AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0620440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0620440 MtrunA17_Chr3g0093391 96.939 98 3 0 1 98 1 98 1.86e-61 194
Msa0620440 MtrunA17_Chr3g0093571 91.837 98 8 0 1 98 3 100 4.02e-58 186
Msa0620440 MtrunA17_Chr4g0039141 85.484 62 9 0 1 62 81 142 4.18e-33 113
Msa0620440 MtrunA17_Chr4g0051261 53.623 69 32 0 23 91 4 72 1.58e-20 83.2
Msa0620440 MtrunA17_Chr2g0293491 53.623 69 32 0 23 91 4 72 2.21e-20 82.8
Msa0620440 MtrunA17_Chr4g0057791 60.000 65 26 0 18 82 213 277 1.51e-19 81.6
Msa0620440 MtrunA17_Chr4g0061141 58.333 72 28 2 21 91 103 173 1.55e-18 79.0
Msa0620440 MtrunA17_Chr3g0122781 58.108 74 31 0 16 89 409 482 2.89e-18 78.2
Msa0620440 MtrunA17_Chr8g0377071 56.000 75 33 0 15 89 377 451 5.36e-18 77.4
Msa0620440 MtrunA17_Chr1g0191221 56.000 75 31 2 18 91 117 190 5.87e-18 77.4
Msa0620440 MtrunA17_Chr4g0002001 60.000 55 22 0 23 77 4 58 8.39e-18 75.9
Msa0620440 MtrunA17_Chr3g0131861 54.667 75 32 2 18 91 92 165 2.03e-17 75.9
Msa0620440 MtrunA17_Chr8g0385971 54.667 75 32 2 18 91 85 158 2.17e-17 75.5
Msa0620440 MtrunA17_Chr4g0066691 56.000 75 31 2 18 91 99 172 2.49e-17 75.5
Msa0620440 MtrunA17_Chr2g0286421 53.333 75 33 2 18 91 97 170 2.60e-17 75.5
Msa0620440 MtrunA17_Chr7g0273601 53.333 75 33 2 18 91 102 175 3.18e-17 75.1
Msa0620440 MtrunA17_Chr2g0317501 54.667 75 32 2 18 91 129 202 5.98e-17 74.3
Msa0620440 MtrunA17_Chr1g0187371 49.275 69 34 1 21 88 16 84 2.62e-16 72.0
Msa0620440 MtrunA17_Chr7g0218071 51.389 72 33 2 21 91 118 188 2.91e-16 72.4
Msa0620440 MtrunA17_Chr6g0453711 47.222 72 36 2 21 91 108 178 2.34e-15 69.7
Msa0620440 MtrunA17_Chr4g0040141 48.000 75 37 2 18 91 124 197 4.03e-15 69.3
Msa0620440 MtrunA17_Chr6g0483151 48.529 68 35 0 18 85 9 76 4.82e-15 68.9
Msa0620440 MtrunA17_Chr5g0396361 48.000 75 37 2 18 91 135 208 8.90e-15 68.2
Msa0620440 MtrunA17_Chr3g0099951 45.714 70 36 1 21 88 12 81 1.24e-13 64.7
Msa0620440 MtrunA17_Chr2g0324461 45.333 75 39 2 18 91 136 209 2.27e-13 64.3
Msa0620440 MtrunA17_Chr1g0201571 40.000 75 45 0 17 91 120 194 4.22e-13 63.5
Msa0620440 MtrunA17_Chr1g0194881 85.294 34 5 0 1 34 3 36 6.19e-13 62.8
Msa0620440 MtrunA17_Chr5g0443551 85.714 28 4 0 1 28 40 67 8.19e-12 57.4
Msa0620440 MtrunA17_Chr8g0358921 37.143 70 44 0 24 93 48 117 3.27e-11 57.8
