AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1162220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1162220 MtrunA17_Chr7g0258071 95.930 172 6 1 1 171 89 260 1.42e-121 343
Msa1162220 MtrunA17_Chr1g0173971 72.093 172 44 2 1 171 1 169 2.31e-89 258
Msa1162220 MtrunA17_Chr2g0328941 60.000 170 66 2 4 171 3 172 1.65e-72 216
Msa1162220 MtrunA17_Chr4g0032621 55.676 185 65 3 4 171 3 187 5.65e-69 207
Msa1162220 MtrunA17_Chr7g0266121 40.341 176 86 3 5 171 3 168 4.04e-43 141
Msa1162220 MtrunA17_Chr2g0321261 41.401 157 76 3 15 171 14 154 1.53e-38 129
Msa1162220 MtrunA17_Chr1g0178851 42.604 169 80 2 5 171 3 156 3.47e-38 128
Msa1162220 MtrunA17_Chr4g0026561 39.535 172 95 4 5 171 3 170 6.05e-37 125
Msa1162220 MtrunA17_Chr1g0203591 36.774 155 79 4 15 169 3 138 3.93e-27 99.4
Msa1162220 MtrunA17_Chr8g0351971 61.765 68 26 0 104 171 173 240 4.48e-27 102
Msa1162220 MtrunA17_Chr3g0087831 37.419 155 78 2 17 171 28 163 9.27e-27 99.4
Msa1162220 MtrunA17_Chr7g0274001 33.766 154 76 3 15 168 3 130 9.52e-25 93.2
Msa1162220 MtrunA17_Chr2g0306911 30.968 155 74 3 15 169 4 125 7.35e-18 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1162220 AT1G51200.4 53.073 179 65 4 4 171 3 173 1.42e-51 163
Msa1162220 AT1G51200.1 53.073 179 65 4 4 171 3 173 1.42e-51 163
Msa1162220 AT1G51200.3 53.073 179 65 4 4 171 3 173 1.42e-51 163
Msa1162220 AT1G51200.2 53.073 179 65 4 4 171 3 173 1.42e-51 163
Msa1162220 AT2G36320.1 44.048 168 84 2 5 171 3 161 7.79e-45 145
Msa1162220 AT3G52800.2 42.690 171 91 3 5 171 3 170 1.75e-39 132
Msa1162220 AT3G52800.1 42.690 171 91 3 5 171 3 170 1.75e-39 132
Msa1162220 AT2G27580.2 37.500 168 84 3 13 171 8 163 1.76e-37 127
Msa1162220 AT2G27580.1 37.500 168 84 3 13 171 8 163 1.76e-37 127
Msa1162220 AT4G12040.2 36.310 168 94 3 12 171 13 175 2.29e-36 124
Msa1162220 AT4G12040.1 36.310 168 94 3 12 171 13 175 2.29e-36 124
Msa1162220 AT1G12440.2 38.788 165 89 2 11 171 12 168 2.55e-36 124
Msa1162220 AT1G12440.1 38.788 165 89 2 11 171 12 168 2.55e-36 124
Msa1162220 AT1G12440.3 38.788 165 89 2 11 171 12 168 2.55e-36 124
Msa1162220 AT4G22820.1 38.750 160 93 3 15 171 19 176 1.39e-34 120
Msa1162220 AT4G22820.2 38.750 160 93 3 15 171 19 176 1.39e-34 120
Msa1162220 AT3G12630.1 38.926 149 72 3 23 171 31 160 9.63e-31 109
Msa1162220 AT4G14225.1 35.032 157 66 4 15 171 5 125 4.58e-26 96.7
Msa1162220 AT4G25380.1 31.013 158 72 3 16 171 8 130 1.33e-24 93.2

Find 45 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTTAATCCAACACGTTTC+CGG 0.268508 7_4:+52772371 None:intergenic
