AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0196660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0196660 MtrunA17_Chr2g0288481 70.652 184 25 2 7 166 66 244 3.63e-86 253
Msa0196660 MtrunA17_Chr2g0310741 54.745 137 58 2 8 144 85 217 2.28e-49 160
Msa0196660 MtrunA17_Chr7g0272991 47.904 167 63 3 7 149 82 248 5.37e-47 153
Msa0196660 MtrunA17_Chr1g0191681 66.667 99 33 0 7 105 82 180 2.69e-46 151
Msa0196660 MtrunA17_Chr3g0132191 52.555 137 52 2 8 131 37 173 2.21e-44 145
Msa0196660 MtrunA17_Chr8g0376351 94.444 72 4 0 44 115 1 72 3.70e-44 140
Msa0196660 MtrunA17_Chr2g0318881 59.740 77 30 1 27 102 23 99 1.88e-24 91.7
Msa0196660 MtrunA17_Chr2g0318921 59.740 77 30 1 27 102 23 99 2.24e-24 91.7
Msa0196660 MtrunA17_Chr3g0081161 42.308 78 45 0 27 104 9 86 7.86e-13 64.7
Msa0196660 MtrunA17_Chr8g0354151 39.744 78 47 0 27 104 9 86 3.39e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0196660 AT1G54830.2 49.701 167 59 4 7 152 51 213 3.52e-46 150
Msa0196660 AT1G54830.3 49.701 167 59 4 7 152 51 213 3.52e-46 150
Msa0196660 AT1G54830.1 49.701 167 59 4 7 152 51 213 3.52e-46 150
Msa0196660 AT1G56170.1 56.452 124 52 1 5 128 55 176 3.56e-46 150
Msa0196660 AT1G56170.2 56.452 124 52 1 5 128 55 176 3.56e-46 150
Msa0196660 AT1G08970.3 64.815 108 36 1 8 115 62 167 3.16e-45 148
Msa0196660 AT1G08970.4 64.815 108 36 1 8 115 62 167 3.16e-45 148
Msa0196660 AT1G08970.2 64.815 108 36 1 8 115 62 167 3.16e-45 148
Msa0196660 AT1G08970.1 64.815 108 36 1 8 115 62 167 3.16e-45 148
Msa0196660 AT3G48590.1 50.000 144 52 2 8 131 47 190 6.52e-45 147
Msa0196660 AT5G63470.2 63.462 104 38 0 8 111 60 163 7.55e-44 145
Msa0196660 AT5G63470.1 63.462 104 38 0 8 111 60 163 7.55e-44 145
Msa0196660 AT5G50480.1 49.286 140 56 3 4 131 35 171 3.67e-38 129
Msa0196660 AT5G27910.1 44.295 149 67 5 3 138 16 161 2.66e-32 114
Msa0196660 AT5G50490.1 46.154 104 53 1 3 106 16 116 1.18e-26 99.8
Msa0196660 AT5G50470.1 40.351 114 59 2 4 111 44 154 1.28e-23 92.4
Msa0196660 AT5G38140.1 39.806 103 60 1 1 103 44 144 8.18e-23 90.1

Find 32 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGCTTAATCTTCTGAATT+TGG 0.096494 2_1:+14012683 None:intergenic
AATGGAGCGTGACATATTTA+TGG 0.230451 2_1:-14012937 Msa0196660:CDS
GGCATGTGAAATGTTTATTA+TGG 0.268895 2_1:-14013093 Msa0196660:CDS
TAGTCCTCCAAGAATGCTTA+TGG 0.282983 2_1:-14012813 Msa0196660:CDS