Msa0620440 MtrunA17_Chr8g0339221 42.424 66 33 2 26 89 7 69 7.50e-11 57.0
Msa0620440 MtrunA17_Chr8g0383451 45.312 64 33 2 29 91 4 66 8.83e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0620440 AT5G10270.1 84.848 99 14 1 1 98 3 101 2.03e-51 168
Msa0620440 AT5G64960.1 85.714 98 13 1 2 98 4 101 1.51e-50 166
Msa0620440 AT1G67580.1 58.667 75 31 0 15 89 398 472 6.78e-24 94.7
Msa0620440 AT1G67580.2 58.667 75 31 0 15 89 398 472 6.78e-24 94.7
Msa0620440 AT3G48750.1 54.167 72 33 0 20 91 1 72 4.35e-21 85.1
Msa0620440 AT5G63370.2 46.154 91 41 2 3 89 147 233 4.77e-19 80.5
Msa0620440 AT5G63370.3 46.154 91 41 2 3 89 147 233 4.77e-19 80.5
Msa0620440 AT5G63370.7 46.154 91 41 2 3 89 281 367 4.79e-19 80.9
Msa0620440 AT5G63370.8 46.154 91 41 2 3 89 281 367 4.79e-19 80.9
Msa0620440 AT5G63370.4 46.154 91 41 2 3 89 281 367 4.79e-19 80.9
Msa0620440 AT5G63370.6 46.154 91 41 2 3 89 281 367 4.79e-19 80.9
Msa0620440 AT5G63370.1 46.154 91 41 2 3 89 281 367 4.79e-19 80.9
Msa0620440 AT5G63370.9 46.154 91 41 2 3 89 147 233 4.82e-19 80.5
Msa0620440 AT5G63370.5 47.191 89 39 2 5 89 283 367 4.96e-19 80.5
Msa0620440 AT5G63370.10 47.191 89 39 2 5 89 283 367 4.96e-19 80.5
Msa0620440 AT1G18670.2 61.111 72 26 2 21 91 129 199 5.75e-19 80.5
Msa0620440 AT1G18670.3 61.111 72 26 2 21 91 129 199 8.87e-19 80.1
Msa0620440 AT1G18670.1 61.111 72 26 2 21 91 129 199 9.39e-19 80.1
Msa0620440 AT1G76540.1 50.704 71 34 1 19 88 10 80 1.09e-17 76.3
Msa0620440 AT1G33770.1 53.247 77 30 2 18 91 136 209 1.56e-17 76.3
Msa0620440 AT1G74330.3 56.944 72 29 2 21 91 119 189 1.94e-17 76.3
Msa0620440 AT5G50860.2 53.333 75 33 2 18 91 109 182 2.64e-17 75.9
Msa0620440 AT1G74330.2 56.944 72 29 2 21 91 119 189 2.77e-17 75.9
Msa0620440 AT1G74330.1 56.944 72 29 2 21 91 119 189 2.77e-17 75.9
Msa0620440 AT3G05050.3 57.333 75 30 2 18 91 133 206 2.99e-17 75.5
Msa0620440 AT3G05050.2 57.333 75 30 2 18 91 133 206 2.99e-17 75.5
Msa0620440 AT3G05050.1 57.333 75 30 2 18 91 133 206 2.99e-17 75.5
Msa0620440 AT5G50860.1 53.333 75 33 2 18 91 109 182 4.23e-17 75.1
Msa0620440 AT1G54610.1 53.333 75 33 2 18 91 113 186 4.48e-17 75.1
Msa0620440 AT1G54610.3 53.333 75 33 2 18 91 113 186 4.48e-17 75.1
Msa0620440 AT1G54610.2 53.333 75 33 2 18 91 113 186 4.48e-17 75.1
Msa0620440 AT1G57700.1 51.948 77 31 2 18 91 141 214 5.37e-17 75.1
