AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38649

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38649.t1 MTR_4g083510 84.133 271 34 1 1 271 1 262 5.02e-158 442
MS.gene38649.t1 MTR_0867s0010 74.539 271 59 2 1 271 1 261 6.60e-131 374
MS.gene38649.t1 MTR_4g063670 67.528 271 78 2 1 271 1 261 3.18e-119 344
MS.gene38649.t1 MTR_1g051185 59.410 271 75 3 1 271 1 236 8.36e-95 280
MS.gene38649.t1 MTR_3g069460 60.109 183 64 1 1 183 1 174 1.92e-73 223
MS.gene38649.t1 MTR_7g088160 45.133 226 105 6 20 240 75 286 5.02e-50 169
MS.gene38649.t1 MTR_8g015750 64.138 145 35 2 127 271 1 128 2.59e-46 154
MS.gene38649.t1 MTR_7g107340 48.026 152 71 6 78 224 98 246 8.08e-37 133
MS.gene38649.t1 MTR_8g015740 70.330 91 18 1 1 91 49 130 7.36e-34 120
MS.gene38649.t1 MTR_2g023560 77.419 62 14 0 55 116 57 118 1.65e-27 103
MS.gene38649.t1 MTR_7g114170 39.344 183 65 9 18 200 61 197 6.46e-22 92.8
MS.gene38649.t1 MTR_6g081150 38.462 156 54 7 79 232 40 155 3.36e-21 88.6
MS.gene38649.t1 MTR_5g044920 77.551 49 2 1 43 91 17 56 4.97e-17 75.1
MS.gene38649.t1 MTR_6g051405 25.767 163 114 3 19 181 96 251 6.18e-12 65.5
MS.gene38649.t1 MTR_4g026120 27.568 185 118 5 33 208 61 238 7.29e-12 65.1
MS.gene38649.t1 MTR_4g036435 27.568 185 118 5 33 208 61 238 7.29e-12 65.1
MS.gene38649.t1 MTR_3g067785 27.568 185 118 5 33 208 61 238 8.01e-12 65.1
MS.gene38649.t1 MTR_5g066280 27.568 185 118 5 33 208 61 238 8.80e-12 64.7
MS.gene38649.t1 MTR_2g022120 26.961 204 120 6 33 227 125 308 1.10e-11 64.7
MS.gene38649.t1 MTR_1g106885 26.961 204 120 6 33 227 122 305 1.17e-11 64.7
MS.gene38649.t1 MTR_5g077245 27.568 185 118 5 33 208 114 291 1.25e-11 64.7
MS.gene38649.t1 MTR_3g450670 25.309 162 114 3 20 181 93 247 1.61e-11 64.3
MS.gene38649.t1 MTR_1g471070 25.309 162 114 3 20 181 93 247 1.61e-11 64.3
MS.gene38649.t1 MTR_2g072860 28.814 118 82 2 64 181 68 183 2.07e-11 63.5
MS.gene38649.t1 MTR_6g092533 28.218 202 108 6 33 227 125 296 2.11e-11 63.9
MS.gene38649.t1 MTR_4g013220 27.027 185 119 5 33 208 61 238 2.29e-11 63.5
MS.gene38649.t1 MTR_7g461350 25.309 162 114 3 20 181 97 251 2.43e-11 63.9
MS.gene38649.t1 MTR_6g016670 25.309 162 114 3 20 181 97 251 2.43e-11 63.9
MS.gene38649.t1 MTR_3g464310 25.309 162 114 3 20 181 97 251 2.43e-11 63.9
MS.gene38649.t1 MTR_3g464170 27.966 118 83 2 64 181 136 251 2.95e-11 63.5
MS.gene38649.t1 MTR_1g100375 27.966 118 83 2 64 181 136 251 2.95e-11 63.5
MS.gene38649.t1 MTR_7g062380 26.380 163 111 4 48 208 18 173 5.32e-11 62.0