GGTGTTCCCATAAGCATTCT+TGG 0.338684 2_1:+14012806 None:intergenic
ATCTTCTTAATCCTTGCTAA+TGG 0.378288 2_1:+14013176 None:intergenic
ACTGTTGATTTCAAAAGTAA+TGG 0.437192 2_1:-14013203 Msa0196660:CDS
ATGGAGCGTGACATATTTAT+GGG 0.438860 2_1:-14012936 Msa0196660:intron
TCAATCAGCCTCATAACAAC+AGG 0.483454 2_1:-14012778 Msa0196660:CDS
AATTTGGAAAATCAACATAA+TGG 0.484356 2_1:+14012699 None:intergenic
CATGCCTTAGCAAACAGAAT+AGG 0.486382 2_1:+14013110 None:intergenic
CCTAGTTGATATTGTCCCTA+GGG 0.487741 2_1:-14012967 Msa0196660:CDS
GGAAACATTTGATTTGCAAG+AGG 0.498129 2_1:+14012743 None:intergenic
TGGAGCTAGCAACAAGGTCA+TGG 0.501489 2_1:-14013073 Msa0196660:CDS
AAGATCATGAAAACAGAAGA+AGG 0.505724 2_1:-14013158 Msa0196660:CDS
AGTCCTCCAAGAATGCTTAT+GGG 0.511667 2_1:-14012812 Msa0196660:CDS
CCCTAGGGACAATATCAACT+AGG 0.511793 2_1:+14012967 None:intergenic
GAAACATTTGATTTGCAAGA+GGG 0.521354 2_1:+14012744 None:intergenic
GGCACCTATTCTGTTTGCTA+AGG 0.530640 2_1:-14013114 Msa0196660:CDS
GAGGGCTGCCTGTTGTTATG+AGG 0.531966 2_1:+14012770 None:intergenic
AATGTTTCCAATCCAAAAGC+AGG 0.532891 2_1:-14012729 Msa0196660:CDS
TTGATTTGCAAGAGGGTGTG+AGG 0.552359 2_1:+14012751 None:intergenic
TCCTAGTTGATATTGTCCCT+AGG 0.558927 2_1:-14012968 Msa0196660:CDS
GGAGCTAGCAACAAGGTCAT+GGG 0.582315 2_1:-14013072 Msa0196660:CDS
ATTCTTGGAGGACTATATGA+TGG 0.593998 2_1:+14012821 None:intergenic
GTAATGGCTTGCCATTAGCA+AGG 0.597965 2_1:-14013187 Msa0196660:CDS
GTTCCCATAAGCATTCTTGG+AGG 0.601037 2_1:+14012809 None:intergenic
TGATTTGCAAGAGGGTGTGA+GGG 0.602521 2_1:+14012752 None:intergenic
AAGGTCATGGGCTAATACAG+AGG 0.637560 2_1:-14013060 Msa0196660:CDS
TTATGAGGCTGATTGAGAGA+AGG 0.649482 2_1:+14012785 None:intergenic
AGTGAGTATGATATCAGCTG+AGG 0.690629 2_1:-14013135 Msa0196660:CDS
TTATTATGGAGCTAGCAACA+AGG 0.697305 2_1:-14013079 Msa0196660:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTGGAAAATCAACATAA+TGG + chr2_1:14013249-14013268 None:intergenic 20.0%
!!! ACTGTTGATTTCAAAAGTAA+TGG - chr2_1:14012742-14012761 Msa0196660:CDS 25.0%
!!! TTCATTTTGTTTTGACCAGA+AGG + chr2_1:14012710-14012729 None:intergenic 30.0%
ATCTTCTTAATCCTTGCTAA+TGG + chr2_1:14012772-14012791 None:intergenic 30.0%
AAGATCATGAAAACAGAAGA+AGG - chr2_1:14012787-14012806 Msa0196660:CDS 30.0%
GGCATGTGAAATGTTTATTA+TGG - chr2_1:14012852-14012871 Msa0196660:intron 30.0%
AGGAACATATATTCCCTATT+GGG + chr2_1:14013056-14013075 None:intergenic 30.0%
