AGG - chr1_4:38015439-38015458 None:intergenic 30.0%
! GAAGAAGATTATGGAAGTTT+TGG + chr1_4:38015516-38015535 Msa0161900:five_prime_UTR 30.0%
TTGTAGAACTAAAGAAACCA+AGG - chr1_4:38015585-38015604 None:intergenic 30.0%
! AGTCTCCAAAGATTTTTGTT+TGG + chr1_4:38015642-38015661 Msa0161900:intron 30.0%
CATTGCCAAACAAAAATCTT+TGG - chr1_4:38015650-38015669 None:intergenic 30.0%
!!! TAAAGGTTTTAGCTTTCGTA+TGG + chr1_4:38016005-38016024 Msa0161900:CDS 30.0%
!!! AAAGGTTTTAGCTTTCGTAT+GGG + chr1_4:38016006-38016025 Msa0161900:CDS 30.0%
! TCGTGTTACTAAATCAAGAA+CGG + chr1_4:38016029-38016048 Msa0161900:CDS 30.0%
TCAAGAGATTCTTTGTTCAA+AGG + chr1_4:38016068-38016087 Msa0161900:CDS 30.0%
!! AATGGTAGTCTTATTGTACA+TGG + chr1_4:38016126-38016145 Msa0161900:CDS 30.0%
TTATTGTACATGGTCAAACA+AGG + chr1_4:38016136-38016155 Msa0161900:CDS 30.0%
TATTGTACATGGTCAAACAA+GGG + chr1_4:38016137-38016156 Msa0161900:CDS 30.0%
!!! TCTCTCTCTTTTTCAATTGA+AGG + chr1_4:38015394-38015413 Msa0161900:five_prime_UTR 30.0%
TCAAACGAACAAAAGAAAGT+AGG - chr1_4:38015439-38015458 None:intergenic 30.0%
! GAAGAAGATTATGGAAGTTT+TGG + chr1_4:38015516-38015535 Msa0161900:five_prime_UTR 30.0%
TTGTAGAACTAAAGAAACCA+AGG - chr1_4:38015585-38015604 None:intergenic 30.0%
! AGTCTCCAAAGATTTTTGTT+TGG + chr1_4:38015642-38015661 Msa0161900:intron 30.0%
CATTGCCAAACAAAAATCTT+TGG - chr1_4:38015650-38015669 None:intergenic 30.0%
!!! TAAAGGTTTTAGCTTTCGTA+TGG + chr1_4:38016005-38016024 Msa0161900:CDS 30.0%
!!! AAAGGTTTTAGCTTTCGTAT+GGG + chr1_4:38016006-38016025 Msa0161900:CDS 30.0%
! TCGTGTTACTAAATCAAGAA+CGG + chr1_4:38016029-38016048 Msa0161900:CDS 30.0%
TCAAGAGATTCTTTGTTCAA+AGG + chr1_4:38016068-38016087 Msa0161900:CDS 30.0%
!! AATGGTAGTCTTATTGTACA+TGG + chr1_4:38016126-38016145 Msa0161900:CDS 30.0%
TTATTGTACATGGTCAAACA+AGG + chr1_4:38016136-38016155 Msa0161900:CDS 30.0%
TATTGTACATGGTCAAACAA+GGG + chr1_4:38016137-38016156 Msa0161900:CDS 30.0%
! TTCTTTTGTTCGTTTGAACG+AGG + chr1_4:38015442-38015461 Msa0161900:five_prime_UTR 35.0%
TCCATAATCTTCTTCGAAGA+CGG - chr1_4:38015511-38015530 None:intergenic 35.0%
AACCACATCTTCAATTACCT+TGG + chr1_4:38015565-38015584 Msa0161900:intron 35.0%
AACCAAGGTAATTGAAGATG+TGG - chr1_4:38015570-38015589 None:intergenic 35.0%
CATGAACATACCAACATGAT+TGG + chr1_4:38015844-38015863 Msa0161900:CDS 35.0%
AATGGTAGTCTATCATTGAG+AGG - chr1_4:38015901-38015920 None:intergenic 35.0%
TCTCAATGATAGACTACCAT+TGG + chr1_4:38015900-38015919 Msa0161900:CDS 35.0%
GTAAACTCCATTCCTTCAAA+GGG - chr1_4:38015940-38015959 None:intergenic 35.0%
GTTACTAAATCAAGAACGGA+TGG + chr1_4:38016033-38016052 Msa0161900:CDS 35.0%
AGAGATTCTTTGTTCAAAGG+AGG + chr1_4:38016071-38016090 Msa0161900:CDS 35.0%
GAGATTCTTTGTTCAAAGGA+GGG + chr1_4:38016072-38016091 Msa0161900:CDS 35.0%
AGATTCTTTGTTCAAAGGAG+GGG + chr1_4:38016073-38016092 Msa0161900:CDS 35.0%
TCAAGAAAAGTGAAGATAGG+TGG + chr1_4:38016184-38016203 Msa0161900:CDS 35.0%
! TTCTTTTGTTCGTTTGAACG+AGG + chr1_4:38015442-38015461 Msa0161900:five_prime_UTR 35.0%
TCCATAATCTTCTTCGAAGA+CGG - chr1_4:38015511-38015530 None:intergenic 35.0%
AACCACATCTTCAATTACCT+TGG + chr1_4:38015565-38015584 Msa0161900:intron 35.0%
AACCAAGGTAATTGAAGATG+TGG - chr1_4:38015570-38015589 None:intergenic 35.0%
CATGAACATACCAACATGAT+TGG + chr1_4:38015844-38015863 Msa0161900:CDS 35.0%
AATGGTAGTCTATCATTGAG+AGG - chr1_4:38015901-38015920 None:intergenic 35.0%
TCTCAATGATAGACTACCAT+TGG + chr1_4:38015900-38015919 Msa0161900:CDS 35.0%
GTAAACTCCATTCCTTCAAA+GGG - chr1_4:38015940-38015959 None:intergenic 35.0%
GTTACTAAATCAAGAACGGA+TGG + chr1_4:38016033-38016052 Msa0161900:CDS 35.0%
AGAGATTCTTTGTTCAAAGG+AGG + chr1_4:38016071-38016090 Msa0161900:CDS 35.0%
GAGATTCTTTGTTCAAAGGA+GGG + chr1_4:38016072-38016091 Msa0161900:CDS 35.0%
AGATTCTTTGTTCAAAGGAG+GGG + chr1_4:38016073-38016092 Msa0161900:CDS 35.0%
TCAAGAAAAGTGAAGATAGG+TGG + chr1_4:38016184-38016203 Msa0161900:CDS 35.0%
ACCGTCTTCGAAGAAGATTA+TGG + chr1_4:38015507-38015526 Msa0161900:five_prime_UTR 40.0%
