AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene013398

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013398.t1 MTR_3g094690 99.029 103 1 0 1 103 30 132 7.38e-73 216
MS.gene013398.t1 MTR_3g094690 98.058 103 1 1 1 103 30 131 3.16e-70 209
MS.gene013398.t1 MTR_5g083960 91.837 98 8 0 6 103 27 124 1.66e-64 194
MS.gene013398.t1 MTR_5g075020 82.828 99 15 1 1 97 24 122 8.67e-59 180
MS.gene013398.t1 MTR_5g075020 82.828 99 15 1 1 97 28 126 1.45e-58 180
MS.gene013398.t1 MTR_5g083230 74.157 89 23 0 17 105 5 93 7.42e-45 143
MS.gene013398.t1 MTR_3g071590 70.652 92 27 0 14 105 4 95 4.22e-44 140
MS.gene013398.t1 MTR_4g083680 72.414 87 24 0 17 103 14 100 5.13e-44 141
MS.gene013398.t1 MTR_2g068760 70.787 89 26 0 15 103 10 98 7.53e-44 140
MS.gene013398.t1 MTR_7g033800 67.816 87 28 0 17 103 10 96 1.90e-40 132
MS.gene013398.t1 MTR_6g005070 66.667 87 29 0 17 103 8 94 1.90e-40 131
MS.gene013398.t1 MTR_3g031660 67.416 89 29 0 17 105 6 94 2.14e-40 132
MS.gene013398.t1 MTR_6g005080 64.368 87 31 0 17 103 9 95 7.56e-39 127
MS.gene013398.t1 MTR_4g105170 66.667 87 29 0 17 103 10 96 8.40e-39 128
MS.gene013398.t1 MTR_3g077240 66.667 87 29 0 17 103 9 95 1.48e-38 127
MS.gene013398.t1 MTR_2g093310 62.500 88 33 0 16 103 31 118 4.76e-38 126
MS.gene013398.t1 MTR_3g073690 65.517 87 30 0 17 103 8 94 1.37e-37 125
MS.gene013398.t1 MTR_3g452660 63.218 87 32 0 17 103 6 92 4.36e-37 127
MS.gene013398.t1 MTR_5g017950 65.517 87 30 0 17 103 7 93 5.34e-37 127
MS.gene013398.t1 MTR_3g071420 65.882 85 29 0 19 103 15 99 7.47e-37 123
MS.gene013398.t1 MTR_8g040900 64.634 82 29 0 17 98 6 87 1.62e-36 123
MS.gene013398.t1 MTR_5g083010 64.706 85 30 0 19 103 12 96 9.10e-36 120
MS.gene013398.t1 MTR_1g095850 62.069 87 33 0 19 105 73 159 2.40e-35 120
MS.gene013398.t1 MTR_4g060950 60.674 89 34 1 16 103 22 110 5.52e-35 118
MS.gene013398.t1 MTR_7g074990 64.368 87 30 1 18 103 20 106 9.08e-34 117
MS.gene013398.t1 MTR_7g096530 55.914 93 40 1 15 106 11 103 3.18e-32 112
MS.gene013398.t1 MTR_7g028905 57.647 85 36 0 19 103 6 90 5.86e-32 108
MS.gene013398.t1 MTR_1g070220 57.471 87 36 1 18 103 15 101 3.78e-30 107
MS.gene013398.t1 MTR_5g093010 56.471 85 37 0 19 103 6 90 4.44e-30 104
MS.gene013398.t1 MTR_6g027710 58.427 89 36 1 16 103 38 126 5.52e-30 107
MS.gene013398.t1 MTR_1g070205 56.818 88 35 2 18 103 12 98 1.25e-28 103
MS.gene013398.t1 MTR_8g036105 58.621 87 35 1 18 103 18 104 1.53e-28 103