Msa0620440 AT1G71530.4 51.948 77 31 2 18 91 142 215 5.80e-17 74.3
Msa0620440 AT1G66750.1 45.946 74 40 0 12 85 2 75 6.78e-17 74.3
Msa0620440 AT1G09600.1 48.649 74 38 0 18 91 158 231 7.94e-17 74.3
Msa0620440 AT5G39420.1 50.704 71 35 0 21 91 103 173 7.96e-17 74.3
Msa0620440 AT1G71530.3 51.948 77 31 2 18 91 142 215 8.37e-17 74.3
Msa0620440 AT1G71530.2 51.948 77 31 2 18 91 142 215 1.32e-16 73.6
Msa0620440 AT1G20930.1 47.887 71 36 1 19 88 12 82 2.18e-16 72.4
Msa0620440 AT1G53050.2 52.000 75 34 2 18 91 129 202 2.78e-16 72.8
Msa0620440 AT1G53050.1 52.000 75 34 2 18 91 129 202 2.78e-16 72.8
Msa0620440 AT1G71530.1 51.948 77 31 2 18 91 142 215 5.47e-16 72.0
Msa0620440 AT2G38620.2 44.578 83 36 1 23 95 4 86 7.09e-16 71.2
Msa0620440 AT4G10010.2 50.649 77 32 2 18 91 151 224 8.39e-16 71.6
Msa0620440 AT1G73690.1 43.210 81 42 1 18 98 6 82 3.24e-15 69.7
Msa0620440 AT1G18040.1 41.860 86 46 1 13 98 2 83 4.94e-15 69.3
Msa0620440 AT2G38620.3 44.578 83 36 1 23 95 4 86 5.11e-15 68.2
Msa0620440 AT2G38620.1 44.578 83 36 1 23 95 4 86 5.11e-15 68.2
Msa0620440 AT3G54180.1 56.364 55 24 0 23 77 4 58 5.25e-15 68.6
Msa0620440 AT1G03740.2 46.053 76 39 2 18 92 208 282 7.39e-15 68.9
Msa0620440 AT1G03740.1 46.053 76 39 2 18 92 208 282 8.42e-15 68.6
Msa0620440 AT5G64960.2 86.111 36 5 0 63 98 13 48 1.70e-14 67.8
Msa0620440 AT5G44290.6 40.217 92 49 3 1 91 119 205 1.13e-13 65.5
Msa0620440 AT3G01085.1 50.000 70 33 2 23 91 115 183 1.31e-13 65.1
Msa0620440 AT3G01085.2 50.000 70 33 2 23 91 115 183 1.31e-13 65.1
Msa0620440 AT3G01085.3 50.000 70 33 2 23 91 115 183 1.47e-13 65.1
Msa0620440 AT5G44290.7 40.217 92 49 3 1 91 119 205 1.99e-13 64.7
Msa0620440 AT5G44290.2 40.217 92 49 3 1 91 119 205 2.05e-13 64.7
Msa0620440 AT5G44290.5 40.217 92 49 3 1 91 119 205 2.05e-13 64.7
Msa0620440 AT5G44290.4 40.217 92 49 3 1 91 119 205 2.05e-13 64.7
Msa0620440 AT5G44290.1 40.217 92 49 3 1 91 119 205 2.05e-13 64.7
Msa0620440 AT5G44290.3 40.217 92 49 3 1 91 119 205 2.05e-13 64.7
Msa0620440 AT4G22940.1 43.333 90 45 3 1 89 85 169 5.08e-12 60.8
Msa0620440 AT4G22940.2 43.333 90 45 3 1 89 85 169 1.23e-11 59.7

Find 25 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCGGCGAAGGCACTTA+TGG 0.185430 4_2:+71991662 Msa0620440:CDS
TGAAAATGTTATCAAGTTAA+AGG 0.254582 4_2:+71991999 Msa0620440:CDS