! TGGTCTGAGACATTATAACC+AGG + chr1_4:38015536-38015555 Msa0161900:five_prime_UTR 40.0%
GAAGATGTGGTTAATTCACC+TGG - chr1_4:38015557-38015576 None:intergenic 40.0%
ATCATCTGAGCCAATCATGT+TGG - chr1_4:38015857-38015876 None:intergenic 40.0%
! ATTCCTTCAAAGGGCTCTAA+GGG - chr1_4:38015931-38015950 None:intergenic 40.0%
CGTAAACTCCATTCCTTCAA+AGG - chr1_4:38015941-38015960 None:intergenic 40.0%
AGAACGGATGGTAGAGTAAT+TGG + chr1_4:38016045-38016064 Msa0161900:CDS 40.0%
ACCGTCTTCGAAGAAGATTA+TGG + chr1_4:38015507-38015526 Msa0161900:five_prime_UTR 40.0%
! TGGTCTGAGACATTATAACC+AGG + chr1_4:38015536-38015555 Msa0161900:five_prime_UTR 40.0%
GAAGATGTGGTTAATTCACC+TGG - chr1_4:38015557-38015576 None:intergenic 40.0%
ATCATCTGAGCCAATCATGT+TGG - chr1_4:38015857-38015876 None:intergenic 40.0%
! ATTCCTTCAAAGGGCTCTAA+GGG - chr1_4:38015931-38015950 None:intergenic 40.0%
CGTAAACTCCATTCCTTCAA+AGG - chr1_4:38015941-38015960 None:intergenic 40.0%
AGAACGGATGGTAGAGTAAT+TGG + chr1_4:38016045-38016064 Msa0161900:CDS 40.0%
!! TTCCTTCAAAGGGCTCTAAG+GGG - chr1_4:38015930-38015949 None:intergenic 45.0%
CATTCCTTCAAAGGGCTCTA+AGG - chr1_4:38015932-38015951 None:intergenic 45.0%
! CTTAGAGCCCTTTGAAGGAA+TGG + chr1_4:38015930-38015949 Msa0161900:CDS 45.0%
AATACTACACAAGGTACGCG+AGG + chr1_4:38015980-38015999 Msa0161900:CDS 45.0%
ACAAGGTACGCGAGGAATAA+AGG + chr1_4:38015988-38016007 Msa0161900:CDS 45.0%
GTACATGGTCAAACAAGGGT+AGG + chr1_4:38016141-38016160 Msa0161900:CDS 45.0%
TCAAACAAGGGTAGGATGCA+AGG + chr1_4:38016149-38016168 Msa0161900:CDS 45.0%
ACTGTTTGTGTTGAAGCTGC+AGG + chr1_4:38016207-38016226 Msa0161900:CDS 45.0%
!! TTCCTTCAAAGGGCTCTAAG+GGG - chr1_4:38015930-38015949 None:intergenic 45.0%
CATTCCTTCAAAGGGCTCTA+AGG - chr1_4:38015932-38015951 None:intergenic 45.0%
! CTTAGAGCCCTTTGAAGGAA+TGG + chr1_4:38015930-38015949 Msa0161900:CDS 45.0%
AATACTACACAAGGTACGCG+AGG + chr1_4:38015980-38015999 Msa0161900:CDS 45.0%
ACAAGGTACGCGAGGAATAA+AGG + chr1_4:38015988-38016007 Msa0161900:CDS 45.0%
GTACATGGTCAAACAAGGGT+AGG + chr1_4:38016141-38016160 Msa0161900:CDS 45.0%
TCAAACAAGGGTAGGATGCA+AGG + chr1_4:38016149-38016168 Msa0161900:CDS 45.0%
ACTGTTTGTGTTGAAGCTGC+AGG + chr1_4:38016207-38016226 Msa0161900:CDS 45.0%
AGACGGTTCTCAGGTCGTAA+CGG - chr1_4:38015494-38015513 None:intergenic 50.0%
CTTCTTCGAAGACGGTTCTC+AGG - chr1_4:38015503-38015522 None:intergenic 50.0%
TTTGTGTTGAAGCTGCAGGC+AGG + chr1_4:38016211-38016230 Msa0161900:CDS 50.0%
AGACGGTTCTCAGGTCGTAA+CGG - chr1_4:38015494-38015513 None:intergenic 50.0%
CTTCTTCGAAGACGGTTCTC+AGG - chr1_4:38015503-38015522 None:intergenic 50.0%
TTTGTGTTGAAGCTGCAGGC+AGG + chr1_4:38016211-38016230 Msa0161900:CDS 50.0%
CTCCCCTTAGAGCCCTTTGA+AGG + chr1_4:38015925-38015944 Msa0161900:CDS 55.0%
CTCCCCTTAGAGCCCTTTGA+AGG + chr1_4:38015925-38015944 Msa0161900:CDS 55.0%
CGGTTCTCAGGTCGTAACGG+CGG - chr1_4:38015491-38015510 None:intergenic 60.0%
!! GGCTCTAAGGGGAGCTCCAA+TGG - chr1_4:38015919-38015938 None:intergenic 60.0%
CGGTTCTCAGGTCGTAACGG+CGG - chr1_4:38015491-38015510 None:intergenic 60.0%
!! GGCTCTAAGGGGAGCTCCAA+TGG - chr1_4:38015919-38015938 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 38015347 38016248 38015347 ID=Msa0161900;Name=Msa0161900
chr1_4 mRNA 38015347 38016248 38015347 ID=Msa0161900-mRNA-1;Parent=Msa0161900;Name=Msa0161900-mRNA-1;_AED=0.11;_eAED=0.13;_QI=235|1|0.5|1|0|0.5|2|0|143
chr1_4 exon 38015347 38015557 38015347 ID=Msa0161900-mRNA-1:exon:11144;Parent=Msa0161900-mRNA-1
chr1_4 exon 38015793 38016248 38015793 ID=Msa0161900-mRNA-1:exon:11145;Parent=Msa0161900-mRNA-1
chr1_4 five_prime_UTR 38015347 38015557 38015347 ID=Msa0161900-mRNA-1:five_prime_utr;Parent=Msa0161900-mRNA-1
chr1_4 five_prime_UTR 38015793 38015816 38015793 ID=Msa0161900-mRNA-1:five_prime_utr;Parent=Msa0161900-mRNA-1
chr1_4 CDS 38015817 38016248 38015817 ID=Msa0161900-mRNA-1:cds;Parent=Msa0161900-mRNA-1
Gene Sequence

