AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00249

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00249.t1 MTR_2g435490 99.454 183 1 0 1 183 1 183 3.27e-138 383
MS.gene00249.t1 MTR_4g050762 58.599 157 60 2 20 174 16 169 6.94e-66 200
MS.gene00249.t1 MTR_2g012370 58.599 157 60 2 20 174 16 169 6.94e-66 200
MS.gene00249.t1 MTR_2g010600 56.962 158 65 2 9 164 6 162 7.89e-66 199
MS.gene00249.t1 MTR_2g010590 53.750 160 73 1 5 164 1 159 1.96e-62 190
MS.gene00249.t1 MTR_2g010580 52.201 159 72 3 8 164 8 164 1.90e-57 178
MS.gene00249.t1 MTR_2g010630 55.844 154 60 4 17 164 14 165 5.91e-57 177
MS.gene00249.t1 MTR_2g010650 54.118 170 67 7 1 164 1 165 6.60e-56 174
MS.gene00249.t1 MTR_2g010610 50.345 145 50 2 20 164 16 138 9.54e-50 157
MS.gene00249.t1 MTR_4g092540 46.541 159 81 4 7 164 4 159 1.28e-48 155
MS.gene00249.t1 MTR_4g128750 51.128 133 64 1 33 164 41 173 1.54e-46 150
MS.gene00249.t1 MTR_2g010700 46.341 164 77 5 10 164 7 168 3.77e-46 149
MS.gene00249.t1 MTR_2g010640 46.584 161 78 5 9 164 6 163 5.06e-44 144
MS.gene00249.t1 MTR_2g010690 44.444 162 81 5 9 164 6 164 9.13e-41 135
MS.gene00249.t1 MTR_2g010670 45.062 162 80 5 9 164 6 164 1.83e-39 132
MS.gene00249.t1 MTR_4g128770 44.928 138 70 3 32 164 70 206 1.77e-38 131
MS.gene00249.t1 MTR_8g078770 37.857 140 83 3 29 164 33 172 4.20e-33 116
MS.gene00249.t1 MTR_5g018770 38.571 140 80 4 31 164 46 185 2.29e-31 112
MS.gene00249.t1 MTR_1g067290 38.971 136 80 3 32 164 73 208 3.09e-31 112
MS.gene00249.t1 MTR_4g092515 51.136 88 42 1 9 95 9 96 3.54e-23 89.7
MS.gene00249.t1 MTR_5g018755 35.165 91 54 4 79 164 13 103 3.93e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00249.t1 AT2G14610 58.228 158 63 2 7 164 7 161 7.21e-69 207
MS.gene00249.t1 AT4G33720 57.325 157 65 2 8 164 9 163 8.73e-68 204
MS.gene00249.t1 AT2G14580 58.228 158 63 2 7 164 7 161 6.76e-67 202
MS.gene00249.t1 AT3G19690 51.829 164 73 3 3 164 2 161 5.44e-58 179
MS.gene00249.t1 AT4G33710 56.028 141 59 2 26 164 27 166 2.42e-53 167
MS.gene00249.t1 AT4G33730 51.923 156 72 3 10 164 19 172 1.02e-52 166
MS.gene00249.t1 AT5G26130 51.266 158 73 3 9 164 11 166 1.17e-52 166
MS.gene00249.t1 AT2G19990 54.074 135 62 0 30 164 42 176 1.75e-52 166
MS.gene00249.t1 AT4G25790 50.370 135 66 1 31 164 76 210 1.82e-49 159