MS.gene38649.t1 MTR_7g083520 28.289 152 99 4 33 179 35 181 6.90e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38649.t1 AT5G41220 37.500 216 113 8 44 245 202 409 8.38e-32 123
MS.gene38649.t1 AT5G41220 37.500 216 113 8 44 245 210 417 8.89e-32 123
MS.gene38649.t1 AT5G41220 37.500 216 113 8 44 245 260 467 1.41e-31 123
MS.gene38649.t1 AT5G41240 37.297 185 103 6 60 232 272 455 2.21e-27 111
MS.gene38649.t1 AT3G47680 35.533 197 113 7 30 223 23 208 4.50e-25 101
MS.gene38649.t1 AT1G66235 29.412 187 116 5 61 232 7 192 2.53e-17 80.5

Find 49 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTCAAAGCATCAAATT+TGG 0.164119 6.2:-55871302 None:intergenic
CATTCTCTTGATCATTTAAT+TGG 0.185656 6.2:-55870616 None:intergenic
CTTTGATCATTCCCAACAAT+TGG 0.310977 6.2:-55870818 None:intergenic
TTCAGCTTCTGGAGCATATT+CGG 0.312536 6.2:+55871168 MS.gene38649:CDS
AGAACAAAGAATTCAGCTTC+TGG 0.340604 6.2:+55871157 MS.gene38649:CDS
GATGAACCGAAATGGCTTGC+AGG 0.369514 6.2:+55871109 MS.gene38649:CDS
TCTTTCAAAGCATCAAATTT+GGG 0.374468 6.2:-55871301 None:intergenic
AGAAAACCAGAGGCACTTAA+AGG 0.378046 6.2:+55870908 MS.gene38649:CDS
CATGCATTCTCAAGTGTGAA+TGG 0.388314 6.2:-55871073 None:intergenic
ACACAACCTGCAAGCCATTT+CGG 0.388495 6.2:-55871115 None:intergenic
CTCCGAGAGCGACAACATTT+CGG 0.391789 6.2:+55871015 MS.gene38649:CDS
ATTTCAAAGGATCCAATTGT+TGG 0.399370 6.2:+55870806 MS.gene38649:CDS
ATGAGAAGTTCATCCTCCTT+TGG 0.406782 6.2:-55870767 None:intergenic
GGTGGATTGTATTCGCTTGT+TGG 0.416563 6.2:-55871211 None:intergenic
GGCTTGGAAACAATTAATCT+TGG 0.423881 6.2:+55870665 MS.gene38649:CDS
AATTGTTTCCAAGCCATCTT+GGG 0.439909 6.2:-55870657 None:intergenic
CATCGACCTTTAAGTGCCTC+TGG 0.445875 6.2:-55870914 None:intergenic
TCCAAGCCATCTTGGGTGCA+AGG 0.447157 6.2:-55870650 None:intergenic
TTTCAAAGGATCCAATTGTT+GGG 0.450141 6.2:+55870807 MS.gene38649:CDS
ATGGCTTGCAGGTTGTGTAT+TGG 0.465781 6.2:+55871120 MS.gene38649:CDS
TAATTGTTTCCAAGCCATCT+TGG 0.472415 6.2:-55870658 None:intergenic
TATTGAGAGATGAACCGAAA+TGG 0.474221 6.2:+55871101 MS.gene38649:CDS
AGCCGAAATGTTGTCGCTCT+CGG 0.477888 6.2:-55871017 None:intergenic
TATTCGCTTGTTGGTGTTGG+TGG 0.480363 6.2:-55871202 None:intergenic
CCATCTTGGGTGCAAGGTTG+TGG 0.481149 6.2:-55870644 None:intergenic
ACAACGTCCAATCGGTCAAA+AGG 0.486049 6.2:+55871234 MS.gene38649:CDS
TCGGTCAAAAGGCGGCAAAA+AGG 0.487566 6.2:+55871245 MS.gene38649:CDS
ACCTTGCACCCAAGATGGCT+TGG 0.489398 6.2:+55870649 MS.gene38649:CDS
ATGAACTTCTCATTCAATCA+TGG 0.496152 6.2:+55870777 MS.gene38649:CDS
CATTTGCACTTCATGAGACA+TGG 0.508686 6.2:-55870579 None:intergenic
TTGTATTCGCTTGTTGGTGT+TGG 0.511913 6.2:-55871205 None:intergenic
