AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1363130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1363130 MtrunA17_Chr4g0070161 94.762 210 10 1 1 209 1 210 2.58e-146 405
Msa1363130 MtrunA17_Chr2g0301381 44.186 172 88 1 33 204 32 195 7.75e-47 153
Msa1363130 MtrunA17_Chr5g0398871 33.166 199 115 6 13 203 29 217 1.86e-27 103
Msa1363130 MtrunA17_Chr4g0018251 31.731 208 114 5 2 196 1 193 8.52e-26 99.0
Msa1363130 MtrunA17_Chr4g0018241 32.536 209 111 5 2 196 1 193 2.24e-25 97.8
Msa1363130 MtrunA17_Chr3g0079381 34.302 172 101 4 28 194 17 181 5.86e-25 96.7
Msa1363130 MtrunA17_Chr3g0079401 32.768 177 107 4 28 199 18 187 2.49e-24 94.7
Msa1363130 MtrunA17_Chr7g0269361 35.366 164 94 5 36 196 34 188 3.26e-24 94.7
Msa1363130 MtrunA17_Chr4g0018281 31.579 209 113 5 2 196 1 193 4.25e-24 94.4
Msa1363130 MtrunA17_Chr8g0391341 29.817 218 127 7 2 198 1 213 5.31e-23 92.0
Msa1363130 MtrunA17_Chr4g0067891 30.144 209 129 6 2 198 1 204 7.90e-23 91.3
Msa1363130 MtrunA17_Chr4g0056601 30.653 199 127 5 7 199 9 202 3.91e-22 89.4
Msa1363130 MtrunA17_Chr7g0230391 34.320 169 101 4 34 193 42 209 4.20e-22 90.1
Msa1363130 MtrunA17_Chr4g0011681 32.547 212 123 7 1 201 1 203 5.37e-21 86.7
Msa1363130 MtrunA17_Chr4g0011721 32.512 203 123 6 10 202 6 204 9.67e-21 86.3
Msa1363130 MtrunA17_Chr1g0195561 29.442 197 128 6 1 196 1 187 2.07e-20 84.7
Msa1363130 MtrunA17_Chr3g0079371 29.310 174 116 4 23 193 54 223 5.36e-20 84.3
Msa1363130 MtrunA17_Chr4g0011701 31.429 210 128 6 1 201 1 203 5.79e-20 84.0
Msa1363130 MtrunA17_Chr4g0011711 31.527 203 123 7 10 201 6 203 1.29e-19 83.2
Msa1363130 MtrunA17_Chr3g0092681 27.957 186 119 3 8 192 50 221 5.22e-13 65.5
Msa1363130 MtrunA17_Chr4g0018231 26.316 209 131 6 2 196 3 202 6.23e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1363130 AT5G20740.1 41.379 203 103 6 8 204 9 201 2.72e-42 142
Msa1363130 AT5G20740.2 41.379 203 103 6 8 204 43 235 2.74e-41 140
Msa1363130 AT1G62770.1 34.314 204 111 7 13 202 8 202 1.03e-26 102
Msa1363130 AT1G14890.1 31.220 205 113 7 3 193 22 212 9.44e-23 92.0
Msa1363130 AT3G47380.1 29.798 198 125 4 8 198 11 201 2.37e-22 90.5
Msa1363130 AT5G62360.1 29.878 164 108 2 34 196 42 199 4.04e-21 87.4
Msa1363130 AT3G62820.1 31.915 188 116 6 11 196 13 190 9.44e-21 85.9
Msa1363130 AT5G62350.1 28.804 184 121 3 19 197 22 200 1.04e-20 86.3
Msa1363130 AT2G01610.1 29.651 172 109 3 34 193 43 214 2.30e-20 85.5