MS.gene013398.t1 MTR_7g096610 55.056 89 37 2 17 103 7 94 6.61e-28 101
MS.gene013398.t1 MTR_8g036085 55.172 87 38 1 18 103 23 109 1.38e-27 100
MS.gene013398.t1 MTR_8g079660 53.409 88 41 0 16 103 6 93 1.45e-27 101
MS.gene013398.t1 MTR_5g080470 51.136 88 42 1 17 103 6 93 2.74e-27 99.4
MS.gene013398.t1 MTR_6g011250 45.000 80 43 1 19 97 10 89 1.25e-24 92.0
MS.gene013398.t1 MTR_7g075230 52.809 89 39 2 18 103 12 100 1.53e-23 89.7
MS.gene013398.t1 MTR_8g079620 47.674 86 45 0 16 101 6 91 1.80e-23 90.5
MS.gene013398.t1 MTR_8g079580 52.273 88 41 1 16 102 6 93 3.30e-23 89.4
MS.gene013398.t1 MTR_6g027700 45.977 87 46 1 18 103 7 93 8.55e-23 88.2
MS.gene013398.t1 MTR_6g011230 42.857 84 48 0 14 97 7 90 1.17e-22 87.4
MS.gene013398.t1 MTR_6g011200 41.573 89 48 2 13 97 1 89 1.01e-21 86.3
MS.gene013398.t1 MTR_4g107450 43.820 89 50 0 15 103 7 95 1.15e-20 84.0
MS.gene013398.t1 MTR_5g085390 40.449 89 49 2 13 97 1 89 1.86e-19 79.7
MS.gene013398.t1 MTR_4g099230 41.250 80 46 1 19 97 3 82 1.07e-18 76.3
MS.gene013398.t1 MTR_8g017090 40.000 90 52 2 15 103 9 97 6.60e-18 76.6
MS.gene013398.t1 MTR_2g100020 40.000 90 52 2 15 103 16 104 4.43e-17 74.3
MS.gene013398.t1 MTR_4g088035 34.483 87 57 0 17 103 5 91 2.13e-15 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013398.t1 AT2G40470 94.792 96 5 0 3 98 5 100 2.65e-63 191
MS.gene013398.t1 AT2G40470 94.792 96 5 0 3 98 30 125 3.86e-63 191
MS.gene013398.t1 AT2G30340 83.810 105 15 2 1 103 33 137 9.26e-61 186
MS.gene013398.t1 AT2G30340 83.810 105 15 2 1 103 34 138 1.05e-60 186
MS.gene013398.t1 AT1G31320 73.563 87 23 0 17 103 12 98 2.16e-43 139
MS.gene013398.t1 AT2G30130 67.677 99 28 1 7 105 1 95 2.19e-43 140
MS.gene013398.t1 AT3G27650 62.626 99 37 0 5 103 26 124 2.17e-41 134
MS.gene013398.t1 AT5G66870 68.966 87 27 0 17 103 6 92 1.90e-39 133
MS.gene013398.t1 AT1G16530 62.222 90 33 1 15 103 11 100 4.47e-39 128
MS.gene013398.t1 AT1G65620 68.235 85 27 0 14 98 5 89 8.90e-39 128
MS.gene013398.t1 AT1G65620 68.235 85 27 0 14 98 5 89 8.90e-39 128
MS.gene013398.t1 AT1G65620 68.235 85 27 0 14 98 5 89 8.90e-39 128
MS.gene013398.t1 AT1G65620 68.235 85 27 0 14 98 5 89 8.90e-39 128
MS.gene013398.t1 AT1G65620 68.235 85 27 0 14 98 5 89 8.90e-39 128
MS.gene013398.t1 AT5G63090 65.517 87 30 0 17 103 10 96 4.26e-38 126
MS.gene013398.t1 AT5G63090 65.517 87 30 0 17 103 10 96 4.26e-38 126
