AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene013397

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013397.t1 MTR_3g094690 99.029 103 1 0 1 103 30 132 5.18e-73 216
MS.gene013397.t1 MTR_3g094690 98.058 103 1 1 1 103 30 131 2.64e-70 209
MS.gene013397.t1 MTR_5g083960 91.837 98 8 0 6 103 27 124 9.90e-65 194
MS.gene013397.t1 MTR_5g075020 82.828 99 15 1 1 97 24 122 6.10e-59 181
MS.gene013397.t1 MTR_5g075020 82.828 99 15 1 1 97 28 126 1.05e-58 180
MS.gene013397.t1 MTR_5g083230 74.713 87 22 0 17 103 5 91 8.46e-45 142
MS.gene013397.t1 MTR_4g083680 72.414 87 24 0 17 103 14 100 4.17e-44 141
MS.gene013397.t1 MTR_3g071590 71.111 90 26 0 14 103 4 93 4.81e-44 140
MS.gene013397.t1 MTR_2g068760 70.787 89 26 0 15 103 10 98 4.97e-44 140
MS.gene013397.t1 MTR_7g033800 67.816 87 28 0 17 103 10 96 1.54e-40 132
MS.gene013397.t1 MTR_6g005070 66.667 87 29 0 17 103 8 94 1.64e-40 131
MS.gene013397.t1 MTR_3g031660 67.816 87 28 0 17 103 6 92 2.58e-40 131
MS.gene013397.t1 MTR_6g005080 64.368 87 31 0 17 103 9 95 5.89e-39 127
MS.gene013397.t1 MTR_4g105170 66.667 87 29 0 17 103 10 96 6.91e-39 128
MS.gene013397.t1 MTR_3g077240 66.667 87 29 0 17 103 9 95 1.14e-38 128
MS.gene013397.t1 MTR_2g093310 62.500 88 33 0 16 103 31 118 3.22e-38 127
MS.gene013397.t1 MTR_3g073690 65.517 87 30 0 17 103 8 94 1.02e-37 125
MS.gene013397.t1 MTR_3g452660 63.218 87 32 0 17 103 6 92 3.30e-37 127
MS.gene013397.t1 MTR_5g017950 65.517 87 30 0 17 103 7 93 4.08e-37 127
MS.gene013397.t1 MTR_3g071420 64.368 87 31 0 17 103 13 99 4.74e-37 123
MS.gene013397.t1 MTR_8g040900 64.634 82 29 0 17 98 6 87 1.36e-36 124
MS.gene013397.t1 MTR_5g083010 63.218 87 32 0 17 103 10 96 6.87e-36 120
MS.gene013397.t1 MTR_1g095850 62.353 85 32 0 19 103 73 157 3.30e-35 120
MS.gene013397.t1 MTR_4g060950 60.674 89 34 1 16 103 22 110 3.95e-35 119
MS.gene013397.t1 MTR_7g074990 64.368 87 30 1 18 103 20 106 5.03e-34 117
MS.gene013397.t1 MTR_7g028905 57.647 85 36 0 19 103 6 90 3.60e-32 109
MS.gene013397.t1 MTR_7g096530 56.667 90 38 1 15 103 11 100 1.26e-31 110
MS.gene013397.t1 MTR_1g070220 57.471 87 36 1 18 103 15 101 2.66e-30 107
MS.gene013397.t1 MTR_5g093010 56.471 85 37 0 19 103 6 90 2.98e-30 105
MS.gene013397.t1 MTR_6g027710 58.427 89 36 1 16 103 38 126 3.27e-30 107
MS.gene013397.t1 MTR_1g070205 56.818 88 35 2 18 103 12 98 7.96e-29 103
MS.gene013397.t1 MTR_8g036105 58.621 87 35 1 18 103 18 104 1.08e-28 103
MS.gene013397.t1 MTR_7g096610 55.056 89 37 2 17 103 7 94 4.18e-28 102
MS.gene013397.t1 MTR_8g036085 55.172 87 38 1 18 103 23 109 8.35e-28 101
MS.gene013397.t1 MTR_8g079660 53.409 88 41 0 16 103 6 93 1.15e-27 101
MS.gene013397.t1 MTR_5g080470 51.136 88 42 1 17 103 6 93 1.78e-27 99.4
MS.gene013397.t1 MTR_6g011250 45.000 80 43 1 19 97 10 89 9.22e-25 92.4
MS.gene013397.t1 MTR_7g075230 52.809 89 39 2 18 103 12 100 8.64e-24 90.1