Msa1363130 AT4G25250.1 31.343 201 108 8 7 192 8 193 4.48e-20 84.3
Msa1363130 AT4G25260.1 29.240 171 111 3 34 199 36 201 8.15e-20 83.6
Msa1363130 AT1G23205.1 30.612 196 127 5 10 198 9 202 2.02e-19 82.8
Msa1363130 AT4G12390.1 31.579 171 106 4 34 198 38 203 3.52e-19 82.0
Msa1363130 AT1G62760.1 33.537 164 98 4 34 193 146 302 5.07e-18 80.9
Msa1363130 AT4G00080.1 31.795 195 117 5 11 193 7 197 7.82e-18 78.6
Msa1363130 AT1G70720.2 29.082 196 118 4 9 198 28 208 6.99e-17 76.3
Msa1363130 AT1G70720.1 28.426 197 120 4 14 198 9 196 1.06e-16 75.5
Msa1363130 AT5G51520.1 26.829 205 137 6 1 195 1 202 2.25e-16 74.7
Msa1363130 AT3G14310.1 29.121 182 117 5 35 209 58 234 4.87e-16 76.3
Msa1363130 AT2G47670.1 31.481 162 104 3 36 196 49 204 1.66e-12 64.3

Find 48 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGAATCAGTTATTGGAAT+TGG 0.301253 tig0018025:+160358 None:intergenic
AACGGTAACTCTTGTATTAA+CGG 0.341964 tig0018025:-160515 Msa1363130:CDS
CTACTTGGCTGGAGAGGGTT+TGG 0.366722 tig0018025:+160822 None:intergenic
TGGATGCAAGAATCAGTTAT+TGG 0.395690 tig0018025:+160352 None:intergenic
TGTGGACCCTGCTACCATAT+TGG 0.402819 tig0018025:+160700 None:intergenic
GAAAACCCTAAAATCCAATA+TGG 0.405587 tig0018025:-160714 Msa1363130:CDS
GAGGCTTGAGCTAGGTCTAA+TGG 0.427815 tig0018025:+160785 None:intergenic
CTAAAATCCAATATGGTAGC+AGG 0.439105 tig0018025:-160707 Msa1363130:CDS
GGGTTTGGACGCAGAGAGTT+GGG 0.447323 tig0018025:+160837 None:intergenic
CTTGCGGCGGTTGCGGATGA+AGG 0.449788 tig0018025:+160905 None:intergenic
TGGTGGTCTTGCGGCGGTTG+CGG 0.461087 tig0018025:+160898 None:intergenic
TGCTGAAAAGAAGGTGAAGT+TGG 0.476788 tig0018025:-160477 Msa1363130:CDS
GGAAGAAAGCAAGGAGTGTG+AGG 0.494383 tig0018025:+160951 None:intergenic
CGTTACTCAAATTTCAGACT+CGG 0.496711 tig0018025:-160642 Msa1363130:CDS
TGTTGTAAGACCTACTTGGC+TGG 0.502726 tig0018025:+160811 None:intergenic
CTTTGACAGAGGCTTGAGCT+AGG 0.508368 tig0018025:+160777 None:intergenic
TTTCTTGAGGTAAACGGAAA+GGG 0.508413 tig0018025:+160733 None:intergenic
AGGGTTTGGACGCAGAGAGT+TGG 0.516504 tig0018025:+160836 None:intergenic
GGTGAGAGTGTGAGTGAGAC+TGG 0.518335 tig0018025:+160754 None:intergenic
AAATGAGTAACGCTCAGACA+TGG 0.525801 tig0018025:-160556 Msa1363130:CDS
TAAGACCTACTTGGCTGGAG+AGG 0.534637 tig0018025:+160816 None:intergenic
AAGACCTACTTGGCTGGAGA+GGG 0.536678 tig0018025:+160817 None:intergenic
TCGAGTTCTAGAAGTGGTTG+TGG 0.540975 tig0018025:+160682 None:intergenic
