AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41499

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41499.t1 MTR_8g036130 62.209 172 63 1 1 170 1 172 2.89e-69 210
MS.gene41499.t1 MTR_4g032620 60.119 168 67 0 1 168 1 168 6.01e-69 209
MS.gene41499.t1 MTR_4g031910 61.078 167 65 0 1 167 1 167 3.13e-67 204
MS.gene41499.t1 MTR_3g065100 62.581 155 57 1 1 155 1 154 5.10e-61 189
MS.gene41499.t1 MTR_4g032290 60.479 167 66 0 1 167 1 167 2.38e-60 187
MS.gene41499.t1 MTR_4g032260 60.897 156 61 0 1 156 1 156 1.04e-56 176
MS.gene41499.t1 MTR_3g466980 50.877 171 83 1 1 171 1 170 2.15e-54 172
MS.gene41499.t1 MTR_2g035610 66.116 121 41 0 1 121 1 121 2.38e-49 155
MS.gene41499.t1 MTR_3g466830 47.682 151 78 1 3 153 2 151 2.00e-47 152
MS.gene41499.t1 MTR_3g466890 44.231 156 86 1 3 158 2 156 1.40e-43 142
MS.gene41499.t1 MTR_4g063790 44.156 154 86 0 1 154 1 154 2.08e-41 137
MS.gene41499.t1 MTR_3g031100 41.667 156 91 0 1 156 1 156 1.24e-37 129
MS.gene41499.t1 MTR_5g047580 42.308 156 88 2 1 156 1 154 5.59e-37 125
MS.gene41499.t1 MTR_3g467080 38.462 156 96 0 1 156 1 156 4.09e-36 123
MS.gene41499.t1 MTR_5g075380 40.260 154 91 1 1 154 1 153 6.64e-36 123
MS.gene41499.t1 MTR_2g016210 39.766 171 97 1 1 171 1 165 2.14e-35 124
MS.gene41499.t1 MTR_1g090783 44.218 147 80 2 3 149 2 146 2.81e-35 121
MS.gene41499.t1 MTR_1g090697 38.608 158 95 2 1 158 1 156 5.51e-35 120
MS.gene41499.t1 MTR_3g031240 35.443 158 102 0 1 158 1 158 1.16e-32 115
MS.gene41499.t1 MTR_1g090710 37.342 158 98 1 1 158 1 157 7.74e-32 112
MS.gene41499.t1 MTR_1g077390 38.312 154 93 2 1 154 1 152 3.30e-31 110
MS.gene41499.t1 MTR_4g028800 69.444 72 20 1 1 72 1 70 1.41e-30 106
MS.gene41499.t1 MTR_3g466900 37.600 125 77 1 34 158 4 127 3.47e-30 107
MS.gene41499.t1 MTR_7g055800 49.580 119 32 3 1 119 1 91 6.35e-30 105
MS.gene41499.t1 MTR_1g084950 40.385 156 91 2 1 156 1 154 1.68e-29 106
MS.gene41499.t1 MTR_7g011950 41.026 156 90 2 1 156 1 154 1.84e-29 106
MS.gene41499.t1 MTR_4g028720 40.385 156 91 2 1 156 1 154 4.82e-29 105
MS.gene41499.t1 MTR_1g077320 41.026 156 90 2 1 156 1 154 9.62e-29 104
MS.gene41499.t1 MTR_1g077300 40.909 154 87 2 1 154 1 150 1.28e-27 101
MS.gene41499.t1 MTR_2g035580 41.026 156 91 1 1 156 1 155 1.58e-27 101
MS.gene41499.t1 MTR_3g465410 39.683 126 76 0 29 154 1 126 6.91e-27 99.4
MS.gene41499.t1 MTR_3g466930 35.200 125 80 1 34 158 4 127 1.15e-26 98.6
MS.gene41499.t1 MTR_5g047560 35.256 156 83 3 1 156 1 138 2.06e-22 87.8
MS.gene41499.t1 MTR_7g055940 46.226 106 29 3 1 106 1 78 2.33e-22 85.9
MS.gene41499.t1 MTR_3g093900 30.282 142 99 0 3 144 6 147 5.46e-22 92.4
MS.gene41499.t1 MTR_7g106510 33.071 127 85 0 3 129 6 132 4.94e-21 89.4
MS.gene41499.t1 MTR_7g055790 46.847 111 41 2 1 111 59 151 3.04e-20 82.4
MS.gene41499.t1 MTR_4g019670 32.520 123 83 0 3 125 6 128 4.14e-19 84.0
