AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29855

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29855.t1 MTR_3g073690 98.413 126 2 0 1 126 2 127 3.38e-91 262
MS.gene29855.t1 MTR_5g017950 76.423 123 29 0 1 123 1 123 5.69e-67 205
MS.gene29855.t1 MTR_3g452660 74.576 118 28 2 1 117 1 117 1.97e-57 179
MS.gene29855.t1 MTR_4g105170 65.254 118 41 0 6 123 9 126 1.53e-50 159
MS.gene29855.t1 MTR_7g033800 66.667 111 37 0 2 112 5 115 7.57e-50 156
MS.gene29855.t1 MTR_3g077240 65.217 115 40 0 2 116 4 118 3.91e-49 155
MS.gene29855.t1 MTR_6g005070 67.290 107 35 0 2 108 3 109 2.13e-48 152
MS.gene29855.t1 MTR_6g005080 63.063 111 41 0 2 112 4 114 7.69e-48 150
MS.gene29855.t1 MTR_5g083230 60.684 117 45 1 6 121 4 120 5.04e-47 149
MS.gene29855.t1 MTR_3g071590 61.111 108 42 0 1 108 1 108 4.62e-46 146
MS.gene29855.t1 MTR_3g031660 60.577 104 41 0 5 108 4 107 1.67e-45 145
MS.gene29855.t1 MTR_8g040900 67.568 111 35 1 1 111 1 110 1.89e-44 144
MS.gene29855.t1 MTR_5g083960 60.377 106 42 0 6 111 37 142 2.00e-43 141
MS.gene29855.t1 MTR_4g083680 60.784 102 40 0 6 107 13 114 4.90e-43 139
MS.gene29855.t1 MTR_2g068760 60.784 102 40 0 7 108 12 113 1.48e-42 137
MS.gene29855.t1 MTR_2g093310 59.804 102 41 0 7 108 32 133 1.95e-42 139
MS.gene29855.t1 MTR_3g094690 60.000 105 42 0 7 111 46 150 6.30e-42 138
MS.gene29855.t1 MTR_3g071420 62.745 102 38 0 5 106 11 112 2.52e-41 135
MS.gene29855.t1 MTR_8g079660 56.364 110 48 0 8 117 8 117 3.43e-41 137
MS.gene29855.t1 MTR_5g083010 60.952 105 41 0 5 109 8 112 1.91e-40 133
MS.gene29855.t1 MTR_3g094690 59.048 105 42 1 7 111 46 149 9.26e-40 133
MS.gene29855.t1 MTR_1g095850 56.863 102 44 0 9 110 73 174 2.65e-39 131
MS.gene29855.t1 MTR_8g079620 53.636 110 51 0 8 117 8 117 3.39e-39 131
MS.gene29855.t1 MTR_4g060950 56.311 103 44 1 7 108 23 125 6.41e-39 129
MS.gene29855.t1 MTR_5g075020 55.738 122 46 1 7 120 42 163 7.70e-39 130
MS.gene29855.t1 MTR_5g075020 55.738 122 46 1 7 120 46 167 1.17e-38 130
MS.gene29855.t1 MTR_8g079580 53.153 111 51 1 8 117 8 118 2.61e-36 124
MS.gene29855.t1 MTR_7g028905 47.619 105 55 0 7 111 4 108 6.27e-35 117
MS.gene29855.t1 MTR_7g096530 53.571 112 51 1 2 112 8 119 9.00e-35 119
MS.gene29855.t1 MTR_8g036085 55.238 105 46 1 8 111 23 127 2.10e-34 119
MS.gene29855.t1 MTR_7g074990 53.846 104 47 1 8 110 20 123 6.27e-34 118
MS.gene29855.t1 MTR_1g070220 54.455 101 45 1 8 107 15 115 9.23e-33 114
MS.gene29855.t1 MTR_5g093010 46.602 103 55 0 9 111 6 108 1.16e-32 112
MS.gene29855.t1 MTR_8g036105 54.206 107 48 1 5 110 15 121 1.18e-32 114
MS.gene29855.t1 MTR_6g027710 50.485 103 50 1 7 108 39 141 6.30e-32 112
MS.gene29855.t1 MTR_7g096610 49.091 110 55 1 1 109 1 110 4.26e-31 110