MS.gene00249.t1 AT1G50060 50.649 154 74 2 12 164 9 161 1.11e-48 155
MS.gene00249.t1 AT5G57625 51.128 133 64 1 33 164 75 207 1.15e-47 154
MS.gene00249.t1 AT4G30320 41.212 165 92 3 1 164 1 161 5.79e-45 146
MS.gene00249.t1 AT3G09590 41.401 157 90 1 10 164 30 186 4.36e-44 145
MS.gene00249.t1 AT1G50050 48.387 155 77 3 12 164 9 162 5.78e-42 139
MS.gene00249.t1 AT1G01310 42.484 153 73 3 32 183 87 225 5.75e-41 138
MS.gene00249.t1 AT4G31470 45.185 135 72 2 31 164 52 185 9.16e-39 131
MS.gene00249.t1 AT1G50050 47.619 147 74 3 12 156 9 154 1.54e-37 129
MS.gene00249.t1 AT4G25780 43.478 138 72 4 32 164 54 190 1.92e-37 128
MS.gene00249.t1 AT5G02730 36.970 165 102 1 11 173 38 202 8.74e-37 127
MS.gene00249.t1 AT4G07820 42.446 139 77 3 26 164 25 160 3.96e-35 121
MS.gene00249.t1 AT5G66590 39.286 140 78 3 31 164 47 185 1.01e-30 110
MS.gene00249.t1 AT2G19970 41.045 134 68 5 30 154 35 166 1.49e-26 99.8
MS.gene00249.t1 AT2G19980 35.542 166 84 8 12 164 10 165 1.85e-22 89.0

Find 46 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTAGTCTTGTGGTGAGTTT+TGG 0.282878 2.1:+57364095 None:intergenic
GACATTATACTCAGGTTGTT+TGG 0.338106 2.1:-57363814 MS.gene00249:CDS
GAAGGAGATGTGAGATCATT+GGG 0.354867 2.1:+57364164 None:intergenic
ATTAAAAGCAAACTGCAAAA+TGG 0.363614 2.1:-57363978 MS.gene00249:CDS
GATCCACCTGGTAATTATAT+TGG 0.367528 2.1:-57363716 MS.gene00249:CDS
TTGTTTGGCGCGATTCGGTT+CGG 0.384031 2.1:-57363799 MS.gene00249:CDS
TTGGTGTTGGCCCAATATCT+TGG 0.387017 2.1:-57364042 MS.gene00249:CDS
TGTTTGGCGCGATTCGGTTC+GGG 0.388041 2.1:-57363798 MS.gene00249:CDS
TCAGGTTGTTTGGCGCGATT+CGG 0.394956 2.1:-57363804 MS.gene00249:CDS
ATCATAGTTACAACTAATAA+TGG 0.408982 2.1:+57363736 None:intergenic
GGAAGGAGATGTGAGATCAT+TGG 0.420420 2.1:+57364163 None:intergenic
AAGCTCAATGGCACTTCAAA+AGG 0.430809 2.1:+57363671 None:intergenic
TGGTGTTGGCCCAATATCTT+GGG 0.465713 2.1:-57364041 MS.gene00249:CDS
GTACACTCCAAGGGTCCATA+TGG 0.472690 2.1:-57363956 MS.gene00249:CDS
AACAAAGCACGCTCTGACGT+TGG 0.488151 2.1:-57364061 MS.gene00249:CDS
TCAAAAGGACTAATATCAAA+AGG 0.488505 2.1:+57363686 None:intergenic
AACAGTAATTCATGTGCTGT+TGG 0.492187 2.1:-57363848 MS.gene00249:CDS
CTCACATCTCCTTCCACTCA+TGG 0.495622 2.1:-57364155 MS.gene00249:CDS
CTACCATGGTTGAAGCTCAA+TGG 0.504277 2.1:+57363659 None:intergenic
CTGCAAAATGGTACACTCCA+AGG 0.542543 2.1:-57363966 MS.gene00249:CDS
