AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46080.t1 MTR_3g040810 96.939 98 3 0 1 98 1 98 6.77e-62 196
MS.gene46080.t1 MTR_3g040520 91.837 98 8 0 1 98 3 100 1.97e-58 187
MS.gene46080.t1 MTR_4g076670 84.127 63 10 0 1 63 1 63 6.42e-34 113
MS.gene46080.t1 MTR_4g094430 52.174 69 33 0 23 91 4 72 5.66e-19 79.3
MS.gene46080.t1 MTR_4g109090 54.930 71 32 0 21 91 103 173 6.48e-19 80.1
MS.gene46080.t1 MTR_2g032060 52.174 69 33 0 23 91 4 72 8.13e-19 79.0
MS.gene46080.t1 MTR_4g103810 58.462 65 27 0 18 82 103 167 9.60e-19 79.7
MS.gene46080.t1 MTR_1g081870 52.703 74 35 0 18 91 117 190 2.63e-18 78.6
MS.gene46080.t1 MTR_4g103810 58.462 65 27 0 18 82 213 277 4.29e-18 77.8
MS.gene46080.t1 MTR_8g099770 52.703 74 35 0 18 91 85 158 6.45e-18 77.4
MS.gene46080.t1 MTR_3g098760 51.351 74 36 0 18 91 92 165 7.19e-18 77.4
MS.gene46080.t1 MTR_4g118780 52.703 74 35 0 18 91 99 172 9.25e-18 77.0
MS.gene46080.t1 MTR_2g020210 50.000 74 37 0 18 91 97 170 9.58e-18 77.0
MS.gene46080.t1 MTR_2g085200 51.351 74 36 0 18 91 129 202 1.81e-17 76.3
MS.gene46080.t1 MTR_7g114300 51.351 74 36 0 18 91 102 175 2.43e-17 75.5
MS.gene46080.t1 MTR_7g114300 51.351 74 36 0 18 91 102 175 2.86e-17 75.5
MS.gene46080.t1 MTR_7g011800 50.704 71 35 0 21 91 118 188 3.06e-17 75.5
MS.gene46080.t1 MTR_8g080190 54.667 75 34 0 15 89 377 451 5.90e-17 74.7
MS.gene46080.t1 MTR_3g085650 56.757 74 32 0 16 89 409 482 6.36e-17 74.7
MS.gene46080.t1 MTR_7g114300 51.351 74 36 0 18 91 102 175 6.50e-17 74.7
MS.gene46080.t1 MTR_3g085650 56.757 74 32 0 16 89 409 482 6.73e-17 74.7
MS.gene46080.t1 MTR_8g080190 54.667 75 34 0 15 89 377 451 7.82e-17 74.3
MS.gene46080.t1 MTR_7g114300 51.351 74 36 0 18 91 102 175 7.99e-17 74.3
MS.gene46080.t1 MTR_3g085650 56.757 74 32 0 16 89 409 482 8.39e-17 74.3
MS.gene46080.t1 MTR_3g085650 56.757 74 32 0 16 89 409 482 8.89e-17 74.3
MS.gene46080.t1 MTR_4g007750 58.182 55 23 0 23 77 4 58 2.09e-16 72.4
MS.gene46080.t1 MTR_6g013030 46.479 71 38 0 21 91 108 178 2.79e-16 72.8
MS.gene46080.t1 MTR_4g078290 45.946 74 40 0 18 91 124 197 1.04e-15 71.2
MS.gene46080.t1 MTR_4g078290 45.946 74 40 0 18 91 124 197 1.05e-15 71.2
MS.gene46080.t1 MTR_5g008860 45.946 74 40 0 18 91 135 208 2.10e-15 70.1
MS.gene46080.t1 MTR_6g080470 48.529 68 35 0 18 85 9 76 4.39e-15 69.3
MS.gene46080.t1 MTR_1g075610 47.826 69 35 1 21 88 16 84 6.29e-15 68.6
MS.gene46080.t1 MTR_8g092290 43.243 74 42 0 18 91 136 209 1.27e-14 68.2
MS.gene46080.t1 MTR_1g098300 41.333 75 44 0 17 91 120 194 3.68e-14 66.6
MS.gene46080.t1 MTR_2g090405 43.243 74 42 0 18 91 136 209 7.36e-14 65.9
MS.gene46080.t1 MTR_3g054080 45.714 70 36 1 21 88 12 81 1.55e-13 64.7
MS.gene46080.t1 MTR_1g087310 85.294 34 5 0 1 34 1 34 1.10e-12 62.4
MS.gene46080.t1 MTR_5g091975 85.714 28 4 0 1 28 1 28 4.48e-12 57.4
MS.gene46080.t1 MTR_1g048630 39.189 74 45 0 19 92 3 76 3.52e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46080.t1 AT5G10270 84.848 99 14 1 1 98 3 101 6.65e-52 169
MS.gene46080.t1 AT5G64960 85.714 98 13 1 2 98 4 101 5.34e-51 167