MS.gene013397.t1 MTR_8g079620 47.674 86 45 0 16 101 6 91 1.37e-23 90.5
MS.gene013397.t1 MTR_8g079580 52.273 88 41 1 16 102 6 93 2.80e-23 89.7
MS.gene013397.t1 MTR_6g027700 45.977 87 46 1 18 103 7 93 4.48e-23 88.6
MS.gene013397.t1 MTR_6g011230 42.857 84 48 0 14 97 7 90 9.10e-23 87.8
MS.gene013397.t1 MTR_6g011200 41.573 89 48 2 13 97 1 89 7.31e-22 86.3
MS.gene013397.t1 MTR_4g107450 43.820 89 50 0 15 103 7 95 8.73e-21 84.3
MS.gene013397.t1 MTR_5g085390 40.449 89 49 2 13 97 1 89 1.38e-19 80.1
MS.gene013397.t1 MTR_4g099230 41.250 80 46 1 19 97 3 82 9.65e-19 76.3
MS.gene013397.t1 MTR_8g017090 40.000 90 52 2 15 103 9 97 5.68e-18 77.0
MS.gene013397.t1 MTR_2g100020 40.000 90 52 2 15 103 16 104 2.89e-17 74.7
MS.gene013397.t1 MTR_4g088035 34.483 87 57 0 17 103 5 91 2.27e-15 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013397.t1 AT2G40470 94.792 96 5 0 3 98 5 100 1.80e-63 191
MS.gene013397.t1 AT2G40470 94.792 96 5 0 3 98 30 125 2.92e-63 191
MS.gene013397.t1 AT2G30340 83.810 105 15 2 1 103 33 137 6.80e-61 187
MS.gene013397.t1 AT2G30340 83.810 105 15 2 1 103 34 138 7.90e-61 187
MS.gene013397.t1 AT1G31320 73.563 87 23 0 17 103 12 98 1.41e-43 140
MS.gene013397.t1 AT2G30130 68.041 97 27 1 7 103 1 93 2.55e-43 140
MS.gene013397.t1 AT3G27650 62.626 99 37 0 5 103 26 124 1.62e-41 134
MS.gene013397.t1 AT5G66870 68.966 87 27 0 17 103 6 92 1.53e-39 133
MS.gene013397.t1 AT1G16530 62.222 90 33 1 15 103 11 100 3.45e-39 128
MS.gene013397.t1 AT1G65620 68.235 85 27 0 14 98 5 89 7.48e-39 129
MS.gene013397.t1 AT1G65620 68.235 85 27 0 14 98 5 89 7.48e-39 129
MS.gene013397.t1 AT1G65620 68.235 85 27 0 14 98 5 89 7.48e-39 129
MS.gene013397.t1 AT1G65620 68.235 85 27 0 14 98 5 89 7.48e-39 129
MS.gene013397.t1 AT1G65620 68.235 85 27 0 14 98 5 89 7.48e-39 129
MS.gene013397.t1 AT5G63090 65.517 87 30 0 17 103 10 96 3.47e-38 126
MS.gene013397.t1 AT5G63090 65.517 87 30 0 17 103 10 96 3.47e-38 126
MS.gene013397.t1 AT5G63090 65.517 87 30 0 17 103 10 96 3.47e-38 126
MS.gene013397.t1 AT5G63090 65.517 87 30 0 17 103 10 96 3.47e-38 126
MS.gene013397.t1 AT1G07900 61.798 89 34 0 15 103 30 118 6.90e-38 125
MS.gene013397.t1 AT2G28500 62.500 88 33 0 16 103 53 140 1.74e-37 126
MS.gene013397.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.26e-37 128
MS.gene013397.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.26e-37 128
MS.gene013397.t1 AT2G23660 65.116 86 30 0 17 102 4 89 2.26e-37 128
MS.gene013397.t1 AT3G11090 62.069 87 33 0 17 103 10 96 8.11e-35 117
MS.gene013397.t1 AT3G26660 58.824 85 35 0 19 103 6 90 1.37e-34 115
MS.gene013397.t1 AT3G26620 58.824 85 35 0 19 103 6 90 1.57e-34 115
MS.gene013397.t1 AT2G42430 54.639 97 43 1 8 103 5 101 1.55e-31 111
MS.gene013397.t1 AT4G00210 59.770 87 34 1 18 103 11 97 1.08e-30 108
MS.gene013397.t1 AT3G58190 56.818 88 35 2 18 103 11 97 1.22e-28 103