AATGGAGATAGAGAGAAAGA+AGG 0.517552 6.2:+55871394 MS.gene38649:CDS
TGAATGGTTCACGTACATCT+TGG 0.533697 6.2:-55871057 None:intergenic
CTTGAAAATTCTCGTCGCGA+TGG 0.533833 6.2:-55870883 None:intergenic
AATCCACCACAACGTCCAAT+CGG 0.536837 6.2:+55871226 MS.gene38649:CDS
CATTCACACTTGAGAATGCA+TGG 0.543088 6.2:+55871074 MS.gene38649:CDS
ATCATGGCTCAATATTTCAA+AGG 0.547059 6.2:+55870793 MS.gene38649:CDS
CCACAACCTTGCACCCAAGA+TGG 0.549550 6.2:+55870644 MS.gene38649:CDS
ATTCGCTTGTTGGTGTTGGT+GGG 0.567081 6.2:-55871201 None:intergenic
GTTGTCGCTCTAAAGAAAAG+TGG 0.594037 6.2:+55870989 MS.gene38649:CDS
AATAAGATTTAAACCAAAGG+AGG 0.598325 6.2:+55870754 MS.gene38649:CDS
TGACCGATTGGACGTTGTGG+TGG 0.605293 6.2:-55871229 None:intergenic
CAGAGGCACTTAAAGGTCGA+TGG 0.621203 6.2:+55870915 MS.gene38649:CDS
GAAAATAAGATTTAAACCAA+AGG 0.637971 6.2:+55870751 MS.gene38649:CDS
GAAGGGAAAAGAAAAGCTTG+TGG 0.644203 6.2:+55871267 MS.gene38649:CDS
CGAAATGTTGTCGCTCTCGG+AGG 0.658068 6.2:-55871014 None:intergenic
ACGTCCAATCGGTCAAAAGG+CGG 0.661921 6.2:+55871237 MS.gene38649:CDS
ATTGTTGGGAATGATCAAAG+AGG 0.674803 6.2:+55870821 MS.gene38649:CDS
TGAAGAAGTCAGAGCTACGT+CGG 0.718655 6.2:+55870688 MS.gene38649:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAATAAGATTTAAACCAA+AGG + chr6.2:55870751-55870770 MS.gene38649:CDS 20.0%
!!! ACATCTATTTCAAAGTTTTT+TGG + chr6.2:55870953-55870972 MS.gene38649:CDS 20.0%
!!! CATCTATTTCAAAGTTTTTT+GGG + chr6.2:55870954-55870973 MS.gene38649:CDS 20.0%
! AATAAGATTTAAACCAAAGG+AGG + chr6.2:55870754-55870773 MS.gene38649:CDS 25.0%
! CATTCTCTTGATCATTTAAT+TGG - chr6.2:55870619-55870638 None:intergenic 25.0%
! GAAAAAAAGATTTCAACCAA+AGG + chr6.2:55870724-55870743 MS.gene38649:CDS 25.0%
!! ATCTTTCAAAGCATCAAATT+TGG - chr6.2:55871305-55871324 None:intergenic 25.0%
!! TCTTTCAAAGCATCAAATTT+GGG - chr6.2:55871304-55871323 None:intergenic 25.0%
!! TGAATTCTTTGTTCTTTTTG+CGG - chr6.2:55871152-55871171 None:intergenic 25.0%
AAAAAGATTTCAACCAAAGG+AGG + chr6.2:55870727-55870746 MS.gene38649:CDS 30.0%
ATCATGGCTCAATATTTCAA+AGG + chr6.2:55870793-55870812 MS.gene38649:CDS 30.0%
ATGAACTTCTCATTCAATCA+TGG + chr6.2:55870777-55870796 MS.gene38649:CDS 30.0%
ATTTCAAAGGATCCAATTGT+TGG + chr6.2:55870806-55870825 MS.gene38649:CDS 30.0%
TTTCAAAGGATCCAATTGTT+GGG + chr6.2:55870807-55870826 MS.gene38649:CDS 30.0%
! ATCAAAGAGGAGATAGTTTT+TGG + chr6.2:55870834-55870853 MS.gene38649:CDS 30.0%
!!! CGTTTTGAGAGTGAAAAAAA+TGG + chr6.2:55871376-55871395 MS.gene38649:CDS 30.0%
AATGGAGATAGAGAGAAAGA+AGG + chr6.2:55871394-55871413 MS.gene38649:CDS 35.0%