MS.gene46080.t1 AT1G67580 57.333 75 32 0 15 89 398 472 8.07e-23 91.3
MS.gene46080.t1 AT1G67580 57.333 75 32 0 15 89 398 472 8.07e-23 91.3
MS.gene46080.t1 AT3G48750 52.778 72 34 0 20 91 1 72 1.23e-19 80.9
MS.gene46080.t1 AT1G18670 57.746 71 30 0 21 91 129 199 1.86e-19 82.0
MS.gene46080.t1 AT1G18670 57.746 71 30 0 21 91 129 199 2.81e-19 81.3
MS.gene46080.t1 AT1G18670 57.746 71 30 0 21 91 129 199 3.07e-19 81.3
MS.gene46080.t1 AT5G39420 52.113 71 34 0 21 91 103 173 5.48e-18 77.8
MS.gene46080.t1 AT1G74330 53.521 71 33 0 21 91 119 189 8.33e-18 77.0
MS.gene46080.t1 AT5G50860 50.000 74 37 0 18 91 109 182 1.11e-17 76.6
MS.gene46080.t1 AT1G74330 53.521 71 33 0 21 91 119 189 1.20e-17 76.6
MS.gene46080.t1 AT1G74330 53.521 71 33 0 21 91 119 189 1.20e-17 76.6
MS.gene46080.t1 AT1G54610 50.000 74 37 0 18 91 113 186 1.38e-17 76.6
MS.gene46080.t1 AT1G54610 50.000 74 37 0 18 91 113 186 1.38e-17 76.6
MS.gene46080.t1 AT1G54610 50.000 74 37 0 18 91 113 186 1.38e-17 76.6
MS.gene46080.t1 AT5G50860 50.000 74 37 0 18 91 109 182 1.42e-17 76.6
MS.gene46080.t1 AT1G71530 51.948 77 31 2 18 91 142 215 1.63e-17 75.9
MS.gene46080.t1 AT1G71530 51.948 77 31 2 18 91 142 215 1.98e-17 75.9
MS.gene46080.t1 AT3G05050 57.333 75 30 2 18 91 133 206 1.99e-17 76.3
MS.gene46080.t1 AT3G05050 57.333 75 30 2 18 91 133 206 1.99e-17 76.3
MS.gene46080.t1 AT3G05050 57.333 75 30 2 18 91 133 206 1.99e-17 76.3
MS.gene46080.t1 AT1G71530 50.000 74 37 0 18 91 142 215 2.20e-17 75.9
MS.gene46080.t1 AT1G33770 51.351 74 36 0 18 91 136 209 2.30e-17 75.9
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 149 241 4.60e-17 75.1
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 149 241 4.60e-17 75.1
MS.gene46080.t1 AT1G53050 48.649 74 38 0 18 91 129 202 4.78e-17 75.1
MS.gene46080.t1 AT1G53050 48.649 74 38 0 18 91 129 202 4.78e-17 75.1
MS.gene46080.t1 AT1G66750 45.946 74 40 0 12 85 2 75 5.18e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 149 241 6.79e-17 74.3
MS.gene46080.t1 AT1G57700 50.000 74 37 0 18 91 141 214 7.62e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 7.70e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 7.70e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 7.70e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 7.70e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 7.70e-17 74.3
MS.gene46080.t1 AT1G71530 50.000 74 37 0 18 91 142 215 8.21e-17 74.3
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 1.11e-16 73.9
MS.gene46080.t1 AT5G63370 43.299 97 47 2 5 97 283 375 1.11e-16 73.9
MS.gene46080.t1 AT1G09600 48.649 74 38 0 18 91 158 231 1.32e-16 73.9
MS.gene46080.t1 AT4G10010 48.649 74 38 0 18 91 151 224 1.50e-16 73.6
MS.gene46080.t1 AT1G76540 49.296 71 35 1 19 88 10 80 2.29e-16 72.4
MS.gene46080.t1 AT1G73690 47.059 68 36 0 18 85 6 73 3.25e-15 69.7
MS.gene46080.t1 AT1G20930 46.479 71 37 1 19 88 12 82 4.56e-15 68.9
MS.gene46080.t1 AT1G18040 45.205 73 40 0 13 85 2 74 4.71e-15 69.3
MS.gene46080.t1 AT1G03740 46.053 76 39 2 18 92 208 282 6.39e-15 68.9