MS.gene29855.t1 MTR_5g080470 46.226 106 56 1 6 110 5 110 1.65e-30 108
MS.gene29855.t1 MTR_1g070205 50.485 103 50 1 8 109 12 114 2.82e-30 108
MS.gene29855.t1 MTR_6g011200 46.078 102 54 1 9 109 10 111 5.81e-29 105
MS.gene29855.t1 MTR_6g011230 46.000 100 54 0 6 105 9 108 8.92e-29 103
MS.gene29855.t1 MTR_7g075230 50.926 108 50 2 5 109 9 116 3.46e-28 102
MS.gene29855.t1 MTR_6g027700 46.602 103 54 1 6 107 5 107 1.51e-27 101
MS.gene29855.t1 MTR_6g011250 46.078 102 54 1 9 109 10 111 3.15e-27 99.8
MS.gene29855.t1 MTR_4g107450 45.000 100 55 0 9 108 11 110 5.53e-26 99.0
MS.gene29855.t1 MTR_4g099230 42.157 102 58 1 9 109 3 104 2.45e-25 94.0
MS.gene29855.t1 MTR_8g017090 38.835 103 63 0 9 111 13 115 2.20e-24 94.7
MS.gene29855.t1 MTR_5g085390 42.157 102 58 1 9 109 10 111 4.20e-22 87.4
MS.gene29855.t1 MTR_2g100020 36.634 101 64 0 9 109 20 120 4.78e-22 88.2
MS.gene29855.t1 MTR_4g088035 37.778 90 56 0 5 94 3 92 3.47e-20 83.2
MS.gene29855.t1 MTR_2g094730 28.571 105 71 3 8 110 2 104 5.52e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29855.t1 AT5G66870 75.214 117 29 0 3 119 2 118 1.42e-61 191
MS.gene29855.t1 AT2G23660 66.379 116 39 0 6 121 3 118 4.52e-56 177
MS.gene29855.t1 AT2G23660 66.379 116 39 0 6 121 3 118 4.52e-56 177
MS.gene29855.t1 AT2G23660 66.379 116 39 0 6 121 3 118 4.52e-56 177
MS.gene29855.t1 AT5G63090 69.643 112 32 1 2 111 3 114 1.34e-50 159
MS.gene29855.t1 AT5G63090 69.643 112 32 1 2 111 3 114 1.34e-50 159
MS.gene29855.t1 AT5G63090 69.643 112 32 1 2 111 3 114 1.34e-50 159
MS.gene29855.t1 AT5G63090 69.643 112 32 1 2 111 3 114 1.34e-50 159
MS.gene29855.t1 AT3G27650 64.602 113 40 0 1 113 32 144 1.05e-49 155
MS.gene29855.t1 AT2G30130 62.963 108 40 0 1 108 1 108 4.81e-48 152
MS.gene29855.t1 AT1G65620 67.227 119 39 0 2 120 3 121 8.59e-48 152
MS.gene29855.t1 AT1G65620 67.227 119 39 0 2 120 3 121 8.59e-48 152
MS.gene29855.t1 AT1G65620 67.227 119 39 0 2 120 3 121 8.59e-48 152
MS.gene29855.t1 AT1G65620 67.227 119 39 0 2 120 3 121 8.59e-48 152
MS.gene29855.t1 AT1G65620 67.227 119 39 0 2 120 3 121 8.59e-48 152
MS.gene29855.t1 AT1G07900 59.615 104 42 0 7 110 32 135 1.72e-43 141
MS.gene29855.t1 AT2G28500 58.182 110 43 1 7 116 54 160 1.87e-42 140
MS.gene29855.t1 AT2G30340 59.804 102 41 0 7 108 51 152 2.53e-41 138
MS.gene29855.t1 AT2G30340 59.804 102 41 0 7 108 52 153 2.76e-41 138
MS.gene29855.t1 AT3G11090 57.798 109 46 0 5 113 8 116 5.88e-41 134
MS.gene29855.t1 AT1G16530 59.223 103 41 1 7 108 13 115 6.56e-41 134
MS.gene29855.t1 AT1G31320 62.921 89 33 0 6 94 11 99 2.31e-39 130
MS.gene29855.t1 AT2G40470 60.000 105 42 0 7 111 19 123 4.55e-38 127
MS.gene29855.t1 AT2G40470 60.000 105 42 0 7 111 44 148 9.89e-38 127