CTTCCTTAATCTTCTTTCTC+AGG 0.290546 4_2:-71992042 None:intergenic
ATTTCTCGTATAGCAGTAAT+AGG 0.291287 4_2:-71991952 None:intergenic
GGCCCTGAGAAAGAAGATTA+AGG 0.391298 4_2:+71992039 Msa0620440:CDS
TAATCTTCTTTCTCAGGGCC+TGG 0.395120 4_2:-71992036 None:intergenic
TTCCTTAATCTTCTTTCTCA+GGG 0.404520 4_2:-71992041 None:intergenic
CAACTAGCAATGGCAGCAGC+TGG 0.409192 4_2:+71991572 None:intergenic
TTCACCGGTTTCGATCTCTT+TGG 0.427011 4_2:-71991787 None:intergenic
TTTGAGAAACTCGAACAAAT+CGG 0.450626 4_2:+71991647 Msa0620440:CDS
AAATCGGCGAAGGCACTTAT+GGG 0.452605 4_2:+71991663 Msa0620440:CDS
AAGGAAATCGTTACGTCTCC+AGG 0.454720 4_2:+71992018 Msa0620440:CDS
TGCTTGCAGTCAAGTTTACA+TGG 0.493561 4_2:+71991764 Msa0620440:intron
CTTGAGAGCAACAATTTCAC+CGG 0.511084 4_2:-71991802 None:intergenic
CTCAAAGCAATCGACGCTAC+GGG 0.511892 4_2:-71991630 None:intergenic
GTATGGATAATGAAAGAGAA+GGG 0.512036 4_2:+71991832 Msa0620440:CDS
AACTAGCAATGGCAGCAGCT+GGG 0.520780 4_2:+71991573 None:intergenic
TGCTCTCAAGCAAATACGTA+TGG 0.526233 4_2:+71991815 Msa0620440:CDS
TCTCAAAGCAATCGACGCTA+CGG 0.534411 4_2:-71991631 None:intergenic
ATGGCCAAAGAGATCGAAAC+CGG 0.536311 4_2:+71991783 Msa0620440:CDS
CGTATGGATAATGAAAGAGA+AGG 0.557605 4_2:+71991831 Msa0620440:CDS
TATGGATAATGAAAGAGAAG+GGG 0.649789 4_2:+71991833 Msa0620440:CDS
ACGCTACGGGAACCACGCGA+AGG 0.656742 4_2:-71991617 None:intergenic
AAACTCGAACAAATCGGCGA+AGG 0.657326 4_2:+71991653 Msa0620440:CDS
TTAATTGATTCACCTTCGCG+TGG 0.661011 4_2:+71991605 Msa0620440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGGAATTTTAAATAGAATT+GGG - chr4_2:71991735-71991754 None:intergenic 15.0%
!!! ATTGGAATTTTAAATAGAAT+TGG - chr4_2:71991736-71991755 None:intergenic 15.0%
!! TGAAAATGTTATCAAGTTAA+AGG + chr4_2:71991999-71992018 Msa0620440:CDS 20.0%
TTTGAGAAACTCGAACAAAT+CGG + chr4_2:71991647-71991666 Msa0620440:CDS 30.0%
ACTGCAAGCATAATAAACAT+TGG - chr4_2:71991754-71991773 None:intergenic 30.0%
GTATGGATAATGAAAGAGAA+GGG + chr4_2:71991832-71991851 Msa0620440:CDS 30.0%
TATGGATAATGAAAGAGAAG+GGG + chr4_2:71991833-71991852 Msa0620440:CDS 30.0%
AATTTCACAGAATTGCACAT+AGG - chr4_2:71991892-71991911 None:intergenic 30.0%
ATTTCTCGTATAGCAGTAAT+AGG - chr4_2:71991955-71991974 None:intergenic 30.0%
CGTATGGATAATGAAAGAGA+AGG + chr4_2:71991831-71991850 Msa0620440:CDS 35.0%