MS.gene013397.t1 AT5G06080 55.682 88 38 1 17 103 6 93 1.70e-28 101
MS.gene013397.t1 AT3G03760 55.682 88 38 1 17 103 50 137 4.07e-28 103
MS.gene013397.t1 AT2G31310 50.000 88 43 1 17 103 6 93 9.77e-28 100
MS.gene013397.t1 AT4G00220 58.333 84 34 1 21 103 20 103 2.56e-27 100
MS.gene013397.t1 AT2G45420 54.762 84 37 1 21 103 40 123 9.65e-27 99.4
MS.gene013397.t1 AT2G42440 51.685 89 40 2 17 103 6 93 2.21e-26 98.2
MS.gene013397.t1 AT2G45410 53.571 84 38 1 21 103 19 102 2.23e-25 94.4
MS.gene013397.t1 AT3G47870 42.529 87 50 0 15 101 33 119 6.66e-23 90.5
MS.gene013397.t1 AT3G50510 45.977 87 47 0 17 103 11 97 9.74e-23 87.4
MS.gene013397.t1 AT3G50510 45.977 87 47 0 17 103 11 97 9.74e-23 87.4
MS.gene013397.t1 AT1G06280 48.052 77 40 0 19 95 25 101 8.53e-21 82.8
MS.gene013397.t1 AT1G72980 42.529 87 50 0 15 101 10 96 2.67e-19 79.0
MS.gene013397.t1 AT3G13850 38.824 85 52 0 19 103 37 121 1.26e-18 78.2
MS.gene013397.t1 AT5G35900 39.080 87 53 0 17 103 4 90 2.96e-18 76.3
MS.gene013397.t1 AT2G19820 34.483 87 56 1 18 103 12 98 1.67e-15 67.0
MS.gene013397.t1 AT5G15060 35.526 76 47 1 16 89 15 90 1.13e-11 57.8
MS.gene013397.t1 AT1G36000 31.034 87 58 2 18 103 9 94 4.88e-11 55.5

Find 21 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAAGGGGTTATAGTATTT+AGG 0.181231 3.4:+86136259 None:intergenic
TGGTTCATGAGGAGAGAAAT+AGG 0.287589 3.4:+86136185 None:intergenic
AGGCTAAGAGATCCAGTTTA+TGG 0.306813 3.4:-86135956 MS.gene013397:CDS
ACAAGGGGTTATAGTATTTA+GGG 0.313905 3.4:+86136260 None:intergenic
GTTATAGTATTTAGGGTTCC+TGG 0.351578 3.4:+86136267 None:intergenic
GCACCCATGCATCCATAAAC+TGG 0.381798 3.4:+86135944 None:intergenic
GGAGAGAAATAGGGAGAAAA+GGG 0.384566 3.4:+86136195 None:intergenic
AGGAGAGAAATAGGGAGAAA+AGG 0.419838 3.4:+86136194 None:intergenic
AATTTCTGCATTGCAACAAC+AGG 0.457176 3.4:-86135921 None:intergenic
ATGGGAAGAAGACATATGTT+AGG 0.472989 3.4:-86136294 MS.gene013397:CDS
GGTTCATGAGGAGAGAAATA+GGG 0.492582 3.4:+86136186 None:intergenic
AGATCCAGTTTATGGATGCA+TGG 0.526865 3.4:-86135948 MS.gene013397:CDS
AATAGCTTACATGCTGCACA+AGG 0.566069 3.4:+86136243 None:intergenic
GATCCAGTTTATGGATGCAT+GGG 0.578062 3.4:-86135947 MS.gene013397:CDS
GCAAACTTCTGTGGTTCATG+AGG 0.583150 3.4:+86136174 None:intergenic
TGAACAGAAGCAAACTTCTG+TGG 0.594520 3.4:+86136165 None:intergenic
TAGCTTACATGCTGCACAAG+GGG 0.599040 3.4:+86136245 None:intergenic
ATAGTATTTAGGGTTCCTGG+TGG 0.604329 3.4:+86136270 None:intergenic
AGACATATGTTAGGTCCACC+AGG 0.627473 3.4:-86136285 MS.gene013397:CDS
TTGTTTATGAAGCAAATGTG+AGG 0.672469 3.4:-86135976 MS.gene013397:CDS
ATAGCTTACATGCTGCACAA+GGG 0.680325 3.4:+86136244 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATATATAATGTTTTAGG+AGG - chr3.4:86136181-86136200 MS.gene013397:CDS 15.0%
ACAAGGGGTTATAGTATTTA+GGG + chr3.4:86135959-86135978 None:intergenic 30.0%