AGTTTATCCGCCTTAATTAC+TGG 0.271098 7_4:+52772235 None:intergenic
CGGAAACGTGTTGGATTAAC+TGG 0.273573 7_4:-52772370 Msa1162220:CDS
TGAATCCAACCCAGTAATTA+AGG 0.350084 7_4:-52772245 Msa1162220:CDS
CAATTATTAACGCACAGAAT+TGG 0.359796 7_4:+52772673 None:intergenic
ATCTCCATCTCATTAGAGAT+TGG 0.379259 7_4:+52772430 None:intergenic
CCAGCAGATGCACTACTTGC+CGG 0.396434 7_4:-52772390 Msa1162220:CDS
GAATTGGACGTTCAGGTGTC+TGG 0.402600 7_4:+52772689 None:intergenic
GTTAATAATTGTGGTTTCTT+CGG 0.432078 7_4:-52772661 Msa1162220:CDS
GCATCTGCTGGGACCAGTCT+TGG 0.436198 7_4:+52772402 None:intergenic
CCGGCAAGTAGTGCATCTGC+TGG 0.450708 7_4:+52772390 None:intergenic
ACGCACAGAATTGGACGTTC+AGG 0.451830 7_4:+52772682 None:intergenic
CCAGCAGTTCTATAATCAAA+AGG 0.452505 7_4:+52772283 None:intergenic
ATCCGCCTTAATTACTGGGT+TGG 0.457754 7_4:+52772240 None:intergenic
TTCCAGCGGCAATGGAAAGC+TGG 0.468107 7_4:-52772530 Msa1162220:CDS
AGCCAGCTTTCCATTGCCGC+TGG 0.484638 7_4:+52772528 None:intergenic
AATGGCAATTCCAGCGGCAA+TGG 0.485507 7_4:-52772538 Msa1162220:CDS
GTTTATCCGCCTTAATTACT+GGG 0.487636 7_4:+52772236 None:intergenic
CATGTGTTCCAAGTGTTACA+AGG 0.489662 7_4:-52772620 Msa1162220:CDS
ACACTTGGAACACATGTTCA+TGG 0.501814 7_4:+52772627 None:intergenic
TACTGGGTTGGATTCAGCTA+TGG 0.503220 7_4:+52772252 None:intergenic
AATGGAGTCTCATGATGAGA+TGG 0.509058 7_4:-52772716 Msa1162220:CDS
ATAATTGTGGTTTCTTCGGA+AGG 0.510786 7_4:-52772657 Msa1162220:CDS
ATTCTGTGCGTTAATAATTG+TGG 0.511147 7_4:-52772670 Msa1162220:CDS
CAGCAGTTCTATAATCAAAA+GGG 0.523968 7_4:+52772284 None:intergenic
CAGTGTGTCCTTGTAACACT+TGG 0.534504 7_4:+52772612 None:intergenic
AGCGATGCATTGAGCAAAAG+AGG 0.535711 7_4:+52772326 None:intergenic
TCAGTTGAAAACATCGTGAA+TGG 0.542840 7_4:-52772556 Msa1162220:CDS
CAAGGACACACTGCTGAAGC+AGG 0.543963 7_4:-52772602 Msa1162220:CDS
ATGGAGATGAAAGCCAAGAC+TGG 0.550708 7_4:-52772415 Msa1162220:CDS
AAATCCAATCTCTAATGAGA+TGG 0.551991 7_4:-52772434 Msa1162220:CDS
CACACTGCTGAAGCAGGAGC+AGG 0.565527 7_4:-52772596 Msa1162220:CDS
CGGCAAGTAGTGCATCTGCT+GGG 0.567957 7_4:+52772391 None:intergenic
ACTGGTTTCAGCTGCAAATG+TGG 0.568603 7_4:-52772352 Msa1162220:CDS
TTATAGAACTGCTGGTCAGA+AGG 0.572119 7_4:-52772275 Msa1162220:CDS
ACTACTTGCCGGAAACGTGT+TGG 0.596630 7_4:-52772379 Msa1162220:CDS
GAAAGCTGGCTGTGACCGCA+AGG 0.603467 7_4:-52772516 Msa1162220:CDS
TAATTGTGGTTTCTTCGGAA+GGG 0.609724 7_4:-52772656 Msa1162220:CDS
ATGGAGTCTCATGATGAGAT+GGG 0.645569 7_4:-52772715 Msa1162220:CDS
TCGCACATCAACGGTCCTTG+CGG 0.652242 7_4:+52772501 None:intergenic
ATCGTGAATGGCAATTCCAG+CGG 0.654212 7_4:-52772544 Msa1162220:CDS