MS.gene013398.t1 AT5G63090 65.517 87 30 0 17 103 10 96 4.26e-38 126
MS.gene013398.t1 AT5G63090 65.517 87 30 0 17 103 10 96 4.26e-38 126
MS.gene013398.t1 AT1G07900 61.538 91 35 0 15 105 30 120 4.86e-38 126
MS.gene013398.t1 AT2G28500 62.222 90 34 0 16 105 53 142 1.68e-37 126
MS.gene013398.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.54e-37 128
MS.gene013398.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.54e-37 128
MS.gene013398.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.54e-37 128
MS.gene013398.t1 AT3G11090 63.529 85 31 0 19 103 12 96 1.20e-34 117
MS.gene013398.t1 AT3G26620 58.824 85 35 0 19 103 6 90 2.53e-34 115
MS.gene013398.t1 AT3G26660 58.824 85 35 0 19 103 6 90 2.64e-34 115
MS.gene013398.t1 AT2G42430 54.639 97 43 1 8 103 5 101 2.45e-31 110
MS.gene013398.t1 AT4G00210 59.770 87 34 1 18 103 11 97 1.28e-30 108
MS.gene013398.t1 AT3G58190 56.818 88 35 2 18 103 11 97 2.24e-28 102
MS.gene013398.t1 AT5G06080 55.682 88 38 1 17 103 6 93 2.66e-28 101
MS.gene013398.t1 AT3G03760 55.682 88 38 1 17 103 50 137 5.71e-28 102
MS.gene013398.t1 AT2G31310 50.000 88 43 1 17 103 6 93 1.78e-27 99.8
MS.gene013398.t1 AT4G00220 57.143 84 35 1 21 103 20 103 3.48e-27 99.8
MS.gene013398.t1 AT2G45420 54.762 84 37 1 21 103 40 123 1.37e-26 99.0
MS.gene013398.t1 AT2G42440 51.685 89 40 2 17 103 6 93 3.17e-26 97.8
MS.gene013398.t1 AT2G45410 53.571 84 38 1 21 103 19 102 2.90e-25 94.0
MS.gene013398.t1 AT3G47870 43.373 83 47 0 19 101 37 119 9.36e-23 90.1
MS.gene013398.t1 AT3G50510 45.977 87 47 0 17 103 11 97 1.39e-22 87.4
MS.gene013398.t1 AT3G50510 45.977 87 47 0 17 103 11 97 1.39e-22 87.4
MS.gene013398.t1 AT1G06280 48.052 77 40 0 19 95 25 101 9.72e-21 82.8
MS.gene013398.t1 AT1G72980 42.529 87 50 0 15 101 10 96 3.93e-19 78.6
MS.gene013398.t1 AT3G13850 38.824 85 52 0 19 103 37 121 1.71e-18 77.8
MS.gene013398.t1 AT5G35900 39.080 87 53 0 17 103 4 90 5.32e-18 75.5
MS.gene013398.t1 AT2G19820 34.483 87 56 1 18 103 12 98 2.13e-15 67.0
MS.gene013398.t1 AT5G15060 35.526 76 47 1 16 89 15 90 1.30e-11 57.4
MS.gene013398.t1 AT1G36000 31.034 87 58 2 18 103 9 94 6.80e-11 55.5

Find 21 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAAGGGGTTATAGTATTT+AGG 0.181231 3.4:+86108174 None:intergenic
TGGTTCATGAGGAGAGAAAT+AGG 0.287589 3.4:+86108100 None:intergenic
AGGCTAAGAGATCCAGTTTA+TGG 0.306813 3.4:-86107871 MS.gene013398:CDS