TTGTTTATGAAGCAAATGTG+AGG - chr3.4:86136240-86136259 MS.gene013397:CDS 30.0%
ATGGGAAGAAGACATATGTT+AGG - chr3.4:86135922-86135941 MS.gene013397:CDS 35.0%
CAACGTCTCAAAAATGCTAA+TGG - chr3.4:86136092-86136111 MS.gene013397:intron 35.0%
CACAAGGGGTTATAGTATTT+AGG + chr3.4:86135960-86135979 None:intergenic 35.0%
! GCTTCTGTTCACAAAGTTTT+TGG - chr3.4:86136063-86136082 MS.gene013397:intron 35.0%
! GTTATAGTATTTAGGGTTCC+TGG + chr3.4:86135952-86135971 None:intergenic 35.0%
AATAGCTTACATGCTGCACA+AGG + chr3.4:86135976-86135995 None:intergenic 40.0%
AGATCCAGTTTATGGATGCA+TGG - chr3.4:86136268-86136287 MS.gene013397:CDS 40.0%
AGGAGAGAAATAGGGAGAAA+AGG + chr3.4:86136025-86136044 None:intergenic 40.0%
AGGCTAAGAGATCCAGTTTA+TGG - chr3.4:86136260-86136279 MS.gene013397:CDS 40.0%
ATAGCTTACATGCTGCACAA+GGG + chr3.4:86135975-86135994 None:intergenic 40.0%
GATCCAGTTTATGGATGCAT+GGG - chr3.4:86136269-86136288 MS.gene013397:CDS 40.0%
GGAGAGAAATAGGGAGAAAA+GGG + chr3.4:86136024-86136043 None:intergenic 40.0%
GGTTCATGAGGAGAGAAATA+GGG + chr3.4:86136033-86136052 None:intergenic 40.0%
TGAACAGAAGCAAACTTCTG+TGG + chr3.4:86136054-86136073 None:intergenic 40.0%
TGGTTCATGAGGAGAGAAAT+AGG + chr3.4:86136034-86136053 None:intergenic 40.0%
! ATAGTATTTAGGGTTCCTGG+TGG + chr3.4:86135949-86135968 None:intergenic 40.0%
!!! TAGCATTTTTGAGACGTTGC+TGG + chr3.4:86136091-86136110 None:intergenic 40.0%
AGACATATGTTAGGTCCACC+AGG - chr3.4:86135931-86135950 MS.gene013397:CDS 45.0%
GCAAACTTCTGTGGTTCATG+AGG + chr3.4:86136045-86136064 None:intergenic 45.0%
TAGCTTACATGCTGCACAAG+GGG + chr3.4:86135974-86135993 None:intergenic 45.0%
!!! AATAATATATATAATGTTTT+AGG - chr3.4:86136178-86136197 MS.gene013397:CDS 5.0%
GCACCCATGCATCCATAAAC+TGG + chr3.4:86136275-86136294 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 86135922 86136316 86135922 ID=MS.gene013397
chr3.4 mRNA 86135922 86136316 86135922 ID=MS.gene013397.t1;Parent=MS.gene013397
chr3.4 exon 86136125 86136316 86136125 ID=MS.gene013397.t1.exon1;Parent=MS.gene013397.t1
chr3.4 CDS 86136125 86136316 86136125 ID=cds.MS.gene013397.t1;Parent=MS.gene013397.t1
chr3.4 exon 86135922 86136038 86135922 ID=MS.gene013397.t1.exon2;Parent=MS.gene013397.t1
chr3.4 CDS 86135922 86136038 86135922 ID=cds.MS.gene013397.t1;Parent=MS.gene013397.t1
Gene Sequence

>MS.gene013397

ATGGGAAGAAGACATATGTTAGGTCCACCAGGAACCCTAAATACTATAACCCCTTGTGCAGCATGTAAGCTATTAAGAAGAAGATGTGCTCAAGAGTGTCCCTTTTCTCCCTATTTCTCTCCTCATGAACCACAGAAGTTTGCTTCTGTTCACAAAGTTTTTGGTGCCAGCAACGTCTCAAAAATGCTAATGGTAAACATTAATTAAATATATCTAATTATATGTCATATATTTCATATATAAAAAGCAATTAAGTAATAATATATATAATGTTTTAGGAGGTAGCAGAATCTTCAAGAGCAGATGCAGCAAATAGTCTTGTTTATGAAGCAAATGTGAGGCTAAGAGATCCAGTTTATGGATGCATGGGTGCAATTTCTGCATTGCAACAACAG
Protein sequence

>MS.gene013397.t1

MGRRHMLGPPGTLNTITPCAACKLLRRRCAQECPFSPYFSPHEPQKFASVHKVFGASNVSKMLMEVAESSRADAANSLVYEANVRLRDPVYGCMGAISALQQQ