>Msa0161900

ATGACAGATCAAGAAATGACAGATATGCATGAACATACCAACATGATTGGCTCAGATGATATGCTTGCAAGTGATGCAGATCCTCTCAATGATAGACTACCATTGGAGCTCCCCTTAGAGCCCTTTGAAGGAATGGAGTTTACGTCAATTGAAGATGTAAAAAAATACTACACAAGGTACGCGAGGAATAAAGGTTTTAGCTTTCGTATGGGTCGTGTTACTAAATCAAGAACGGATGGTAGAGTAATTGGTCAAGAGATTCTTTGTTCAAAGGAGGGGTTTAGATCCCAAAAAAATTTGAAAAAAGAAAATGGTAGTCTTATTGTACATGGTCAAACAAGGGTAGGATGCAAGGCACTCTTGTATATCAAGAAAAGTGAAGATAGGTGGACTGTTTGTGTTGAAGCTGCAGGCAGGTTGTTTTTAATCTGA

Protein sequence

>Msa0161900

MTDQEMTDMHEHTNMIGSDDMLASDADPLNDRLPLELPLEPFEGMEFTSIEDVKKYYTRYARNKGFSFRMGRVTKSRTDGRVIGQEILCSKEGFRSQKNLKKENGSLIVHGQTRVGCKALLYIKKSEDRWTVCVEAAGRLFLI*