ACAAGGGGTTATAGTATTTA+GGG 0.313905 3.4:+86108175 None:intergenic
GTTATAGTATTTAGGGTTCC+TGG 0.351578 3.4:+86108182 None:intergenic
GCACCCATGCATCCATAAAC+TGG 0.381798 3.4:+86107859 None:intergenic
GGAGAGAAATAGGGAGAAAA+GGG 0.384566 3.4:+86108110 None:intergenic
AGGAGAGAAATAGGGAGAAA+AGG 0.419838 3.4:+86108109 None:intergenic
AATTTCTGCATTGCAACAAC+AGG 0.457176 3.4:-86107836 MS.gene013398:intron
ATGGGAAGAAGACATATGTT+AGG 0.472989 3.4:-86108209 MS.gene013398:CDS
GGTTCATGAGGAGAGAAATA+GGG 0.492582 3.4:+86108101 None:intergenic
AGATCCAGTTTATGGATGCA+TGG 0.526865 3.4:-86107863 MS.gene013398:CDS
AATAGCTTACATGCTGCACA+AGG 0.566069 3.4:+86108158 None:intergenic
GATCCAGTTTATGGATGCAT+GGG 0.578062 3.4:-86107862 MS.gene013398:CDS
GCAAACTTCTGTGGTTCATG+AGG 0.583150 3.4:+86108089 None:intergenic
TGAACAGAAGCAAACTTCTG+TGG 0.594520 3.4:+86108080 None:intergenic
TAGCTTACATGCTGCACAAG+GGG 0.599040 3.4:+86108160 None:intergenic
ATAGTATTTAGGGTTCCTGG+TGG 0.604329 3.4:+86108185 None:intergenic
AGACATATGTTAGGTCCACC+AGG 0.627473 3.4:-86108200 MS.gene013398:CDS
TTGTTTATGAAGCAAATGTG+AGG 0.672469 3.4:-86107891 MS.gene013398:CDS
ATAGCTTACATGCTGCACAA+GGG 0.680325 3.4:+86108159 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTAAATACAAATTA+AGG - chr3.4:86108198-86108217 MS.gene013398:CDS 10.0%
!! AATACTTAAATACAAATTAA+GGG - chr3.4:86108199-86108218 MS.gene013398:CDS 10.0%
!!! AATATATATAATGTTTTAGG+AGG - chr3.4:86108022-86108041 MS.gene013398:intron 15.0%
ACAAGGGGTTATAGTATTTA+GGG + chr3.4:86107800-86107819 None:intergenic 30.0%
TTGTTTATGAAGCAAATGTG+AGG - chr3.4:86108081-86108100 MS.gene013398:CDS 30.0%
AATTTCTGCATTGCAACAAC+AGG - chr3.4:86108136-86108155 MS.gene013398:CDS 35.0%
ATGGGAAGAAGACATATGTT+AGG - chr3.4:86107763-86107782 MS.gene013398:intron 35.0%
CAACGTCTCAAAAATGCTAA+TGG - chr3.4:86107933-86107952 MS.gene013398:CDS 35.0%
CACAAGGGGTTATAGTATTT+AGG + chr3.4:86107801-86107820 None:intergenic 35.0%
GCAGAACTCAATCTATTAAG+AGG - chr3.4:86108173-86108192 MS.gene013398:CDS 35.0%
! GCTTCTGTTCACAAAGTTTT+TGG - chr3.4:86107904-86107923 MS.gene013398:CDS 35.0%
! GTTATAGTATTTAGGGTTCC+TGG + chr3.4:86107793-86107812 None:intergenic 35.0%
AATAGCTTACATGCTGCACA+AGG + chr3.4:86107817-86107836 None:intergenic 40.0%
AGATCCAGTTTATGGATGCA+TGG - chr3.4:86108109-86108128 MS.gene013398:CDS 40.0%
AGGAGAGAAATAGGGAGAAA+AGG + chr3.4:86107866-86107885 None:intergenic 40.0%
