AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055657

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055657.t1 MTR_4g119428 54.772 241 98 2 12 251 15 245 1.90e-84 252
MS.gene055657.t1 MTR_1g057270 61.582 177 67 1 77 252 72 248 1.68e-74 227
MS.gene055657.t1 MTR_7g105870 51.042 192 85 3 62 246 39 228 1.82e-52 170
MS.gene055657.t1 MTR_7g106030 40.526 190 101 5 46 231 34 215 3.33e-40 139
MS.gene055657.t1 MTR_7g106010 42.328 189 97 5 48 231 30 211 3.75e-40 138
MS.gene055657.t1 MTR_7g106000 35.784 204 116 5 46 245 33 225 1.16e-38 134
MS.gene055657.t1 MTR_1g057230 91.045 67 6 0 186 252 30 96 1.17e-38 130
MS.gene055657.t1 MTR_7g105970 36.170 188 108 4 46 229 33 212 6.43e-37 130
MS.gene055657.t1 MTR_1g057400 35.354 198 119 4 51 243 13 206 1.85e-34 123
MS.gene055657.t1 MTR_6g471090 40.782 179 93 8 57 225 2 177 2.46e-32 117
MS.gene055657.t1 MTR_6g071410 37.696 191 101 7 40 225 2 179 8.25e-32 116
MS.gene055657.t1 MTR_6g070890 37.696 191 101 7 40 225 2 179 8.25e-32 116
MS.gene055657.t1 MTR_6g070900 38.202 178 100 6 58 225 2 179 9.33e-32 116
MS.gene055657.t1 MTR_6g071400 38.202 178 100 6 58 225 2 179 9.33e-32 116
MS.gene055657.t1 MTR_6g471080 36.957 184 94 8 47 225 8 174 1.33e-24 97.8
MS.gene055657.t1 MTR_2g048270 41.860 129 71 4 100 225 2 129 2.21e-22 90.9
MS.gene055657.t1 MTR_2g011350 28.249 177 113 3 73 245 35 201 2.87e-20 85.9
MS.gene055657.t1 MTR_1g057290 34.568 162 101 2 86 242 52 213 3.59e-19 83.6
MS.gene055657.t1 MTR_7g106050 26.923 182 130 3 62 241 20 200 7.65e-16 74.3
MS.gene055657.t1 MTR_3g063310 32.639 144 95 2 81 223 88 230 1.08e-14 72.0
MS.gene055657.t1 MTR_7g118270 28.750 160 110 3 69 226 53 210 2.87e-14 70.5
MS.gene055657.t1 MTR_5g087760 27.072 181 118 5 47 223 64 234 1.58e-13 68.6
MS.gene055657.t1 MTR_3g078800 26.994 163 116 3 63 223 71 232 7.30e-13 67.0
MS.gene055657.t1 MTR_2g100060 30.986 142 94 3 81 220 84 223 2.67e-12 65.1
MS.gene055657.t1 MTR_4g094322 43.662 71 38 1 184 252 1 71 4.04e-12 60.5
MS.gene055657.t1 MTR_5g076170 30.556 144 98 2 81 223 99 241 4.19e-12 64.7
MS.gene055657.t1 MTR_1g057420 26.582 158 113 3 81 236 39 195 1.63e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055657.t1 AT3G11650 44.037 218 103 6 35 245 33 238 3.13e-52 170
MS.gene055657.t1 AT5G06320 44.865 185 99 2 62 245 48 230 3.48e-50 164
MS.gene055657.t1 AT2G35460 40.000 195 101 4 38 225 33 218 2.36e-46 155
MS.gene055657.t1 AT2G35980 45.977 174 88 4 57 225 34 206 2.83e-44 149
MS.gene055657.t1 AT1G32270 39.860 143 86 0 83 225 1 143 1.71e-29 113
MS.gene055657.t1 AT1G32270 39.860 143 86 0 83 225 1 143 7.27e-29 113