MS.gene41499.t1 MTR_2g035590 54.762 84 38 0 80 163 7 90 5.85e-17 72.4
MS.gene41499.t1 MTR_6g018920 31.056 161 96 6 1 155 1 152 1.42e-13 67.8
MS.gene41499.t1 MTR_4g084780 56.863 51 22 0 75 125 2 52 3.47e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41499.t1 AT5G48670 52.903 155 72 1 1 155 1 154 2.11e-48 159
MS.gene41499.t1 AT5G26630 46.452 155 82 1 1 155 1 154 2.81e-36 125
MS.gene41499.t1 AT1G65300 43.137 153 86 1 3 155 2 153 4.84e-34 121
MS.gene41499.t1 AT3G05860 41.509 159 86 3 1 152 1 159 1.30e-33 118
MS.gene41499.t1 AT5G26650 42.484 153 87 1 4 156 2 153 1.42e-33 122
MS.gene41499.t1 AT3G05860 41.509 159 86 3 1 152 1 159 6.95e-33 117
MS.gene41499.t1 AT3G05860 41.509 159 86 3 1 152 1 159 1.03e-32 117
MS.gene41499.t1 AT5G27960 41.176 153 89 1 4 156 2 153 2.72e-32 118
MS.gene41499.t1 AT1G31630 39.189 148 88 2 3 150 2 147 2.87e-31 115
MS.gene41499.t1 AT1G65330 42.484 153 87 1 3 155 2 153 3.22e-31 114
MS.gene41499.t1 AT5G27810 49.474 95 48 0 29 123 1 95 1.07e-29 105
MS.gene41499.t1 AT1G31640 37.086 151 93 2 3 153 2 150 9.35e-28 108
MS.gene41499.t1 AT2G28700 38.158 152 89 2 1 150 1 149 1.25e-27 105
MS.gene41499.t1 AT1G22590 36.076 158 93 2 1 156 1 152 1.88e-25 96.3
MS.gene41499.t1 AT5G26580 36.774 155 83 2 1 155 1 140 2.33e-24 97.4
MS.gene41499.t1 AT2G40210 37.956 137 78 2 1 137 1 130 3.69e-18 80.9
MS.gene41499.t1 AT5G06500 32.051 156 104 1 1 156 1 154 1.69e-15 72.0
MS.gene41499.t1 AT5G58890 37.692 130 68 5 1 120 1 127 2.89e-15 72.0
MS.gene41499.t1 AT5G55690 41.489 94 48 2 1 87 1 94 5.29e-15 71.2
MS.gene41499.t1 AT5G55690 41.489 94 48 2 1 87 1 94 5.29e-15 71.2

Find 38 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGCATGCGCTGTAATTTA+TGG 0.162014 3.1:-51552852 MS.gene41499:CDS
AAAGGGTGCTCTCAAACTTT+AGG 0.264431 3.1:-51552782 MS.gene41499:CDS
AAGATAAACTGGCGAAATTA+AGG 0.283159 3.1:-51552683 MS.gene41499:CDS
CTCTTGATTTGCCATTTGTT+TGG 0.294475 3.1:+51552737 None:intergenic
GGAAAACAACGTATAATAAA+AGG 0.303343 3.1:-51552926 MS.gene41499:CDS
AAGGGTGCTCTCAAACTTTA+GGG 0.347136 3.1:-51552781 MS.gene41499:CDS
TACCAAGGTCCTTCAATTTG+TGG 0.355617 3.1:+51552544 None:intergenic
TGTTTGGTTTGTATAACTTC+AGG 0.374091 3.1:+51552753 None:intergenic
GAAATTAAGGAAGGACAATA+AGG 0.381252 3.1:-51552670 MS.gene41499:CDS
GTGGTTGATTTGAATTATCT+TGG 0.384051 3.1:-51552579 MS.gene41499:CDS
CTTTCGCTTTCAAAACCCTT+TGG 0.384247 3.1:+51552703 None:intergenic
AACATCAGGTTGAGGTTCAT+AGG 0.388824 3.1:+51552827 None:intergenic
TTTGAAAGCGAAAGATAAAC+TGG 0.405272 3.1:-51552694 MS.gene41499:CDS
AATTGAAGGACCTTGGTAGA+AGG 0.412835 3.1:-51552539 MS.gene41499:CDS
ATGAACCTCAACCTGATGTT+TGG 0.413174 3.1:-51552824 MS.gene41499:CDS
TTGGTAGAAGGTTGGAATCA+TGG 0.444725 3.1:-51552527 MS.gene41499:CDS
CATCACCATGTGAAGTCAAA+AGG 0.449362 3.1:-51552800 MS.gene41499:CDS