GAAGAAAGCAAGGAGTGTGA+GGG 0.545789 tig0018025:+160952 None:intergenic
CGAGTTAAAACATCTTCGCA+TGG 0.548359 tig0018025:-160594 Msa1363130:CDS
TAGATCTTGTGGTGGTCTTG+CGG 0.549941 tig0018025:+160889 None:intergenic
AATGAGTAACGCTCAGACAT+GGG 0.558891 tig0018025:-160555 Msa1363130:CDS
CAAACCCTCTCCAGCCAAGT+AGG 0.559754 tig0018025:-160821 Msa1363130:CDS
TAGAAGTGATGCTGAAAAGA+AGG 0.562772 tig0018025:-160486 Msa1363130:CDS
TGAACAAGAGGAAGAAAGCA+AGG 0.567651 tig0018025:+160942 None:intergenic
AGTGAGACTGGCTTTGACAG+AGG 0.569007 tig0018025:+160766 None:intergenic
ACTTATAAACATAGATGCAT+CGG 0.583299 tig0018025:+160436 None:intergenic
GCTTTGTTGTAAGACCTACT+TGG 0.588353 tig0018025:+160807 None:intergenic
TAGCTTGTGCACATGATGAA+CGG 0.606340 tig0018025:+160864 None:intergenic
TTCGCATGGGAACGTTTGAG+TGG 0.606924 tig0018025:-160580 Msa1363130:CDS
CAGTTATTGGAATTGGAGCG+AGG 0.609889 tig0018025:+160365 None:intergenic
TAAAATCCAATATGGTAGCA+GGG 0.622725 tig0018025:-160706 Msa1363130:CDS
GAGTTAAAACATCTTCGCAT+GGG 0.632660 tig0018025:-160593 Msa1363130:CDS
AGAGTTACCGTTGGTAAAAG+CGG 0.632853 tig0018025:+160526 None:intergenic
ATCTTGTGGTGGTCTTGCGG+CGG 0.641744 tig0018025:+160892 None:intergenic
AGCAACTCGAGTTCTAGAAG+TGG 0.643944 tig0018025:+160676 None:intergenic
GTTAATACAAGAGTTACCGT+TGG 0.650175 tig0018025:+160517 None:intergenic
ACGTCGGTGACATGAACAAG+AGG 0.653665 tig0018025:+160930 None:intergenic
TGAAAAGAAGGTGAAGTTGG+AGG 0.659594 tig0018025:-160474 Msa1363130:CDS
TCAATCGTCTTAGTGAACGC+AGG 0.698607 tig0018025:-160397 Msa1363130:CDS
GTTGCGGATGAAGGAAACGT+CGG 0.705406 tig0018025:+160914 None:intergenic
GATGAACGGATTAGATCTTG+TGG 0.710690 tig0018025:+160878 None:intergenic
GAACGGATTAGATCTTGTGG+TGG 0.733908 tig0018025:+160881 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACTTATAAACATAGATGCAT+CGG + tig0018025:160902-160921 None:intergenic 25.0%
GAAAACCCTAAAATCCAATA+TGG - tig0018025:160621-160640 Msa1363130:CDS 30.0%
! TGCTACCATATTGGATTTTA+GGG + tig0018025:160629-160648 None:intergenic 30.0%
TAAAATCCAATATGGTAGCA+GGG - tig0018025:160629-160648 Msa1363130:CDS 30.0%
AACGGTAACTCTTGTATTAA+CGG - tig0018025:160820-160839 Msa1363130:CDS 30.0%
TTTCTTGAGGTAAACGGAAA+GGG + tig0018025:160605-160624 None:intergenic 35.0%
! TTTTCTTGAGGTAAACGGAA+AGG + tig0018025:160606-160625 None:intergenic 35.0%
! TAGGGTTTTCTTGAGGTAAA+CGG + tig0018025:160611-160630 None:intergenic 35.0%