MS.gene46080.t1 AT1G03740 46.053 76 39 2 18 92 208 282 7.21e-15 68.9
MS.gene46080.t1 AT2G38620 42.353 85 39 1 23 97 4 88 9.39e-15 68.2
MS.gene46080.t1 AT5G64960 86.111 36 5 0 63 98 13 48 4.18e-14 66.6
MS.gene46080.t1 AT3G01085 47.826 69 36 0 23 91 115 183 4.62e-14 66.6
MS.gene46080.t1 AT3G01085 47.826 69 36 0 23 91 115 183 4.62e-14 66.6
MS.gene46080.t1 AT3G01085 47.826 69 36 0 23 91 115 183 5.51e-14 66.2
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 5.78e-14 66.2
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 8.88e-14 65.9
MS.gene46080.t1 AT2G38620 42.353 85 39 1 23 97 4 88 9.07e-14 64.7
MS.gene46080.t1 AT2G38620 42.353 85 39 1 23 97 4 88 9.07e-14 64.7
MS.gene46080.t1 AT3G54180 54.545 55 25 0 23 77 4 58 9.50e-14 65.1
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 9.52e-14 65.5
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 9.52e-14 65.5
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 9.52e-14 65.5
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 9.52e-14 65.5
MS.gene46080.t1 AT5G44290 38.462 91 52 1 1 91 119 205 9.52e-14 65.5
MS.gene46080.t1 AT4G22940 41.573 89 48 1 1 89 85 169 1.83e-12 62.0
MS.gene46080.t1 AT4G22940 41.573 89 48 1 1 89 85 169 2.84e-12 61.2
MS.gene46080.t1 AT5G25110 45.312 64 34 1 29 91 49 112 3.97e-11 58.2

Find 24 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCGGCGAAGGCACTTA+TGG 0.185430 7.2:+41941681 MS.gene46080:CDS
TGAAAATGTTATCAAGTTAA+AGG 0.254582 7.2:+41942018 MS.gene46080:CDS
CTTCCTTAATCATCTTTCTC+AGG 0.318392 7.2:-41942061 None:intergenic
GGCCCTGAGAAAGATGATTA+AGG 0.402221 7.2:+41942058 MS.gene46080:CDS
CAACTAGCAATGGCAGCAGC+TGG 0.409192 7.2:+41941591 None:intergenic
TAATCATCTTTCTCAGGGCC+TGG 0.414426 7.2:-41942055 None:intergenic
TTCACCGGTTTCGATCTCTT+TGG 0.427011 7.2:-41941806 None:intergenic
AAGGAAATTGTTACGTCTCC+AGG 0.439484 7.2:+41942037 MS.gene46080:CDS
TTCCTTAATCATCTTTCTCA+GGG 0.448783 7.2:-41942060 None:intergenic
TTTGAGAAACTCGAACAAAT+CGG 0.450626 7.2:+41941666 MS.gene46080:CDS
AAATCGGCGAAGGCACTTAT+GGG 0.452605 7.2:+41941682 MS.gene46080:CDS
TGCTTGCAGTCAAGTTTACA+TGG 0.493561 7.2:+41941783 MS.gene46080:intron
CTTGAGAGCAACAATTTCAC+CGG 0.511084 7.2:-41941821 None:intergenic
CTCAAAGCAATCGACGCTAC+GGG 0.511892 7.2:-41941649 None:intergenic
GTATGGATAATGAAAGAGAA+GGG 0.512036 7.2:+41941851 MS.gene46080:CDS
AACTAGCAATGGCAGCAGCT+GGG 0.520780 7.2:+41941592 None:intergenic
TGCTCTCAAGCAAATACGTA+TGG 0.526233 7.2:+41941834 MS.gene46080:CDS
TCTCAAAGCAATCGACGCTA+CGG 0.534411 7.2:-41941650 None:intergenic
ATGGCCAAAGAGATCGAAAC+CGG 0.536311 7.2:+41941802 MS.gene46080:CDS
CGTATGGATAATGAAAGAGA+AGG 0.557605 7.2:+41941850 MS.gene46080:CDS
TATGGATAATGAAAGAGAAG+GGG 0.649789 7.2:+41941852 MS.gene46080:CDS
ACGCTACGGGAACCACGCGA+AGG 0.656742 7.2:-41941636 None:intergenic
AAACTCGAACAAATCGGCGA+AGG 0.657326 7.2:+41941672 MS.gene46080:CDS
TTAATTGATTCACCTTCGCG+TGG 0.661011 7.2:+41941624 MS.gene46080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGGAATTTTAAATAGAAT+TGG - chr7.2:41941755-41941774 None:intergenic 15.0%