AGGCTAAGAGATCCAGTTTA+TGG - chr3.4:86108101-86108120 MS.gene013398:CDS 40.0%
ATAGCTTACATGCTGCACAA+GGG + chr3.4:86107816-86107835 None:intergenic 40.0%
GATCCAGTTTATGGATGCAT+GGG - chr3.4:86108110-86108129 MS.gene013398:CDS 40.0%
GGAGAGAAATAGGGAGAAAA+GGG + chr3.4:86107865-86107884 None:intergenic 40.0%
GGTTCATGAGGAGAGAAATA+GGG + chr3.4:86107874-86107893 None:intergenic 40.0%
TGAACAGAAGCAAACTTCTG+TGG + chr3.4:86107895-86107914 None:intergenic 40.0%
TGGTTCATGAGGAGAGAAAT+AGG + chr3.4:86107875-86107894 None:intergenic 40.0%
! ATAGTATTTAGGGTTCCTGG+TGG + chr3.4:86107790-86107809 None:intergenic 40.0%
!!! TAGCATTTTTGAGACGTTGC+TGG + chr3.4:86107932-86107951 None:intergenic 40.0%
AGACATATGTTAGGTCCACC+AGG - chr3.4:86107772-86107791 MS.gene013398:intron 45.0%
GCAAACTTCTGTGGTTCATG+AGG + chr3.4:86107886-86107905 None:intergenic 45.0%
TAGCTTACATGCTGCACAAG+GGG + chr3.4:86107815-86107834 None:intergenic 45.0%
!!! AATAATATATATAATGTTTT+AGG - chr3.4:86108019-86108038 MS.gene013398:intron 5.0%
GCACCCATGCATCCATAAAC+TGG + chr3.4:86108116-86108135 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 86107763 86108231 86107763 ID=MS.gene013398
chr3.4 mRNA 86107763 86108231 86107763 ID=MS.gene013398.t1;Parent=MS.gene013398
chr3.4 exon 86108040 86108231 86108040 ID=MS.gene013398.t1.exon1;Parent=MS.gene013398.t1
chr3.4 CDS 86108040 86108231 86108040 ID=cds.MS.gene013398.t1;Parent=MS.gene013398.t1
chr3.4 exon 86107837 86107953 86107837 ID=MS.gene013398.t1.exon2;Parent=MS.gene013398.t1
chr3.4 CDS 86107837 86107953 86107837 ID=cds.MS.gene013398.t1;Parent=MS.gene013398.t1
chr3.4 exon 86107763 86107774 86107763 ID=MS.gene013398.t1.exon3;Parent=MS.gene013398.t1
chr3.4 CDS 86107763 86107774 86107763 ID=cds.MS.gene013398.t1;Parent=MS.gene013398.t1
Gene Sequence

>MS.gene013398

ATGGGAAGAAGACATATGTTAGGTCCACCAGGAACCCTAAATACTATAACCCCTTGTGCAGCATGTAAGCTATTAAGAAGAAGATGTGCTCAAGAGTGTCCCTTTTCTCCCTATTTCTCTCCTCATGAACCACAGAAGTTTGCTTCTGTTCACAAAGTTTTTGGTGCCAGCAACGTCTCAAAAATGCTAATGGTAAACATTAATTAAATATATCTAATTATATGTCATATATTTCATATATAAAAAGCAATTAAGTAATAATATATATAATGTTTTAGGAGGTAGCAGAATCTTCAAGAGCAGATGCAGCAAATAGTCTTGTTTATGAAGCAAATGTGAGGCTAAGAGATCCAGTTTATGGATGCATGGGTGCAATTTCTGCATTGCAACAACAGGTTCAATCTTTACAAGCAGAACTCAATCTATTAAGAGGTGAAATACTTAAATACAAATTAAGGGAAGCTGCTAA
Protein sequence

>MS.gene013398.t1

MGRRHMLGPPGTLNTITPCAACKLLRRRCAQECPFSPYFSPHEPQKFASVHKVFGASNVSKMLMEVAESSRADAANSLVYEANVRLRDPVYGCMGAISALQQQGSC