!!! TGGATTTTAGGGTTTTCTTG+AGG + tig0018025:160618-160637 None:intergenic 35.0%
! CTGCTACCATATTGGATTTT+AGG + tig0018025:160630-160649 None:intergenic 35.0%
CTAAAATCCAATATGGTAGC+AGG - tig0018025:160628-160647 Msa1363130:CDS 35.0%
CGTTACTCAAATTTCAGACT+CGG - tig0018025:160693-160712 Msa1363130:CDS 35.0%
!!! GTTTTAACTCGTTCAACGTT+TGG + tig0018025:160732-160751 None:intergenic 35.0%
GAGTTAAAACATCTTCGCAT+GGG - tig0018025:160742-160761 Msa1363130:CDS 35.0%
GTTAATACAAGAGTTACCGT+TGG + tig0018025:160821-160840 None:intergenic 35.0%
TAGAAGTGATGCTGAAAAGA+AGG - tig0018025:160849-160868 Msa1363130:CDS 35.0%
TGAACAAGAGGAAGAAAGCA+AGG + tig0018025:160396-160415 None:intergenic 40.0%
!! GATGAACGGATTAGATCTTG+TGG + tig0018025:160460-160479 None:intergenic 40.0%
! TAGCTTGTGCACATGATGAA+CGG + tig0018025:160474-160493 None:intergenic 40.0%
! GCTTTGTTGTAAGACCTACT+TGG + tig0018025:160531-160550 None:intergenic 40.0%
CGAGTTAAAACATCTTCGCA+TGG - tig0018025:160741-160760 Msa1363130:CDS 40.0%
AAATGAGTAACGCTCAGACA+TGG - tig0018025:160779-160798 Msa1363130:CDS 40.0%
AATGAGTAACGCTCAGACAT+GGG - tig0018025:160780-160799 Msa1363130:CDS 40.0%
! AGAGTTACCGTTGGTAAAAG+CGG + tig0018025:160812-160831 None:intergenic 40.0%
TGCTGAAAAGAAGGTGAAGT+TGG - tig0018025:160858-160877 Msa1363130:CDS 40.0%
TGAAAAGAAGGTGAAGTTGG+AGG - tig0018025:160861-160880 Msa1363130:CDS 40.0%
! GAAGAAAGCAAGGAGTGTGA+GGG + tig0018025:160386-160405 None:intergenic 45.0%
! TAGATCTTGTGGTGGTCTTG+CGG + tig0018025:160449-160468 None:intergenic 45.0%
!! GAACGGATTAGATCTTGTGG+TGG + tig0018025:160457-160476 None:intergenic 45.0%
TGTTGTAAGACCTACTTGGC+TGG + tig0018025:160527-160546 None:intergenic 45.0%
!! TCGAGTTCTAGAAGTGGTTG+TGG + tig0018025:160656-160675 None:intergenic 45.0%
!! AGCAACTCGAGTTCTAGAAG+TGG + tig0018025:160662-160681 None:intergenic 45.0%
TCAATCGTCTTAGTGAACGC+AGG - tig0018025:160938-160957 Msa1363130:CDS 45.0%
CAGTTATTGGAATTGGAGCG+AGG + tig0018025:160973-160992 None:intergenic 45.0%
! GGAAGAAAGCAAGGAGTGTG+AGG + tig0018025:160387-160406 None:intergenic 50.0%
ACGTCGGTGACATGAACAAG+AGG + tig0018025:160408-160427 None:intergenic 50.0%
GTTGCGGATGAAGGAAACGT+CGG + tig0018025:160424-160443 None:intergenic 50.0%
AAGACCTACTTGGCTGGAGA+GGG + tig0018025:160521-160540 None:intergenic 50.0%
TAAGACCTACTTGGCTGGAG+AGG + tig0018025:160522-160541 None:intergenic 50.0%