GCACGCTCTGACGTTGGTGT+TGG 0.542698 2.1:-57364055 MS.gene00249:CDS
CTTTGACCAATATAATTACC+AGG 0.549756 2.1:+57363710 None:intergenic
ACAAGATAGCCATGAGTGGA+AGG 0.552738 2.1:+57364146 None:intergenic
TGGCGCGATTCGGTTCGGGT+TGG 0.564234 2.1:-57363794 MS.gene00249:CDS
TGGAGCAGTGGTGACATGAC+AGG 0.569134 2.1:-57363920 MS.gene00249:CDS
GGTTCGGGTTGGATGTGCTA+AGG 0.572627 2.1:-57363783 MS.gene00249:CDS
GCTGCTGTTACCATGTGGAT+TGG 0.573532 2.1:-57363893 MS.gene00249:CDS
CTGGTAATTATATTGGTCAA+AGG 0.577693 2.1:-57363709 MS.gene00249:CDS
GCTAAGGTAAAATGTAATGA+TGG 0.577870 2.1:-57363767 MS.gene00249:CDS
GTTTACATAGGTTTGTGCAT+AGG 0.587350 2.1:+57364003 None:intergenic
GAAAATTTAGCATGGAGCAG+TGG 0.597306 2.1:-57363932 MS.gene00249:CDS
TGCAAAATGGTACACTCCAA+GGG 0.616230 2.1:-57363965 MS.gene00249:CDS
CATATGGAGAAAATTTAGCA+TGG 0.617244 2.1:-57363940 MS.gene00249:CDS
ACTTGTCATCAAAACTACCA+TGG 0.632716 2.1:+57363645 None:intergenic
TGTGCTGTTGGTTATCAGTG+TGG 0.633545 2.1:-57363836 MS.gene00249:CDS
GTGCCATTGAGCTTCAACCA+TGG 0.637543 2.1:-57363662 MS.gene00249:CDS
GTGCTTTGTTGTGAATCTTG+AGG 0.640090 2.1:+57364074 None:intergenic
ATATGAGATTTGTGTTAGTG+TGG 0.642003 2.1:+57364120 None:intergenic
TGAATCTTGAGGTAGTCTTG+TGG 0.649652 2.1:+57364085 None:intergenic
TCAGTGTGGACATTATACTC+AGG 0.656601 2.1:-57363822 MS.gene00249:CDS
TTTCTTCTCTCCAATCCACA+TGG 0.658038 2.1:+57363883 None:intergenic
AGTTGTAACTATGATCCACC+TGG 0.667304 2.1:-57363728 MS.gene00249:CDS
GCTAACAAGATAGCCATGAG+TGG 0.671580 2.1:+57364142 None:intergenic
GAACAGCTGCTGTTACCATG+TGG 0.688628 2.1:-57363898 MS.gene00249:CDS
TGACCAATATAATTACCAGG+TGG 0.723440 2.1:+57363713 None:intergenic
AAGGAGATGTGAGATCATTG+GGG 0.724704 2.1:+57364165 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCATAGTTACAACTAATAA+TGG + chr2.1:57364082-57364101 None:intergenic 20.0%
!!! TGCTTTTAATTTGTTTACAT+AGG + chr2.1:57363827-57363846 None:intergenic 20.0%
! ATTAAAAGCAAACTGCAAAA+TGG - chr2.1:57363837-57363856 MS.gene00249:CDS 25.0%
! TCAAAAGGACTAATATCAAA+AGG + chr2.1:57364132-57364151 None:intergenic 25.0%
ATATGAGATTTGTGTTAGTG+TGG + chr2.1:57363698-57363717 None:intergenic 30.0%
CATATGGAGAAAATTTAGCA+TGG - chr2.1:57363875-57363894 MS.gene00249:CDS 30.0%
CTGGTAATTATATTGGTCAA+AGG - chr2.1:57364106-57364125 MS.gene00249:CDS 30.0%