AAGGAACATATATTCCCTAT+TGG + chr2_1:14013057-14013076 None:intergenic 30.0%
!! GAAACATTTGATTTGCAAGA+GGG + chr2_1:14013204-14013223 None:intergenic 30.0%
AGAAAAAACTTGACACCTTC+TGG - chr2_1:14012692-14012711 Msa0196660:CDS 35.0%
TTATTATGGAGCTAGCAACA+AGG - chr2_1:14012866-14012885 Msa0196660:intron 35.0%
AATGGAGCGTGACATATTTA+TGG - chr2_1:14013008-14013027 Msa0196660:CDS 35.0%
ATGGAGCGTGACATATTTAT+GGG - chr2_1:14013009-14013028 Msa0196660:CDS 35.0%
ATTCTTGGAGGACTATATGA+TGG + chr2_1:14013127-14013146 None:intergenic 35.0%
!! GGAAACATTTGATTTGCAAG+AGG + chr2_1:14013205-14013224 None:intergenic 35.0%
AATGTTTCCAATCCAAAAGC+AGG - chr2_1:14013216-14013235 Msa0196660:CDS 35.0%
!! TCATTTTCCTGCTTTTGGAT+TGG + chr2_1:14013226-14013245 None:intergenic 35.0%
!! AATGGTCATTTTCCTGCTTT+TGG + chr2_1:14013231-14013250 None:intergenic 35.0%
AGTGAGTATGATATCAGCTG+AGG - chr2_1:14012810-14012829 Msa0196660:CDS 40.0%
CATGCCTTAGCAAACAGAAT+AGG + chr2_1:14012838-14012857 None:intergenic 40.0%
! TCCTAGTTGATATTGTCCCT+AGG - chr2_1:14012977-14012996 Msa0196660:CDS 40.0%
! CCTAGTTGATATTGTCCCTA+GGG - chr2_1:14012978-14012997 Msa0196660:CDS 40.0%
TGTCCCTAGGGAAAAAACAA+TGG - chr2_1:14012990-14013009 Msa0196660:CDS 40.0%
!!! GCTCCATTGTTTTTTCCCTA+GGG + chr2_1:14012996-14013015 None:intergenic 40.0%
ATGGGTATACCAAGAAGAGA+AGG - chr2_1:14013027-14013046 Msa0196660:CDS 40.0%
TCCTTATTATGTGCCTATGC+CGG - chr2_1:14013072-14013091 Msa0196660:CDS 40.0%
TAGTCCTCCAAGAATGCTTA+TGG - chr2_1:14013132-14013151 Msa0196660:CDS 40.0%
AGTCCTCCAAGAATGCTTAT+GGG - chr2_1:14013133-14013152 Msa0196660:CDS 40.0%
TTATGAGGCTGATTGAGAGA+AGG + chr2_1:14013163-14013182 None:intergenic 40.0%
TCAATCAGCCTCATAACAAC+AGG - chr2_1:14013167-14013186 Msa0196660:CDS 40.0%
! GTAATGGCTTGCCATTAGCA+AGG - chr2_1:14012758-14012777 Msa0196660:CDS 45.0%
! GGCACCTATTCTGTTTGCTA+AGG - chr2_1:14012831-14012850 Msa0196660:intron 45.0%
! AAGGTCATGGGCTAATACAG+AGG - chr2_1:14012885-14012904 Msa0196660:intron 45.0%
CCCTAGGGACAATATCAACT+AGG + chr2_1:14012981-14013000 None:intergenic 45.0%
!!! CGCTCCATTGTTTTTTCCCT+AGG + chr2_1:14012997-14013016 None:intergenic 45.0%
ATTGGGACACCTTCTCTTCT+TGG + chr2_1:14013039-14013058 None:intergenic 45.0%
!! AGAAGAGAAGGTGTCCCAAT+AGG - chr2_1:14013039-14013058 Msa0196660:CDS 45.0%
!! GAAGAGAAGGTGTCCCAATA+GGG - chr2_1:14013040-14013059 Msa0196660:CDS 45.0%