AATTGTTTCCAAGCCATCTT+GGG - chr6.2:55870660-55870679 None:intergenic 35.0%
AGAACAAAGAATTCAGCTTC+TGG + chr6.2:55871157-55871176 MS.gene38649:CDS 35.0%
ATTGTTGGGAATGATCAAAG+AGG + chr6.2:55870821-55870840 MS.gene38649:CDS 35.0%
CTTTGATCATTCCCAACAAT+TGG - chr6.2:55870821-55870840 None:intergenic 35.0%
GGCTTGGAAACAATTAATCT+TGG + chr6.2:55870665-55870684 MS.gene38649:CDS 35.0%
TAATTGTTTCCAAGCCATCT+TGG - chr6.2:55870661-55870680 None:intergenic 35.0%
TATTGAGAGATGAACCGAAA+TGG + chr6.2:55871101-55871120 MS.gene38649:CDS 35.0%
! TTCTTTGTTCTTTTTGCGGA+CGG - chr6.2:55871148-55871167 None:intergenic 35.0%
!! GATAGTTTTTGGAAGAGGAT+TGG + chr6.2:55870845-55870864 MS.gene38649:CDS 35.0%
!! TTTTCAAGAGAGAAAACCAG+AGG + chr6.2:55870898-55870917 MS.gene38649:CDS 35.0%
!!! AATCTTATTTTCGCCTCCTT+TGG - chr6.2:55870743-55870762 None:intergenic 35.0%
ATGAGAAGTTCATCCTCCTT+TGG - chr6.2:55870770-55870789 None:intergenic 40.0%
CATGCATTCTCAAGTGTGAA+TGG - chr6.2:55871076-55871095 None:intergenic 40.0%
CATTCACACTTGAGAATGCA+TGG + chr6.2:55871074-55871093 MS.gene38649:CDS 40.0%
GAAGGGAAAAGAAAAGCTTG+TGG + chr6.2:55871267-55871286 MS.gene38649:CDS 40.0%
TGAATGGTTCACGTACATCT+TGG - chr6.2:55871060-55871079 None:intergenic 40.0%
! TTGTATTCGCTTGTTGGTGT+TGG - chr6.2:55871208-55871227 None:intergenic 40.0%
!! AGAAAACCAGAGGCACTTAA+AGG + chr6.2:55870908-55870927 MS.gene38649:CDS 40.0%
!! GAGGAGATAGTTTTTGGAAG+AGG + chr6.2:55870840-55870859 MS.gene38649:CDS 40.0%
!! GTTGTCGCTCTAAAGAAAAG+TGG + chr6.2:55870989-55871008 MS.gene38649:CDS 40.0%
!! TTCAGCTTCTGGAGCATATT+CGG + chr6.2:55871168-55871187 MS.gene38649:CDS 40.0%
AATCCACCACAACGTCCAAT+CGG + chr6.2:55871226-55871245 MS.gene38649:CDS 45.0%
ACAACGTCCAATCGGTCAAA+AGG + chr6.2:55871234-55871253 MS.gene38649:CDS 45.0%
ACACAACCTGCAAGCCATTT+CGG - chr6.2:55871118-55871137 None:intergenic 45.0%
CAAAAGGCGGCAAAAAGGAA+GGG + chr6.2:55871250-55871269 MS.gene38649:CDS 45.0%
CTTGAAAATTCTCGTCGCGA+TGG - chr6.2:55870886-55870905 None:intergenic 45.0%
TCAAAAGGCGGCAAAAAGGA+AGG + chr6.2:55871249-55871268 MS.gene38649:CDS 45.0%
TGAAGAAGTCAGAGCTACGT+CGG + chr6.2:55870688-55870707 MS.gene38649:CDS 45.0%
! ATGGCTTGCAGGTTGTGTAT+TGG + chr6.2:55871120-55871139 MS.gene38649:CDS 45.0%
! TTTTGACCGATTGGACGTTG+TGG - chr6.2:55871235-55871254 None:intergenic 45.0%
!! ATTCGCTTGTTGGTGTTGGT+GGG - chr6.2:55871204-55871223 None:intergenic 45.0%
!! GGTGGATTGTATTCGCTTGT+TGG - chr6.2:55871214-55871233 None:intergenic 45.0%
!! TATTCGCTTGTTGGTGTTGG+TGG - chr6.2:55871205-55871224 None:intergenic 45.0%
ACGTCCAATCGGTCAAAAGG+CGG + chr6.2:55871237-55871256 MS.gene38649:CDS 50.0%