CTTTGACCAATATAATTACC+AGG + chr2.1:57364108-57364127 None:intergenic 30.0%
GCTAAGGTAAAATGTAATGA+TGG - chr2.1:57364048-57364067 MS.gene00249:CDS 30.0%
! CATGCTAAATTTTCTCCATA+TGG + chr2.1:57363877-57363896 None:intergenic 30.0%
AACAGTAATTCATGTGCTGT+TGG - chr2.1:57363967-57363986 MS.gene00249:CDS 35.0%
ACTTGTCATCAAAACTACCA+TGG + chr2.1:57364173-57364192 None:intergenic 35.0%
GATCCACCTGGTAATTATAT+TGG - chr2.1:57364099-57364118 MS.gene00249:CDS 35.0%
GTTTACATAGGTTTGTGCAT+AGG + chr2.1:57363815-57363834 None:intergenic 35.0%
TGACCAATATAATTACCAGG+TGG + chr2.1:57364105-57364124 None:intergenic 35.0%
! ACTTTTGCATCCCAAGATAT+TGG + chr2.1:57363787-57363806 None:intergenic 35.0%
! CTTTTGCATCCCAAGATATT+GGG + chr2.1:57363786-57363805 None:intergenic 35.0%
! GACATTATACTCAGGTTGTT+TGG - chr2.1:57364001-57364020 MS.gene00249:CDS 35.0%
AAGCTCAATGGCACTTCAAA+AGG + chr2.1:57364147-57364166 None:intergenic 40.0%
AAGGAGATGTGAGATCATTG+GGG + chr2.1:57363653-57363672 None:intergenic 40.0%
AGTTGTAACTATGATCCACC+TGG - chr2.1:57364087-57364106 MS.gene00249:CDS 40.0%
GAAAATTTAGCATGGAGCAG+TGG - chr2.1:57363883-57363902 MS.gene00249:CDS 40.0%
GAAGGAGATGTGAGATCATT+GGG + chr2.1:57363654-57363673 None:intergenic 40.0%
TCAGTGTGGACATTATACTC+AGG - chr2.1:57363993-57364012 MS.gene00249:CDS 40.0%
TGCAAAATGGTACACTCCAA+GGG - chr2.1:57363850-57363869 MS.gene00249:CDS 40.0%
TTTCTTCTCTCCAATCCACA+TGG + chr2.1:57363935-57363954 None:intergenic 40.0%
! ATTTTCTCCATATGGACCCT+TGG + chr2.1:57363869-57363888 None:intergenic 40.0%
! GTGCTTTGTTGTGAATCTTG+AGG + chr2.1:57363744-57363763 None:intergenic 40.0%
! TGAATCTTGAGGTAGTCTTG+TGG + chr2.1:57363733-57363752 None:intergenic 40.0%
!!! GTAGTCTTGTGGTGAGTTTT+GGG + chr2.1:57363722-57363741 None:intergenic 40.0%
ACAAGATAGCCATGAGTGGA+AGG + chr2.1:57363672-57363691 None:intergenic 45.0%
CTACCATGGTTGAAGCTCAA+TGG + chr2.1:57364159-57364178 None:intergenic 45.0%
CTGCAAAATGGTACACTCCA+AGG - chr2.1:57363849-57363868 MS.gene00249:CDS 45.0%
GCTAACAAGATAGCCATGAG+TGG + chr2.1:57363676-57363695 None:intergenic 45.0%
GGAAGGAGATGTGAGATCAT+TGG + chr2.1:57363655-57363674 None:intergenic 45.0%
! TGTGCTGTTGGTTATCAGTG+TGG - chr2.1:57363979-57363998 MS.gene00249:CDS 45.0%
!! TGGTGTTGGCCCAATATCTT+GGG - chr2.1:57363774-57363793 MS.gene00249:CDS 45.0%