MS.gene055657.t1 AT5G22870 27.841 176 121 2 61 231 28 202 2.61e-18 80.9
MS.gene055657.t1 AT3G52470 27.528 178 127 2 66 242 23 199 1.05e-16 76.6
MS.gene055657.t1 AT4G09590 26.966 178 128 2 65 241 25 201 1.05e-16 76.6
MS.gene055657.t1 AT4G05220 28.834 163 105 5 53 214 42 194 4.53e-16 75.1
MS.gene055657.t1 AT4G01410 30.303 165 103 5 65 221 43 203 1.78e-15 73.6
MS.gene055657.t1 AT2G35970 28.025 157 111 2 65 220 25 180 4.71e-15 72.0
MS.gene055657.t1 AT5G53730 30.714 140 90 4 75 211 40 175 1.30e-14 70.9
MS.gene055657.t1 AT5G36970 29.167 144 100 2 81 223 84 226 1.55e-14 71.2
MS.gene055657.t1 AT2G35960 26.667 165 119 2 78 241 37 200 2.15e-14 70.5
MS.gene055657.t1 AT3G11660 24.581 179 130 4 62 236 18 195 9.30e-14 68.6
MS.gene055657.t1 AT1G61760 26.490 151 105 4 65 214 47 192 1.59e-13 68.2
MS.gene055657.t1 AT1G65690 28.205 156 108 3 69 221 74 228 2.56e-13 68.2
MS.gene055657.t1 AT5G06330 25.904 166 118 4 81 242 39 203 7.10e-13 66.2
MS.gene055657.t1 AT2G27080 25.424 177 121 4 48 223 73 239 1.10e-12 66.2
MS.gene055657.t1 AT2G27080 25.424 177 121 4 48 223 73 239 1.10e-12 66.2
MS.gene055657.t1 AT3G44220 27.027 148 103 3 65 211 23 166 1.13e-12 65.5
MS.gene055657.t1 AT1G17620 29.412 153 88 5 81 220 84 229 9.72e-12 63.9
MS.gene055657.t1 AT5G22200 26.772 127 91 2 81 206 43 168 4.88e-11 60.8

Find 48 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAAGTTCTGATCAGATTT+TGG 0.182041 1.4:+48131508 MS.gene055657:CDS
AAAATCTGATCAGAACTTAA+AGG 0.258777 1.4:-48131506 None:intergenic
CTTAAAGTGAGGCTTAAAAT+TGG 0.279126 1.4:+48131584 MS.gene055657:CDS
TTCAAGTCACTTATTGTGAT+TGG 0.286998 1.4:+48131699 MS.gene055657:CDS
CAACTCTTCGATTAGGGTTT+CGG 0.289591 1.4:-48131346 None:intergenic
TAAATACCAACTCTTCGATT+AGG 0.295908 1.4:-48131353 None:intergenic
AAATACCAACTCTTCGATTA+GGG 0.315325 1.4:-48131352 None:intergenic
ACGGTGAATTTGACGTAGTT+AGG 0.341252 1.4:-48131245 None:intergenic
GGAGGGATTCGGCCGCAAAA+TGG 0.365204 1.4:-48131024 None:intergenic
TCATAGGAACACGAGTTTCT+TGG 0.368767 1.4:+48131454 MS.gene055657:CDS
CAATCTTTGCTTTCTTCTCA+TGG 0.377112 1.4:+48131210 MS.gene055657:CDS
CTTTCTAGGCGGGAGGGATT+CGG 0.378754 1.4:-48131035 None:intergenic
TATAGTTCGTTGTGATTTGA+AGG 0.386616 1.4:+48131634 MS.gene055657:CDS
AGCAGTCGTCATCACTTTCT+AGG 0.403243 1.4:-48131049 None:intergenic
CATAGGAACACGAGTTTCTT+GGG 0.412608 1.4:+48131455 MS.gene055657:CDS
TCAAGTCACTTATTGTGATT+GGG 0.413813 1.4:+48131700 MS.gene055657:CDS
GAACATTCTTTCAACGTCAT+AGG 0.415486 1.4:+48131438 MS.gene055657:CDS
TTCAAATCACAACGAACTAT+AGG 0.420716 1.4:-48131632 None:intergenic
CGGTGAATTTGACGTAGTTA+GGG 0.436190 1.4:-48131244 None:intergenic