AGCCGAAATGTTGTCGCTCT+CGG - chr6.2:55871020-55871039 None:intergenic 50.0%
CATCGACCTTTAAGTGCCTC+TGG - chr6.2:55870917-55870936 None:intergenic 50.0%
CTCCGAGAGCGACAACATTT+CGG + chr6.2:55871015-55871034 MS.gene38649:CDS 50.0%
TCGGTCAAAAGGCGGCAAAA+AGG + chr6.2:55871245-55871264 MS.gene38649:CDS 50.0%
! GATGAACCGAAATGGCTTGC+AGG + chr6.2:55871109-55871128 MS.gene38649:CDS 50.0%
! TTTGCCGCCTTTTGACCGAT+TGG - chr6.2:55871244-55871263 None:intergenic 50.0%
!! CAGAGGCACTTAAAGGTCGA+TGG + chr6.2:55870915-55870934 MS.gene38649:CDS 50.0%
ACCTTGCACCCAAGATGGCT+TGG + chr6.2:55870649-55870668 MS.gene38649:CDS 55.0%
CCACAACCTTGCACCCAAGA+TGG + chr6.2:55870644-55870663 MS.gene38649:CDS 55.0%
CCATCTTGGGTGCAAGGTTG+TGG - chr6.2:55870647-55870666 None:intergenic 55.0%
CGAAATGTTGTCGCTCTCGG+AGG - chr6.2:55871017-55871036 None:intergenic 55.0%
TCCAAGCCATCTTGGGTGCA+AGG - chr6.2:55870653-55870672 None:intergenic 55.0%
TGACCGATTGGACGTTGTGG+TGG - chr6.2:55871232-55871251 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 55870581 55871420 55870581 ID=MS.gene38649
chr6.2 mRNA 55870581 55871420 55870581 ID=MS.gene38649.t1;Parent=MS.gene38649
chr6.2 exon 55870581 55871420 55870581 ID=MS.gene38649.t1.exon1;Parent=MS.gene38649.t1
chr6.2 CDS 55870581 55871420 55870581 ID=cds.MS.gene38649.t1;Parent=MS.gene38649.t1
Gene Sequence

>MS.gene38649

ATGTCTCATGAAGTGCAAATGAATAATAGTGATGTCCAATTAAATGATCAAGAGAATGAAACACCACAACCTTGCACCCAAGATGGCTTGGAAACAATTAATCTTGGTGAAGAAGTCAGAGCTACGTCGGTTGCGAATACTTCGAAAAAAAGATTTCAACCAAAGGAGGCGAAAATAAGATTTAAACCAAAGGAGGATGAACTTCTCATTCAATCATGGCTCAATATTTCAAAGGATCCAATTGTTGGGAATGATCAAAGAGGAGATAGTTTTTGGAAGAGGATTGGTGAAGCTTATAACAACCATCGCGACGAGAATTTTCAAGAGAGAAAACCAGAGGCACTTAAAGGTCGATGGCACAAAAAAATCAATACATCTATTTCAAAGTTTTTTGGGTGCTACAAAGATGTTGTCGCTCTAAAGAAAAGTGGTGCCTCCGAGAGCGACAACATTTCGGCTGCAAAAGATATTTATTACCAAGATGTACGTGAACCATTCACACTTGAGAATGCATGGAAATTATTGAGAGATGAACCGAAATGGCTTGCAGGTTGTGTATTGGAACCGTCCGCAAAAAGAACAAAGAATTCAGCTTCTGGAGCATATTCGGCATCTTCTAACCCACCAACACCAACAAGCGAATACAATCCACCACAACGTCCAATCGGTCAAAAGGCGGCAAAAAGGAAGGGAAAAGAAAAGCTTGTGGAAATTTCTACTCCCAAATTTGATGCTTTGAAAGATGATTTCAACAAAAAATTTGAATTAATGTCAGAGTTTGCACGTGATTATGCACGTTTTGAGAGTGAAAAAAATGGAGATAGAGAGAAAGAAGGTTGA
Protein sequence

>MS.gene38649.t1

MSHEVQMNNSDVQLNDQENETPQPCTQDGLETINLGEEVRATSVANTSKKRFQPKEAKIRFKPKEDELLIQSWLNISKDPIVGNDQRGDSFWKRIGEAYNNHRDENFQERKPEALKGRWHKKINTSISKFFGCYKDVVALKKSGASESDNISAAKDIYYQDVREPFTLENAWKLLRDEPKWLAGCVLEPSAKRTKNSASGAYSASSNPPTPTSEYNPPQRPIGQKAAKRKGKEKLVEISTPKFDALKDDFNKKFELMSEFARDYARFESEKNGDREKEG