TTTGATCAATGTCTTTATGC+AGG 0.450902 3.1:-51552627 MS.gene41499:CDS
CATGGTGATGGCCAAACATC+AGG 0.452042 3.1:+51552813 None:intergenic
TTGATTTGAATTATCTTGGT+TGG 0.461781 3.1:-51552575 MS.gene41499:CDS
ACATCAGGTTGAGGTTCATA+GGG 0.479711 3.1:+51552828 None:intergenic
TATGAAATAAGCACACTTTG+CGG 0.483205 3.1:-51552879 MS.gene41499:CDS
GTTGATAGACCACAAATTGA+AGG 0.494814 3.1:-51552553 MS.gene41499:CDS
AGTTATACAAACCAAACAAA+TGG 0.499169 3.1:-51552748 MS.gene41499:CDS
TGGTAGAAGGTTGGAATCAT+GGG 0.503221 3.1:-51552526 MS.gene41499:CDS
AGCAGCATCATTCACAATGA+AGG 0.512306 3.1:+51552950 None:intergenic
GAAGGACCTTGGTAGAAGGT+TGG 0.528423 3.1:-51552535 MS.gene41499:CDS
AGAGACTTTCATGAACCAAA+GGG 0.550845 3.1:-51552718 MS.gene41499:CDS
ATCACCATGTGAAGTCAAAA+GGG 0.555553 3.1:-51552799 MS.gene41499:CDS
AAGAGACTTTCATGAACCAA+AGG 0.558441 3.1:-51552719 MS.gene41499:CDS
GACCACAAATTGAAGGACCT+TGG 0.566187 3.1:-51552546 MS.gene41499:CDS
GATGGCCAAACATCAGGTTG+AGG 0.599557 3.1:+51552819 None:intergenic
ATGATTCCAACCTTCTACCA+AGG 0.601006 3.1:+51552529 None:intergenic
TCATTGTGAATGATGCTGCT+AGG 0.624411 3.1:-51552947 MS.gene41499:CDS
TAAACTGGCGAAATTAAGGA+AGG 0.626838 3.1:-51552679 MS.gene41499:CDS
TCAAATTCAAAGTCAAAACA+CGG 0.694826 3.1:-51552487 MS.gene41499:CDS
CATCAGGTTGAGGTTCATAG+GGG 0.720052 3.1:+51552829 None:intergenic
TGTGAACAACGATATGTCAG+TGG 0.740913 3.1:-51552598 MS.gene41499:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTTATACAAACCAAACAAA+TGG - chr3.1:51552697-51552716 MS.gene41499:CDS 25.0%
! GGAAAACAACGTATAATAAA+AGG - chr3.1:51552519-51552538 MS.gene41499:CDS 25.0%
! TCAAATTCAAAGTCAAAACA+CGG - chr3.1:51552958-51552977 MS.gene41499:CDS 25.0%
!! TTGATTTGAATTATCTTGGT+TGG - chr3.1:51552870-51552889 MS.gene41499:CDS 25.0%
AAGATAAACTGGCGAAATTA+AGG - chr3.1:51552762-51552781 MS.gene41499:CDS 30.0%
GAAATTAAGGAAGGACAATA+AGG - chr3.1:51552775-51552794 MS.gene41499:CDS 30.0%
TATGAAATAAGCACACTTTG+CGG - chr3.1:51552566-51552585 MS.gene41499:CDS 30.0%
TTTGAAAGCGAAAGATAAAC+TGG - chr3.1:51552751-51552770 MS.gene41499:CDS 30.0%
TTTGATCAATGTCTTTATGC+AGG - chr3.1:51552818-51552837 MS.gene41499:CDS 30.0%
!! GTGGTTGATTTGAATTATCT+TGG - chr3.1:51552866-51552885 MS.gene41499:CDS 30.0%
!! TGTTTGGTTTGTATAACTTC+AGG + chr3.1:51552695-51552714 None:intergenic 30.0%
AAGAGACTTTCATGAACCAA+AGG - chr3.1:51552726-51552745 MS.gene41499:CDS 35.0%
AGAGACTTTCATGAACCAAA+GGG - chr3.1:51552727-51552746 MS.gene41499:CDS 35.0%
ATCACCATGTGAAGTCAAAA+GGG - chr3.1:51552646-51552665 MS.gene41499:CDS 35.0%
TAAACTGGCGAAATTAAGGA+AGG - chr3.1:51552766-51552785 MS.gene41499:CDS 35.0%
! GTTGATAGACCACAAATTGA+AGG - chr3.1:51552892-51552911 MS.gene41499:CDS 35.0%
!! CTCTTGATTTGCCATTTGTT+TGG + chr3.1:51552711-51552730 None:intergenic 35.0%
AATTGAAGGACCTTGGTAGA+AGG - chr3.1:51552906-51552925 MS.gene41499:CDS 40.0%