ACTTTCAACTCGCACATCAA+CGG 0.654662 7_4:+52772492 None:intergenic
GCTCAATACAGTGTCTCCCG+AGG 0.676644 7_4:-52772464 Msa1162220:CDS
ATCCAACCCAGTAATTAAGG+CGG 0.681546 7_4:-52772242 Msa1162220:CDS
TGATGTGCGAGTTGAAAGTG+TGG 0.707716 7_4:-52772488 Msa1162220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTTAATAATTGTGGTTTCTT+CGG - chr7_4:52772276-52772295 Msa1162220:CDS 25.0%
CAATTATTAACGCACAGAAT+TGG + chr7_4:52772267-52772286 None:intergenic 30.0%
ATTCTGTGCGTTAATAATTG+TGG - chr7_4:52772267-52772286 Msa1162220:CDS 30.0%
! TCATTAGAGATTGGATTTTC+TGG + chr7_4:52772501-52772520 None:intergenic 30.0%
AAATCCAATCTCTAATGAGA+TGG - chr7_4:52772503-52772522 Msa1162220:CDS 30.0%
CAGCAGTTCTATAATCAAAA+GGG + chr7_4:52772656-52772675 None:intergenic 30.0%
ATAATTGTGGTTTCTTCGGA+AGG - chr7_4:52772280-52772299 Msa1162220:CDS 35.0%
TAATTGTGGTTTCTTCGGAA+GGG - chr7_4:52772281-52772300 Msa1162220:CDS 35.0%
TCAGTTGAAAACATCGTGAA+TGG - chr7_4:52772381-52772400 Msa1162220:CDS 35.0%
ATCTCCATCTCATTAGAGAT+TGG + chr7_4:52772510-52772529 None:intergenic 35.0%
CCAGCAGTTCTATAATCAAA+AGG + chr7_4:52772657-52772676 None:intergenic 35.0%
!! CCTTTTGATTATAGAACTGC+TGG - chr7_4:52772654-52772673 Msa1162220:CDS 35.0%
TGAATCCAACCCAGTAATTA+AGG - chr7_4:52772692-52772711 Msa1162220:CDS 35.0%
GTTTATCCGCCTTAATTACT+GGG + chr7_4:52772704-52772723 None:intergenic 35.0%
AGTTTATCCGCCTTAATTAC+TGG + chr7_4:52772705-52772724 None:intergenic 35.0%
ATGGAGTCTCATGATGAGAT+GGG - chr7_4:52772222-52772241 Msa1162220:CDS 40.0%
ACACTTGGAACACATGTTCA+TGG + chr7_4:52772313-52772332 None:intergenic 40.0%
CATGTGTTCCAAGTGTTACA+AGG - chr7_4:52772317-52772336 Msa1162220:CDS 40.0%
ACTTTCAACTCGCACATCAA+CGG + chr7_4:52772448-52772467 None:intergenic 40.0%
!!! ATTGGATTTTCTGGAACCTC+GGG + chr7_4:52772492-52772511 None:intergenic 40.0%
!!! GATTGGATTTTCTGGAACCT+CGG + chr7_4:52772493-52772512 None:intergenic 40.0%
CAGTTAATCCAACACGTTTC+CGG + chr7_4:52772569-52772588 None:intergenic 40.0%
TTATAGAACTGCTGGTCAGA+AGG - chr7_4:52772662-52772681 Msa1162220:CDS 40.0%
ATCCAACCCAGTAATTAAGG+CGG - chr7_4:52772695-52772714 Msa1162220:CDS 40.0%
CAGTGTGTCCTTGTAACACT+TGG + chr7_4:52772328-52772347 None:intergenic 45.0%
ATCGTGAATGGCAATTCCAG+CGG - chr7_4:52772393-52772412 Msa1162220:CDS 45.0%
! TGATGTGCGAGTTGAAAGTG+TGG - chr7_4:52772449-52772468 Msa1162220:CDS 45.0%
ATGGAGATGAAAGCCAAGAC+TGG - chr7_4:52772522-52772541 Msa1162220:CDS 45.0%
CGGAAACGTGTTGGATTAAC+TGG - chr7_4:52772567-52772586 Msa1162220:CDS 45.0%
! ACTGGTTTCAGCTGCAAATG+TGG - chr7_4:52772585-52772604 Msa1162220:CDS 45.0%