AATTGTTGACCGCTAAAAGT+TGG 0.437052 1.4:-48131479 None:intergenic
TTCTGCTGCATATCTATCTT+CGG 0.438567 1.4:+48131137 MS.gene055657:CDS
ACCACGCAATGGAACGTTGA+TGG 0.440472 1.4:+48131667 MS.gene055657:CDS
ATTGTTGACCGCTAAAAGTT+GGG 0.441762 1.4:-48131478 None:intergenic
AAAATGGTGGTTGTTCCGTT+AGG 0.481068 1.4:+48131727 MS.gene055657:CDS
GCAGCAGAAGCAGCAACAGC+TGG 0.481203 1.4:-48131123 None:intergenic
AGTAAGGGATGCGTCTGTTA+CGG 0.503165 1.4:-48131264 None:intergenic
GACGTTGAAAGAATGTTCCT+AGG 0.509172 1.4:-48131433 None:intergenic
CCACGCAATGGAACGTTGAT+GGG 0.509706 1.4:+48131668 MS.gene055657:CDS
CGAAACCCTAATCGAAGAGT+TGG 0.512484 1.4:+48131347 MS.gene055657:CDS
AGGTTTGGTTCTCAAACCCT+AGG 0.515800 1.4:+48131416 MS.gene055657:CDS
CCCATCAACGTTCCATTGCG+TGG 0.523920 1.4:-48131668 None:intergenic
GTTTATTGAAGACATGGAAA+GGG 0.527374 1.4:+48131606 MS.gene055657:CDS
GGTTTATTGAAGACATGGAA+AGG 0.532065 1.4:+48131605 MS.gene055657:CDS
GTCGTCATCACTTTCTAGGC+GGG 0.533584 1.4:-48131045 None:intergenic
ACGTTGAAAGAATGTTCCTA+GGG 0.533748 1.4:-48131432 None:intergenic
GCCGCAGAGACATTTGCAGC+AGG 0.535250 1.4:-48131072 None:intergenic
AAATTGGTTTATTGAAGACA+TGG 0.541017 1.4:+48131600 MS.gene055657:CDS
CGGCCGCAAAATGGAAGAAG+TGG 0.581964 1.4:-48131015 None:intergenic
TTTGAAATTGAACTGAGTAA+GGG 0.583763 1.4:-48131279 None:intergenic
GTCATCACTTTCTAGGCGGG+AGG 0.588472 1.4:-48131042 None:intergenic
GGAGTATGTGTAGTGAATGC+TGG 0.589528 1.4:-48130994 None:intergenic
TCATCACTTTCTAGGCGGGA+GGG 0.609571 1.4:-48131041 None:intergenic
TAACATCTTTATAAAACACA+AGG 0.619107 1.4:-48131394 None:intergenic
AACATCTTTATAAAACACAA+GGG 0.631367 1.4:-48131393 None:intergenic
AGTTTATGGAATTGTTGTGA+AGG 0.646720 1.4:+48131556 MS.gene055657:CDS
GTTCCTCTAAAACCACGCAA+TGG 0.663668 1.4:+48131656 MS.gene055657:CDS
AGTCGTCATCACTTTCTAGG+CGG 0.691693 1.4:-48131046 None:intergenic
TCCTGCTGCAAATGTCTCTG+CGG 0.706881 1.4:+48131071 MS.gene055657:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATCTTTATAAAACACAA+GGG - chr1.4:48131396-48131415 None:intergenic 20.0%
!! TAACATCTTTATAAAACACA+AGG - chr1.4:48131397-48131416 None:intergenic 20.0%
!!! TTGTGTTTTATAAAGATGTT+AGG + chr1.4:48131396-48131415 MS.gene055657:CDS 20.0%
!!! TTTTATAAAGATGTTAGGTT+TGG + chr1.4:48131401-48131420 MS.gene055657:CDS 20.0%
! AAAATCTGATCAGAACTTAA+AGG - chr1.4:48131509-48131528 None:intergenic 25.0%
!! AAATTGGTTTATTGAAGACA+TGG + chr1.4:48131600-48131619 MS.gene055657:CDS 25.0%
!! TTTGAAATTGAACTGAGTAA+GGG - chr1.4:48131282-48131301 None:intergenic 25.0%
!!! TTTAAGTTCTGATCAGATTT+TGG + chr1.4:48131508-48131527 MS.gene055657:CDS 25.0%