AGCAGCATCATTCACAATGA+AGG + chr3.1:51552498-51552517 None:intergenic 40.0%
ATGAACCTCAACCTGATGTT+TGG - chr3.1:51552621-51552640 MS.gene41499:CDS 40.0%
ATGATTCCAACCTTCTACCA+AGG + chr3.1:51552919-51552938 None:intergenic 40.0%
CAAGCATGCGCTGTAATTTA+TGG - chr3.1:51552593-51552612 MS.gene41499:CDS 40.0%
CATCACCATGTGAAGTCAAA+AGG - chr3.1:51552645-51552664 MS.gene41499:CDS 40.0%
CTTTCGCTTTCAAAACCCTT+TGG + chr3.1:51552745-51552764 None:intergenic 40.0%
TACCAAGGTCCTTCAATTTG+TGG + chr3.1:51552904-51552923 None:intergenic 40.0%
TCATTGTGAATGATGCTGCT+AGG - chr3.1:51552498-51552517 MS.gene41499:CDS 40.0%
TGGTAGAAGGTTGGAATCAT+GGG - chr3.1:51552919-51552938 MS.gene41499:CDS 40.0%
TGTGAACAACGATATGTCAG+TGG - chr3.1:51552847-51552866 MS.gene41499:CDS 40.0%
TTGGTAGAAGGTTGGAATCA+TGG - chr3.1:51552918-51552937 MS.gene41499:CDS 40.0%
!! AAAGGGTGCTCTCAAACTTT+AGG - chr3.1:51552663-51552682 MS.gene41499:CDS 40.0%
!! AACATCAGGTTGAGGTTCAT+AGG + chr3.1:51552621-51552640 None:intergenic 40.0%
!! AAGGGTGCTCTCAAACTTTA+GGG - chr3.1:51552664-51552683 MS.gene41499:CDS 40.0%
!! ACATCAGGTTGAGGTTCATA+GGG + chr3.1:51552620-51552639 None:intergenic 40.0%
!!! CTTTTGACTTCACATGGTGA+TGG + chr3.1:51552647-51552666 None:intergenic 40.0%
GACCACAAATTGAAGGACCT+TGG - chr3.1:51552899-51552918 MS.gene41499:CDS 45.0%
!! CATCAGGTTGAGGTTCATAG+GGG + chr3.1:51552619-51552638 None:intergenic 45.0%
!!! AGCACCCTTTTGACTTCACA+TGG + chr3.1:51552653-51552672 None:intergenic 45.0%
GAAGGACCTTGGTAGAAGGT+TGG - chr3.1:51552910-51552929 MS.gene41499:CDS 50.0%
! GATGGCCAAACATCAGGTTG+AGG + chr3.1:51552629-51552648 None:intergenic 50.0%
!! CATGGTGATGGCCAAACATC+AGG + chr3.1:51552635-51552654 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 51552470 51552997 51552470 ID=MS.gene41499
chr3.1 mRNA 51552470 51552997 51552470 ID=MS.gene41499.t1;Parent=MS.gene41499
chr3.1 exon 51552470 51552997 51552470 ID=MS.gene41499.t1.exon1;Parent=MS.gene41499.t1
chr3.1 CDS 51552470 51552997 51552470 ID=cds.MS.gene41499.t1;Parent=MS.gene41499.t1
Gene Sequence

>MS.gene41499

ATGGCTAGAAAAAAGGTGAAACTCGCCTTCATTGTGAATGATGCTGCTAGGAAAACAACGTATAATAAAAGGAAGAAGAGTCTACTGAAGAAAGCTTATGAAATAAGCACACTTTGCGGAGTTCAAGCATGCGCTGTAATTTATGGCCCCTATGAACCTCAACCTGATGTTTGGCCATCACCATGTGAAGTCAAAAGGGTGCTCTCAAACTTTAGGGCAAAGCCTGAAGTTATACAAACCAAACAAATGGCAAATCAAGAGACTTTCATGAACCAAAGGGTTTTGAAAGCGAAAGATAAACTGGCGAAATTAAGGAAGGACAATAAGGAAAAAGAGATGACAATGCTCTTTGATCAATGTCTTTATGCAGGTAAACTTGTGAACAACGATATGTCAGTGGTTGATTTGAATTATCTTGGTTGGTTGATAGACCACAAATTGAAGGACCTTGGTAGAAGGTTGGAATCATGGGATGATTGCAATAATGTTCAAATTCAAAGTCAAAACACGGCTATTGTTTGTAAGTGA
Protein sequence

>MS.gene41499.t1

MARKKVKLAFIVNDAARKTTYNKRKKSLLKKAYEISTLCGVQACAVIYGPYEPQPDVWPSPCEVKRVLSNFRAKPEVIQTKQMANQETFMNQRVLKAKDKLAKLRKDNKEKEMTMLFDQCLYAGKLVNNDMSVVDLNYLGWLIDHKLKDLGRRLESWDDCNNVQIQSQNTAIVCK