AGCGATGCATTGAGCAAAAG+AGG + chr7_4:52772614-52772633 None:intergenic 45.0%
! TACTGGGTTGGATTCAGCTA+TGG + chr7_4:52772688-52772707 None:intergenic 45.0%
ATCCGCCTTAATTACTGGGT+TGG + chr7_4:52772700-52772719 None:intergenic 45.0%
GAATTGGACGTTCAGGTGTC+TGG + chr7_4:52772251-52772270 None:intergenic 50.0%
ACGCACAGAATTGGACGTTC+AGG + chr7_4:52772258-52772277 None:intergenic 50.0%
AATGGCAATTCCAGCGGCAA+TGG - chr7_4:52772399-52772418 Msa1162220:CDS 50.0%
ACTACTTGCCGGAAACGTGT+TGG - chr7_4:52772558-52772577 Msa1162220:CDS 50.0%
CAAGGACACACTGCTGAAGC+AGG - chr7_4:52772335-52772354 Msa1162220:CDS 55.0%
TTCCAGCGGCAATGGAAAGC+TGG - chr7_4:52772407-52772426 Msa1162220:CDS 55.0%
TCGCACATCAACGGTCCTTG+CGG + chr7_4:52772439-52772458 None:intergenic 55.0%
GCTCAATACAGTGTCTCCCG+AGG - chr7_4:52772473-52772492 Msa1162220:CDS 55.0%
CGGCAAGTAGTGCATCTGCT+GGG + chr7_4:52772549-52772568 None:intergenic 55.0%
CCAGCAGATGCACTACTTGC+CGG - chr7_4:52772547-52772566 Msa1162220:CDS 55.0%
CACACTGCTGAAGCAGGAGC+AGG - chr7_4:52772341-52772360 Msa1162220:CDS 60.0%
AGCCAGCTTTCCATTGCCGC+TGG + chr7_4:52772412-52772431 None:intergenic 60.0%
GAAAGCTGGCTGTGACCGCA+AGG - chr7_4:52772421-52772440 Msa1162220:CDS 60.0%
GCATCTGCTGGGACCAGTCT+TGG + chr7_4:52772538-52772557 None:intergenic 60.0%
CCGGCAAGTAGTGCATCTGC+TGG + chr7_4:52772550-52772569 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 52772222 52772737 52772222 ID=Msa1162220;Name=Msa1162220
chr7_4 mRNA 52772222 52772737 52772222 ID=Msa1162220-mRNA-1;Parent=Msa1162220;Name=Msa1162220-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|171
chr7_4 exon 52772222 52772737 52772222 ID=Msa1162220-mRNA-1:exon:15212;Parent=Msa1162220-mRNA-1
chr7_4 CDS 52772222 52772737 52772222 ID=Msa1162220-mRNA-1:cds;Parent=Msa1162220-mRNA-1
Gene Sequence

>Msa1162220

ATGGAGTCTCATGATGAGATGGGATGCCAGACACCTGAACGTCCAATTCTGTGCGTTAATAATTGTGGTTTCTTCGGAAGGGAAGCTACCATGAACATGTGTTCCAAGTGTTACAAGGACACACTGCTGAAGCAGGAGCAGGAAAAACTTGTTGCGACGTCAGTTGAAAACATCGTGAATGGCAATTCCAGCGGCAATGGAAAGCTGGCTGTGACCGCAAGGACCGTTGATGTGCGAGTTGAAAGTGTGGAGCTCAATACAGTGTCTCCCGAGGTTCCAGAAAATCCAATCTCTAATGAGATGGAGATGAAAGCCAAGACTGGTCCCAGCAGATGCACTACTTGCCGGAAACGTGTTGGATTAACTGGTTTCAGCTGCAAATGTGGCAACCTCTTTTGCTCAATGCATCGCTATTCTGATAAACACGATTGCCCTTTTGATTATAGAACTGCTGGTCAGAAGGCCATAGCTGAATCCAACCCAGTAATTAAGGCGGATAAACTCGATAAAATCTAG
Protein sequence

>Msa1162220

MESHDEMGCQTPERPILCVNNCGFFGREATMNMCSKCYKDTLLKQEQEKLVATSVENIVNGNSSGNGKLAVTARTVDVRVESVELNTVSPEVPENPISNEMEMKAKTGPSRCTTCRKRVGLTGFSCKCGNLFCSMHRYSDKHDCPFDYRTAGQKAIAESNPVIKADKLDKI*