!!! TTTTGAAATTGAACTGAGTA+AGG - chr1.4:48131283-48131302 None:intergenic 25.0%
AAATACCAACTCTTCGATTA+GGG - chr1.4:48131355-48131374 None:intergenic 30.0%
AGTTTATGGAATTGTTGTGA+AGG + chr1.4:48131556-48131575 MS.gene055657:CDS 30.0%
ATTGTGATTGGGATCAAAAA+TGG + chr1.4:48131711-48131730 MS.gene055657:CDS 30.0%
CTCAATCAAGAGAAAAAAGA+TGG + chr1.4:48131533-48131552 MS.gene055657:CDS 30.0%
CTTAAAGTGAGGCTTAAAAT+TGG + chr1.4:48131584-48131603 MS.gene055657:CDS 30.0%
GAGAAAAAAGATGGAGTTTA+TGG + chr1.4:48131542-48131561 MS.gene055657:CDS 30.0%
GTTTATTGAAGACATGGAAA+GGG + chr1.4:48131606-48131625 MS.gene055657:CDS 30.0%
TAAATACCAACTCTTCGATT+AGG - chr1.4:48131356-48131375 None:intergenic 30.0%
TATAGTTCGTTGTGATTTGA+AGG + chr1.4:48131634-48131653 MS.gene055657:CDS 30.0%
TCAAGTCACTTATTGTGATT+GGG + chr1.4:48131700-48131719 MS.gene055657:CDS 30.0%
TTCAAATCACAACGAACTAT+AGG - chr1.4:48131635-48131654 None:intergenic 30.0%
TTCAAGTCACTTATTGTGAT+TGG + chr1.4:48131699-48131718 MS.gene055657:CDS 30.0%
AATTGTTGACCGCTAAAAGT+TGG - chr1.4:48131482-48131501 None:intergenic 35.0%
ACGTTGAAAGAATGTTCCTA+GGG - chr1.4:48131435-48131454 None:intergenic 35.0%
ATTGTTGACCGCTAAAAGTT+GGG - chr1.4:48131481-48131500 None:intergenic 35.0%
CAATCTTTGCTTTCTTCTCA+TGG + chr1.4:48131210-48131229 MS.gene055657:CDS 35.0%
GAACATTCTTTCAACGTCAT+AGG + chr1.4:48131438-48131457 MS.gene055657:CDS 35.0%
GGTTTATTGAAGACATGGAA+AGG + chr1.4:48131605-48131624 MS.gene055657:CDS 35.0%
TTCTGCTGCATATCTATCTT+CGG + chr1.4:48131137-48131156 MS.gene055657:CDS 35.0%
! TGAAGGTTTTGCTTAAAGTG+AGG + chr1.4:48131573-48131592 MS.gene055657:CDS 35.0%
ACGGTGAATTTGACGTAGTT+AGG - chr1.4:48131248-48131267 None:intergenic 40.0%
CAACTCTTCGATTAGGGTTT+CGG - chr1.4:48131349-48131368 None:intergenic 40.0%
CATAGGAACACGAGTTTCTT+GGG + chr1.4:48131455-48131474 MS.gene055657:CDS 40.0%
CGGTGAATTTGACGTAGTTA+GGG - chr1.4:48131247-48131266 None:intergenic 40.0%
GACGTTGAAAGAATGTTCCT+AGG - chr1.4:48131436-48131455 None:intergenic 40.0%
GTGATTGGGATCAAAAATGG+TGG + chr1.4:48131714-48131733 MS.gene055657:CDS 40.0%
TCATAGGAACACGAGTTTCT+TGG + chr1.4:48131454-48131473 MS.gene055657:CDS 40.0%
! ACTCCACTTCTTCCATTTTG+CGG + chr1.4:48131012-48131031 MS.gene055657:CDS 40.0%
AGCAGTCGTCATCACTTTCT+AGG - chr1.4:48131052-48131071 None:intergenic 45.0%
AGTAAGGGATGCGTCTGTTA+CGG - chr1.4:48131267-48131286 None:intergenic 45.0%
AGTCGTCATCACTTTCTAGG+CGG - chr1.4:48131049-48131068 None:intergenic 45.0%
CGAAACCCTAATCGAAGAGT+TGG + chr1.4:48131347-48131366 MS.gene055657:CDS 45.0%
GGAGTATGTGTAGTGAATGC+TGG - chr1.4:48130997-48131016 None:intergenic 45.0%
! TTCTTGGGCCCAACTTTTAG+CGG + chr1.4:48131470-48131489 MS.gene055657:CDS 45.0%