GAGGCTTGAGCTAGGTCTAA+TGG + tig0018025:160553-160572 None:intergenic 50.0%
CTTTGACAGAGGCTTGAGCT+AGG + tig0018025:160561-160580 None:intergenic 50.0%
!! AGTGAGACTGGCTTTGACAG+AGG + tig0018025:160572-160591 None:intergenic 50.0%
TGTGGACCCTGCTACCATAT+TGG + tig0018025:160638-160657 None:intergenic 50.0%
TTCGCATGGGAACGTTTGAG+TGG - tig0018025:160755-160774 Msa1363130:CDS 50.0%
!! GCTAGCACCGCTTTTACCAA+CGG - tig0018025:160802-160821 Msa1363130:CDS 50.0%
! ATCTTGTGGTGGTCTTGCGG+CGG + tig0018025:160446-160465 None:intergenic 55.0%
GGGTTTGGACGCAGAGAGTT+GGG + tig0018025:160501-160520 None:intergenic 55.0%
AGGGTTTGGACGCAGAGAGT+TGG + tig0018025:160502-160521 None:intergenic 55.0%
CTACTTGGCTGGAGAGGGTT+TGG + tig0018025:160516-160535 None:intergenic 55.0%
CAAACCCTCTCCAGCCAAGT+AGG - tig0018025:160514-160533 Msa1363130:CDS 55.0%
! GGTGAGAGTGTGAGTGAGAC+TGG + tig0018025:160584-160603 None:intergenic 55.0%
CTTGCGGCGGTTGCGGATGA+AGG + tig0018025:160433-160452 None:intergenic 65.0%
! TGGTGGTCTTGCGGCGGTTG+CGG + tig0018025:160440-160459 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0018025 gene 160364 160993 160364 ID=Msa1363130;Name=Msa1363130
tig0018025 mRNA 160364 160993 160364 ID=Msa1363130-mRNA-1;Parent=Msa1363130;Name=Msa1363130-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|209
tig0018025 exon 160364 160993 160364 ID=Msa1363130-mRNA-1:exon:13408;Parent=Msa1363130-mRNA-1
tig0018025 CDS 160364 160993 160364 ID=Msa1363130-mRNA-1:cds;Parent=Msa1363130-mRNA-1
Gene Sequence

>Msa1363130

ATGATGCAAACATATAACTCCCTCACACTCCTTGCTTTCTTCCTCTTGTTCATGTCACCGACGTTTCCTTCATCCGCAACCGCCGCAAGACCACCACAAGATCTAATCCGTTCATCATGTGCACAAGCTAGATACCCAACTCTCTGCGTCCAAACCCTCTCCAGCCAAGTAGGTCTTACAACAAAGCCATTAGACCTAGCTCAAGCCTCTGTCAAAGCCAGTCTCACTCACACTCTCACCCTTTCCGTTTACCTCAAGAAAACCCTAAAATCCAATATGGTAGCAGGGTCCACAACCACTTCTAGAACTCGAGTTGCTTTGAGAGACTGCGTTACTCAAATTTCAGACTCGGTTCTTCAGTTAAACCAAACGTTGAACGAGTTAAAACATCTTCGCATGGGAACGTTTGAGTGGCAAATGAGTAACGCTCAGACATGGGCTAGCACCGCTTTTACCAACGGTAACTCTTGTATTAACGGTTTGAATAGAAGTGATGCTGAAAAGAAGGTGAAGTTGGAGGTGAAAAGAAAAGTTACCGATGCATCTATGTTTATAAGTAACGCTCTCTACTTGATCAATCGTCTTAGTGAACGCAGGAATCAAAAGCCTCGCTCCAATTCCAATAACTGA
Protein sequence

>Msa1363130

MMQTYNSLTLLAFFLLFMSPTFPSSATAARPPQDLIRSSCAQARYPTLCVQTLSSQVGLTTKPLDLAQASVKASLTHTLTLSVYLKKTLKSNMVAGSTTTSRTRVALRDCVTQISDSVLQLNQTLNELKHLRMGTFEWQMSNAQTWASTAFTNGNSCINGLNRSDAEKKVKLEVKRKVTDASMFISNALYLINRLSERRNQKPRSNSNN*