MS.gene29855.t1 AT4G00210 55.556 117 47 2 6 121 9 121 1.63e-37 127
MS.gene29855.t1 AT3G26620 50.476 105 52 0 5 109 2 106 2.63e-37 123
MS.gene29855.t1 AT3G26660 50.476 105 52 0 5 109 2 106 2.84e-37 123
MS.gene29855.t1 AT3G50510 50.420 119 58 1 6 123 10 128 2.93e-37 125
MS.gene29855.t1 AT3G50510 50.420 119 58 1 6 123 10 128 2.93e-37 125
MS.gene29855.t1 AT5G35900 50.459 109 54 0 5 113 2 110 7.94e-37 124
MS.gene29855.t1 AT3G03760 54.369 103 46 1 7 108 50 152 7.25e-35 121
MS.gene29855.t1 AT4G00220 55.446 101 44 1 11 110 20 120 2.27e-32 114
MS.gene29855.t1 AT2G42430 52.336 107 50 1 6 111 13 119 2.33e-32 114
MS.gene29855.t1 AT3G58190 52.427 103 48 1 8 109 11 113 3.75e-32 113
MS.gene29855.t1 AT2G45420 54.455 101 45 1 11 110 40 140 3.14e-31 112
MS.gene29855.t1 AT2G42440 47.115 104 54 1 5 107 4 107 3.19e-30 108
MS.gene29855.t1 AT2G31310 47.748 111 56 2 6 115 5 114 1.52e-29 105
MS.gene29855.t1 AT2G45410 52.475 101 47 1 11 110 19 119 2.03e-29 105
MS.gene29855.t1 AT5G06080 44.444 108 59 1 5 111 4 111 5.28e-28 101
MS.gene29855.t1 AT1G72980 43.519 108 61 0 1 108 6 113 1.54e-27 101
MS.gene29855.t1 AT3G13850 39.806 103 62 0 9 111 37 139 8.04e-27 100
MS.gene29855.t1 AT3G47870 40.566 106 63 0 6 111 34 139 3.21e-26 100
MS.gene29855.t1 AT4G22700 41.284 109 62 2 6 113 3 110 3.85e-23 89.4
MS.gene29855.t1 AT1G06280 45.977 87 47 0 9 95 25 111 4.14e-21 84.3
MS.gene29855.t1 AT2G19820 34.021 97 63 1 7 102 11 107 4.59e-17 72.0
MS.gene29855.t1 AT3G27940 30.769 117 81 0 5 121 2 118 1.34e-15 68.9
MS.gene29855.t1 AT3G27940 30.769 117 81 0 5 121 2 118 1.34e-15 68.9
MS.gene29855.t1 AT3G27940 30.769 117 81 0 5 121 2 118 1.34e-15 68.9
MS.gene29855.t1 AT5G15060 41.096 73 41 1 9 79 18 90 1.88e-13 63.2
MS.gene29855.t1 AT1G36000 27.778 90 65 0 5 94 6 95 1.10e-11 58.2

Find 15 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTGAGAGATCCTGTTTA+TGG 0.254736 3.4:-72336819 MS.gene29855:CDS
AAAGAACTTGCTTCTTATGT+TGG 0.411259 3.4:-72336726 MS.gene29855:CDS
ACCTACGTTCACAAAGTGTT+TGG 0.430629 3.4:-72336930 MS.gene29855:CDS
AGACCAACACAACCATAAAC+AGG 0.459225 3.4:+72336807 None:intergenic
GATCCTGTTTATGGTTGTGT+TGG 0.503197 3.4:-72336810 MS.gene29855:CDS
TGAATCTTGCACGCTGCACA+CGG 0.560567 3.4:+72337020 None:intergenic
GAACTCGACGCCGCCGTCAT+CGG 0.569433 3.4:+72336681 None:intergenic
GACGCCGCCGTCATCGGTGT+AGG 0.623332 3.4:+72336687 None:intergenic
CATGCTTCCTACACCGATGA+CGG 0.624741 3.4:-72336694 MS.gene29855:CDS
GGTGTAGGAAGCATGATCTG+AGG 0.695632 3.4:+72336702 None:intergenic
GCTTCCTACACCGATGACGG+CGG 0.697155 3.4:-72336691 MS.gene29855:CDS
CGTGGCAAAGTTACTCAACG+AGG 0.719799 3.4:-72336898 MS.gene29855:CDS