!! TTGGTGTTGGCCCAATATCT+TGG - chr2.1:57363773-57363792 MS.gene00249:CDS 45.0%
!!! GGTAGTCTTGTGGTGAGTTT+TGG + chr2.1:57363723-57363742 None:intergenic 45.0%
AACAAAGCACGCTCTGACGT+TGG - chr2.1:57363754-57363773 MS.gene00249:CDS 50.0%
CTCACATCTCCTTCCACTCA+TGG - chr2.1:57363660-57363679 MS.gene00249:CDS 50.0%
GAACAGCTGCTGTTACCATG+TGG - chr2.1:57363917-57363936 MS.gene00249:CDS 50.0%
GCTGCTGTTACCATGTGGAT+TGG - chr2.1:57363922-57363941 MS.gene00249:CDS 50.0%
GTACACTCCAAGGGTCCATA+TGG - chr2.1:57363859-57363878 MS.gene00249:CDS 50.0%
! GTGCCATTGAGCTTCAACCA+TGG - chr2.1:57364153-57364172 MS.gene00249:CDS 50.0%
! TCAGGTTGTTTGGCGCGATT+CGG - chr2.1:57364011-57364030 MS.gene00249:CDS 50.0%
!! TTGTTTGGCGCGATTCGGTT+CGG - chr2.1:57364016-57364035 MS.gene00249:CDS 50.0%
TGGAGCAGTGGTGACATGAC+AGG - chr2.1:57363895-57363914 MS.gene00249:CDS 55.0%
!! GGTTCGGGTTGGATGTGCTA+AGG - chr2.1:57364032-57364051 MS.gene00249:CDS 55.0%
!! TGTTTGGCGCGATTCGGTTC+GGG - chr2.1:57364017-57364036 MS.gene00249:CDS 55.0%
GCACGCTCTGACGTTGGTGT+TGG - chr2.1:57363760-57363779 MS.gene00249:CDS 60.0%
!! TGGCGCGATTCGGTTCGGGT+TGG - chr2.1:57364021-57364040 MS.gene00249:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 57363643 57364194 57363643 ID=MS.gene00249
chr2.1 mRNA 57363643 57364194 57363643 ID=MS.gene00249.t1;Parent=MS.gene00249
chr2.1 exon 57363643 57364194 57363643 ID=MS.gene00249.t1.exon1;Parent=MS.gene00249.t1
chr2.1 CDS 57363643 57364194 57363643 ID=cds.MS.gene00249.t1;Parent=MS.gene00249.t1
Gene Sequence

>MS.gene00249

ATGGGATCCCCAATGATCTCACATCTCCTTCCACTCATGGCTATCTTGTTAGCCACACTAACACAAATCTCATATGCCCAAAACTCACCACAAGACTACCTCAAGATTCACAACAAAGCACGCTCTGACGTTGGTGTTGGCCCAATATCTTGGGATGCAAAAGTTGCTTCCTATGCACAAACCTATGTAAACAAATTAAAAGCAAACTGCAAAATGGTACACTCCAAGGGTCCATATGGAGAAAATTTAGCATGGAGCAGTGGTGACATGACAGGAACAGCTGCTGTTACCATGTGGATTGGAGAGAAGAAATACTATAATTACAACAGTAATTCATGTGCTGTTGGTTATCAGTGTGGACATTATACTCAGGTTGTTTGGCGCGATTCGGTTCGGGTTGGATGTGCTAAGGTAAAATGTAATGATGGACGTAGCACCATTATTAGTTGTAACTATGATCCACCTGGTAATTATATTGGTCAAAGGCCTTTTGATATTAGTCCTTTTGAAGTGCCATTGAGCTTCAACCATGGTAGTTTTGATGACAAGTAA
Protein sequence

>MS.gene00249.t1

MGSPMISHLLPLMAILLATLTQISYAQNSPQDYLKIHNKARSDVGVGPISWDAKVASYAQTYVNKLKANCKMVHSKGPYGENLAWSSGDMTGTAAVTMWIGEKKYYNYNSNSCAVGYQCGHYTQVVWRDSVRVGCAKVKCNDGRSTIISCNYDPPGNYIGQRPFDISPFEVPLSFNHGSFDDK