!!! TTGGAATTTTAAATAGAATT+GGG - chr7.2:41941754-41941773 None:intergenic 15.0%
!! TGAAAATGTTATCAAGTTAA+AGG + chr7.2:41942018-41942037 MS.gene46080:CDS 20.0%
AATTACACAGAATTGCACAT+AGG - chr7.2:41941911-41941930 None:intergenic 30.0%
ACTGCAAGCATAATAAACAT+TGG - chr7.2:41941773-41941792 None:intergenic 30.0%
GTATGGATAATGAAAGAGAA+GGG + chr7.2:41941851-41941870 MS.gene46080:CDS 30.0%
TATGGATAATGAAAGAGAAG+GGG + chr7.2:41941852-41941871 MS.gene46080:CDS 30.0%
TTTGAGAAACTCGAACAAAT+CGG + chr7.2:41941666-41941685 MS.gene46080:CDS 30.0%
CGTATGGATAATGAAAGAGA+AGG + chr7.2:41941850-41941869 MS.gene46080:CDS 35.0%
AAGGAAATTGTTACGTCTCC+AGG + chr7.2:41942037-41942056 MS.gene46080:CDS 40.0%
CTTGAGAGCAACAATTTCAC+CGG - chr7.2:41941824-41941843 None:intergenic 40.0%
TGCTCTCAAGCAAATACGTA+TGG + chr7.2:41941834-41941853 MS.gene46080:CDS 40.0%
TGCTTGCAGTCAAGTTTACA+TGG + chr7.2:41941783-41941802 MS.gene46080:intron 40.0%
! TTAATTGATTCACCTTCGCG+TGG + chr7.2:41941624-41941643 MS.gene46080:CDS 40.0%
AAACTCGAACAAATCGGCGA+AGG + chr7.2:41941672-41941691 MS.gene46080:CDS 45.0%
ATGGCCAAAGAGATCGAAAC+CGG + chr7.2:41941802-41941821 MS.gene46080:CDS 45.0%
TAATCATCTTTCTCAGGGCC+TGG - chr7.2:41942058-41942077 None:intergenic 45.0%
TCTCAAAGCAATCGACGCTA+CGG - chr7.2:41941653-41941672 None:intergenic 45.0%
!! AAATCGGCGAAGGCACTTAT+GGG + chr7.2:41941682-41941701 MS.gene46080:CDS 45.0%
!! TTCACCGGTTTCGATCTCTT+TGG - chr7.2:41941809-41941828 None:intergenic 45.0%
CTCAAAGCAATCGACGCTAC+GGG - chr7.2:41941652-41941671 None:intergenic 50.0%
!! CAAATCGGCGAAGGCACTTA+TGG + chr7.2:41941681-41941700 MS.gene46080:CDS 50.0%
ACGCTACGGGAACCACGCGA+AGG - chr7.2:41941639-41941658 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 41941600 41942078 41941600 ID=MS.gene46080
chr7.2 mRNA 41941600 41942078 41941600 ID=MS.gene46080.t1;Parent=MS.gene46080
chr7.2 exon 41941600 41941703 41941600 ID=MS.gene46080.t1.exon1;Parent=MS.gene46080.t1
chr7.2 CDS 41941600 41941703 41941600 ID=cds.MS.gene46080.t1;Parent=MS.gene46080.t1
chr7.2 exon 41941792 41941873 41941792 ID=MS.gene46080.t1.exon2;Parent=MS.gene46080.t1
chr7.2 CDS 41941792 41941873 41941792 ID=cds.MS.gene46080.t1;Parent=MS.gene46080.t1
chr7.2 exon 41941968 41942078 41941968 ID=MS.gene46080.t1.exon3;Parent=MS.gene46080.t1
chr7.2 CDS 41941968 41942078 41941968 ID=cds.MS.gene46080.t1;Parent=MS.gene46080.t1
Gene Sequence

>MS.gene46080

ATGGCAGCAGCTGGGCAACTAAACTTAATTGATTCACCTTCGCGTGGTTCCCGTAGCGTCGATTGCTTTGAGAAACTCGAACAAATCGGCGAAGGCACTTATGGGTACTTACTTTTTCTCAATTTCACTTTCATCTTTTTCTTCAACACTTCCCAATTCTATTTAAAATTCCAATGTTTATTATGCTTGCAGTCAAGTTTACATGGCCAAAGAGATCGAAACCGGTGAAATTGTTGCTCTCAAGCAAATACGTATGGATAATGAAAGAGAAGGGGTATGAATATGAATGTATTTTCAAACATTTCATTCCTATGTGCAATTCTGTGTAATTAATTAATTTATACTGTAAATTATGCTTGTCATTGTAGTTTATTATTACTGCTATACGAGAAATCAAAATTCTAAAGAAACTACATCATGAAAATGTTATCAAGTTAAAGGAAATTGTTACGTCTCCAGGCCCTGAGAAAGATGATTAA
Protein sequence

>MS.gene46080.t1

MAAAGQLNLIDSPSRGSRSVDCFEKLEQIGEGTYGQVYMAKEIETGEIVALKQIRMDNEREGFIITAIREIKILKKLHHENVIKLKEIVTSPGPEKDD