TCAGCGTCGAAAATGCACAA+AGG 0.734134 3.4:-72337000 MS.gene29855:CDS
AGTGTTTGGTGCTAGCAACG+TGG 0.743523 3.4:-72336916 MS.gene29855:CDS
ACCAAACACTTTGTGAACGT+AGG 0.770701 3.4:+72336929 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAACTTGCTTCTTATGT+TGG - chr3.4:72337000-72337019 MS.gene29855:CDS 30.0%
!! GTAAACTTTTGAGGATTTTC+CGG + chr3.4:72336778-72336797 None:intergenic 30.0%
! TGAACGTAGGTAAACTTTTG+AGG + chr3.4:72336787-72336806 None:intergenic 35.0%
ACCAAACACTTTGTGAACGT+AGG + chr3.4:72336800-72336819 None:intergenic 40.0%
AGACCAACACAACCATAAAC+AGG + chr3.4:72336922-72336941 None:intergenic 40.0%
CGTTTGAGAGATCCTGTTTA+TGG - chr3.4:72336907-72336926 MS.gene29855:CDS 40.0%
GATCCTGTTTATGGTTGTGT+TGG - chr3.4:72336916-72336935 MS.gene29855:CDS 40.0%
! ACCTACGTTCACAAAGTGTT+TGG - chr3.4:72336796-72336815 MS.gene29855:CDS 40.0%
!! AACTTTTGAGGATTTTCCGG+CGG + chr3.4:72336775-72336794 None:intergenic 40.0%
! AGGATTTTCCGGCGGAAAAT+AGG + chr3.4:72336767-72336786 None:intergenic 45.0%
! GGATTTTCCGGCGGAAAATA+GGG + chr3.4:72336766-72336785 None:intergenic 45.0%
! TCAGCGTCGAAAATGCACAA+AGG - chr3.4:72336726-72336745 MS.gene29855:CDS 45.0%
! TTTTGCACCCTATTTTCCGC+CGG - chr3.4:72336756-72336775 MS.gene29855:CDS 45.0%
CATGCTTCCTACACCGATGA+CGG - chr3.4:72337032-72337051 MS.gene29855:CDS 50.0%
CGTGGCAAAGTTACTCAACG+AGG - chr3.4:72336828-72336847 MS.gene29855:CDS 50.0%
TGAATCTTGCACGCTGCACA+CGG + chr3.4:72336709-72336728 None:intergenic 50.0%
! GGTGTAGGAAGCATGATCTG+AGG + chr3.4:72337027-72337046 None:intergenic 50.0%
!! AGTGTTTGGTGCTAGCAACG+TGG - chr3.4:72336810-72336829 MS.gene29855:CDS 50.0%
! GCTTCCTACACCGATGACGG+CGG - chr3.4:72337035-72337054 MS.gene29855:CDS 60.0%
GACGCCGCCGTCATCGGTGT+AGG + chr3.4:72337042-72337061 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 72336685 72337063 72336685 ID=MS.gene29855
chr3.4 mRNA 72336685 72337063 72336685 ID=MS.gene29855.t1;Parent=MS.gene29855
chr3.4 exon 72336685 72337063 72336685 ID=MS.gene29855.t1.exon1;Parent=MS.gene29855.t1
chr3.4 CDS 72336685 72337063 72336685 ID=cds.MS.gene29855.t1;Parent=MS.gene29855.t1
Gene Sequence

>MS.gene29855

ATGTCGTCGTGTAATTCTTCTCCGTGTGCAGCGTGCAAGATTCAGCGTCGAAAATGCACAAAGGAATGCATTTTTGCACCCTATTTTCCGCCGGAAAATCCTCAAAAGTTTACCTACGTTCACAAAGTGTTTGGTGCTAGCAACGTGGCAAAGTTACTCAACGAGGTTGATGCTTCTCAGCGTGAAGATGCTGTTAAGTCTTTAGCTTATGAAGCAGAAGCGCGTTTGAGAGATCCTGTTTATGGTTGTGTTGGTCTTATTTCACATCTTCAGAATAAGCTTAAGAATTTGCAGAATGAACTTAATGTTGCTAAGAAAGAACTTGCTTCTTATGTTGGTCCTCAGATCATGCTTCCTACACCGATGACGGCGGCGTCGA
Protein sequence

>MS.gene29855.t1

MSSCNSSPCAACKIQRRKCTKECIFAPYFPPENPQKFTYVHKVFGASNVAKLLNEVDASQREDAVKSLAYEAEARLRDPVYGCVGLISHLQNKLKNLQNELNVAKKELASYVGPQIMLPTPMTAAS