GTTCCCATAAGCATTCTTGG+AGG + chr2_1:14013139-14013158 None:intergenic 45.0%
GGTGTTCCCATAAGCATTCT+TGG + chr2_1:14013142-14013161 None:intergenic 45.0%
! TGATTTGCAAGAGGGTGTGA+GGG + chr2_1:14013196-14013215 None:intergenic 45.0%
!! TTGATTTGCAAGAGGGTGTG+AGG + chr2_1:14013197-14013216 None:intergenic 45.0%
TGGAGCTAGCAACAAGGTCA+TGG - chr2_1:14012872-14012891 Msa0196660:intron 50.0%
GGAGCTAGCAACAAGGTCAT+GGG - chr2_1:14012873-14012892 Msa0196660:intron 50.0%
GCCGGCATAGGCACATAATA+AGG + chr2_1:14013076-14013095 None:intergenic 50.0%
TACTGAGGTGGCATATGAGC+CGG + chr2_1:14013094-14013113 None:intergenic 50.0%
ATGCCACCTCAGTATGATGC+AGG - chr2_1:14013100-14013119 Msa0196660:CDS 50.0%
GATGGACCTGCATCATACTG+AGG + chr2_1:14013109-14013128 None:intergenic 50.0%
GGACCTGCATCATACTGAGG+TGG + chr2_1:14013106-14013125 None:intergenic 55.0%
GAGGGCTGCCTGTTGTTATG+AGG + chr2_1:14013178-14013197 None:intergenic 55.0%
GGTGGCATATGAGCCGGCAT+AGG + chr2_1:14013088-14013107 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 14012688 14013279 14012688 ID=Msa0196660;Name=Msa0196660
chr2_1 mRNA 14012688 14013279 14012688 ID=Msa0196660-mRNA-1;Parent=Msa0196660;Name=Msa0196660-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|0|0|1|1|1|2|0|166
chr2_1 exon 14012937 14013279 14012937 ID=Msa0196660-mRNA-1:exon:6044;Parent=Msa0196660-mRNA-1
chr2_1 exon 14012688 14012845 14012688 ID=Msa0196660-mRNA-1:exon:6043;Parent=Msa0196660-mRNA-1
chr2_1 CDS 14012937 14013279 14012937 ID=Msa0196660-mRNA-1:cds;Parent=Msa0196660-mRNA-1
chr2_1 CDS 14012688 14012845 14012688 ID=Msa0196660-mRNA-1:cds;Parent=Msa0196660-mRNA-1
Gene Sequence

>Msa0196660

TTGCAGAAAAAACTTGACACCTTCTGGTCAAAACAAAATGAAGAAGTTCAGAAGACTGTTGATTTCAAAAGTAATGGCTTGCCATTAGCAAGGATTAAGAAGATCATGAAAACAGAAGAAGGAGTGAGTATGATATCAGCTGAGGCACCTATTCTGTTTGCTAAGGCATGTGAAATGTTTATTATGGAGCTAGCAACAAGGTCATGGGCTAATACAGAGGTGAACAAAAGAAAGACACTTCAAAAGAGTGACATTGCATCTGCTGTCTCAAGTAATGAAGTGTTTGATTTCCTAGTTGATATTGTCCCTAGGGAAAAAACAATGGAGCGTGACATATTTATGGGTCCATCATATAGTCCTCCAAGAATGCTTATGGGAACACCTTCTCTCAATCAGCCTCATAACAACAGGCAGCCCTCACACCCTCTTGCAAATCAAATGTTTCCAATCCAAAAGCAGGAAAATGACCATTATGTTGATTTTCCAAATTCAGAAGATTAA
Protein sequence

>Msa0196660

LQKKLDTFWSKQNEEVQKTVDFKSNGLPLARIKKIMKTEEGVSMISAEAPILFAKACEMFIMELATRSWANTEVNKRKTLQKSDIASAVSSNEVFDFLVDIVPREKTMERDIFMGPSYSPPRMLMGTPSLNQPHNNRQPSHPLANQMFPIQKQENDHYVDFPNSED*