!! AGGTTTGGTTCTCAAACCCT+AGG + chr1.4:48131416-48131435 MS.gene055657:CDS 45.0%
!! GTTCCTCTAAAACCACGCAA+TGG + chr1.4:48131656-48131675 MS.gene055657:CDS 45.0%
!!! GTTCCATTGCGTGGTTTTAG+AGG - chr1.4:48131662-48131681 None:intergenic 45.0%
ACCACGCAATGGAACGTTGA+TGG + chr1.4:48131667-48131686 MS.gene055657:CDS 50.0%
CCACGCAATGGAACGTTGAT+GGG + chr1.4:48131668-48131687 MS.gene055657:CDS 50.0%
GTCGTCATCACTTTCTAGGC+GGG - chr1.4:48131048-48131067 None:intergenic 50.0%
TCATCACTTTCTAGGCGGGA+GGG - chr1.4:48131044-48131063 None:intergenic 50.0%
TCCTGCTGCAAATGTCTCTG+CGG + chr1.4:48131071-48131090 MS.gene055657:CDS 50.0%
CCCATCAACGTTCCATTGCG+TGG - chr1.4:48131671-48131690 None:intergenic 55.0%
CGGCCGCAAAATGGAAGAAG+TGG - chr1.4:48131018-48131037 None:intergenic 55.0%
CTTTCTAGGCGGGAGGGATT+CGG - chr1.4:48131038-48131057 None:intergenic 55.0%
GTCATCACTTTCTAGGCGGG+AGG - chr1.4:48131045-48131064 None:intergenic 55.0%
GCAGCAGAAGCAGCAACAGC+TGG - chr1.4:48131126-48131145 None:intergenic 60.0%
GCCGCAGAGACATTTGCAGC+AGG - chr1.4:48131075-48131094 None:intergenic 60.0%
GGAGGGATTCGGCCGCAAAA+TGG - chr1.4:48131027-48131046 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 48130990 48131748 48130990 ID=MS.gene055657
chr1.4 mRNA 48130990 48131748 48130990 ID=MS.gene055657.t1;Parent=MS.gene055657
chr1.4 exon 48130990 48131748 48130990 ID=MS.gene055657.t1.exon1;Parent=MS.gene055657.t1
chr1.4 CDS 48130990 48131748 48130990 ID=cds.MS.gene055657.t1;Parent=MS.gene055657.t1
Gene Sequence

>MS.gene055657

ATGGCCAGCATTCACTACACATACTCCACTTCTTCCATTTTGCGGCCGAATCCCTCCCGCCTAGAAAGTGATGACGACTGCTCCTGCTGCAAATGTCTCTGCGGCTCTTGCTGCTTCTGCTGCAAATGTCTCTCCAGCTGTTGCTGCTTCTGCTGCATATCTATCTTCGGCTGTTGCGAATACGTATTCAACGTAATCTGCAACTTCATTTTCGTCGTAGCAATCTTTGCTTTCTTCTCATGGCTTATCATACACCCTAACTACGTCAAATTCACCGTAACAGACGCATCCCTTACTCAGTTCAATTTCAAAAACAACATCACACTTCACTATGATCTCGCTCTCAACATCACAATCCGAAACCCTAATCGAAGAGTTGGTATTTACTATGATAACATCGAAACCCTTGTGTTTTATAAAGATGTTAGGTTTGGTTCTCAAACCCTAGGAACATTCTTTCAACGTCATAGGAACACGAGTTTCTTGGGCCCAACTTTTAGCGGTCAACAATTGATTCCTTTAAGTTCTGATCAGATTTTGGAACTCAATCAAGAGAAAAAAGATGGAGTTTATGGAATTGTTGTGAAGGTTTTGCTTAAAGTGAGGCTTAAAATTGGTTTATTGAAGACATGGAAAGGGAAGCCTATAGTTCGTTGTGATTTGAAGGTTCCTCTAAAACCACGCAATGGAACGTTGATGGGTAAAGAATTTCAAGTCACTTATTGTGATTGGGATCAAAAATGGTGGTTGTTCCGTTAG
Protein sequence

>MS.gene055657.t1

MASIHYTYSTSSILRPNPSRLESDDDCSCCKCLCGSCCFCCKCLSSCCCFCCISIFGCCEYVFNVICNFIFVVAIFAFFSWLIIHPNYVKFTVTDASLTQFNFKNNITLHYDLALNITIRNPNRRVGIYYDNIETLVFYKDVRFGSQTLGTFFQRHRNTSFLGPTFSGQQLIPLSSDQILELNQEKKDGVYGIVVKVLLKVRLKIGLLKTWKGKPIVRCDLKVPLKPRNGTLMGKEFQVTYCDWDQKWWLFR