! TTAATTGATTCACCTTCGCG+TGG + chr4_2:71991605-71991624 Msa0620440:CDS 40.0%
TGCTTGCAGTCAAGTTTACA+TGG + chr4_2:71991764-71991783 Msa0620440:intron 40.0%
CTTGAGAGCAACAATTTCAC+CGG - chr4_2:71991805-71991824 None:intergenic 40.0%
TGCTCTCAAGCAAATACGTA+TGG + chr4_2:71991815-71991834 Msa0620440:CDS 40.0%
TCTCAAAGCAATCGACGCTA+CGG - chr4_2:71991634-71991653 None:intergenic 45.0%
AAACTCGAACAAATCGGCGA+AGG + chr4_2:71991653-71991672 Msa0620440:CDS 45.0%
!! AAATCGGCGAAGGCACTTAT+GGG + chr4_2:71991663-71991682 Msa0620440:CDS 45.0%
ATGGCCAAAGAGATCGAAAC+CGG + chr4_2:71991783-71991802 Msa0620440:CDS 45.0%
!! TTCACCGGTTTCGATCTCTT+TGG - chr4_2:71991790-71991809 None:intergenic 45.0%
AAGGAAATCGTTACGTCTCC+AGG + chr4_2:71992018-71992037 Msa0620440:CDS 45.0%
TAATCTTCTTTCTCAGGGCC+TGG - chr4_2:71992039-71992058 None:intergenic 45.0%
CTCAAAGCAATCGACGCTAC+GGG - chr4_2:71991633-71991652 None:intergenic 50.0%
!! CAAATCGGCGAAGGCACTTA+TGG + chr4_2:71991662-71991681 Msa0620440:CDS 50.0%
ACGCTACGGGAACCACGCGA+AGG - chr4_2:71991620-71991639 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 71991581 71992059 71991581 ID=Msa0620440;Name=Msa0620440
chr4_2 mRNA 71991581 71992059 71991581 ID=Msa0620440-mRNA-1;Parent=Msa0620440;Name=Msa0620440-mRNA-1;_AED=0.28;_eAED=0.29;_QI=0|0|0|0.66|1|1|3|0|98
chr4_2 exon 71991581 71991684 71991581 ID=Msa0620440-mRNA-1:exon:21432;Parent=Msa0620440-mRNA-1
chr4_2 exon 71991773 71991854 71991773 ID=Msa0620440-mRNA-1:exon:21433;Parent=Msa0620440-mRNA-1
chr4_2 exon 71991949 71992059 71991949 ID=Msa0620440-mRNA-1:exon:21434;Parent=Msa0620440-mRNA-1
chr4_2 CDS 71991581 71991684 71991581 ID=Msa0620440-mRNA-1:cds;Parent=Msa0620440-mRNA-1
chr4_2 CDS 71991773 71991854 71991773 ID=Msa0620440-mRNA-1:cds;Parent=Msa0620440-mRNA-1
chr4_2 CDS 71991949 71992059 71991949 ID=Msa0620440-mRNA-1:cds;Parent=Msa0620440-mRNA-1
Gene Sequence

>Msa0620440

ATGGCAGCAGCTGGGCAACTAAACTTAATTGATTCACCTTCGCGTGGTTCCCGTAGCGTCGATTGCTTTGAGAAACTCGAACAAATCGGCGAAGGCACTTATGGTCAAGTTTACATGGCCAAAGAGATCGAAACCGGTGAAATTGTTGCTCTCAAGCAAATACGTATGGATAATGAAAGAGAAGGGTTTCCTATTACTGCTATACGAGAAATCAAAATTCTAAAGAAACTACATCATGAAAATGTTATCAAGTTAAAGGAAATCGTTACGTCTCCAGGCCCTGAGAAAGAAGATTAA
Protein sequence

>Msa0620440

MAAAGQLNLIDSPSRGSRSVDCFEKLEQIGEGTYGQVYMAKEIETGEIVALKQIRMDNEREGFPITAIREIKILKKLHHENVIKLKEIVTSPGPEKED*