AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47253

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47253.t1 MTR_6g027290 88.636 176 20 0 1 176 1 176 4.17e-116 327
MS.gene47253.t1 MTR_2g030570 43.750 176 98 1 1 176 1 175 3.16e-44 155
MS.gene47253.t1 MTR_2g030600 44.318 176 95 2 1 176 1 173 2.85e-42 149
MS.gene47253.t1 MTR_6g477820 35.882 170 100 3 1 164 1 167 1.10e-27 108
MS.gene47253.t1 MTR_4g047800 33.094 139 92 1 26 164 61 198 3.97e-23 95.5
MS.gene47253.t1 MTR_2g088470 30.189 159 107 2 9 164 48 205 3.28e-22 93.2
MS.gene47253.t1 MTR_0198s0030 35.000 160 92 4 11 164 40 193 9.14e-20 85.9
MS.gene47253.t1 MTR_7g076080 29.885 174 114 3 4 174 74 242 1.20e-19 85.9
MS.gene47253.t1 MTR_1g101280 31.724 145 90 2 24 164 55 194 3.37e-18 81.6
MS.gene47253.t1 MTR_7g027265 35.849 106 67 1 40 145 32 136 2.28e-17 74.7
MS.gene47253.t1 MTR_5g046040 37.931 116 69 2 50 164 59 172 5.23e-17 77.4
MS.gene47253.t1 MTR_8g432540 27.950 161 108 2 11 164 94 253 9.23e-17 77.4
MS.gene47253.t1 MTR_5g029320 31.858 113 77 0 49 161 113 225 1.06e-16 77.0
MS.gene47253.t1 MTR_7g427700 31.746 126 74 1 48 173 39 152 1.94e-15 73.2
MS.gene47253.t1 MTR_2g101720 29.710 138 90 2 29 162 143 277 2.07e-15 73.6
MS.gene47253.t1 MTR_7g427710 32.479 117 67 1 40 156 31 135 2.17e-15 73.6
MS.gene47253.t1 MTR_2g030720 33.333 129 73 3 21 149 14 129 4.79e-14 66.6
MS.gene47253.t1 MTR_5g005600 34.545 110 68 3 40 148 60 166 3.63e-13 67.0
MS.gene47253.t1 MTR_2g030660 32.110 109 65 2 40 147 30 130 5.33e-13 66.6
MS.gene47253.t1 MTR_2g030700 27.692 130 84 2 21 150 14 133 1.75e-11 59.7
MS.gene47253.t1 MTR_2g030680 27.692 130 84 2 21 150 14 133 7.83e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47253.t1 AT1G73360 39.860 143 83 2 23 164 30 170 9.09e-30 114
MS.gene47253.t1 AT1G17920 41.880 117 65 2 49 164 45 159 9.42e-25 100
MS.gene47253.t1 AT1G17920 41.880 117 65 2 49 164 45 159 9.42e-25 100
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.18e-22 94.4
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 1.20e-22 94.4
MS.gene47253.t1 AT4G21750 32.026 153 99 2 13 161 46 197 2.28e-21 90.9
MS.gene47253.t1 AT4G21750 32.026 153 99 2 13 161 46 197 2.28e-21 90.9
MS.gene47253.t1 AT4G21750 32.026 153 99 2 13 161 46 197 2.28e-21 90.9
MS.gene47253.t1 AT4G21750 32.026 153 99 2 13 161 46 197 2.28e-21 90.9
MS.gene47253.t1 AT1G05230 32.051 156 102 2 9 164 51 202 8.97e-21 89.0
MS.gene47253.t1 AT3G03260 36.364 121 77 0 40 160 38 158 2.45e-20 87.8
MS.gene47253.t1 AT3G03260 31.818 154 105 0 7 160 5 158 2.61e-20 87.4
MS.gene47253.t1 AT4G04890 32.450 151 100 2 11 161 49 197 3.75e-20 87.0
MS.gene47253.t1 AT4G04890 32.450 151 100 2 11 161 49 197 3.75e-20 87.0
MS.gene47253.t1 AT3G61150 30.137 146 100 2 11 156 97 240 1.89e-17 79.3
MS.gene47253.t1 AT5G46880 27.273 154 96 3 12 156 93 239 8.39e-17 77.4
MS.gene47253.t1 AT5G46880 27.273 154 96 3 12 156 93 239 8.39e-17 77.4
MS.gene47253.t1 AT5G46880 27.273 154 96 3 12 156 93 239 8.39e-17 77.4
MS.gene47253.t1 AT5G17320 31.915 141 96 0 16 156 17 157 9.47e-17 77.4
MS.gene47253.t1 AT5G52170 33.582 134 88 1 29 162 61 193 1.99e-16 76.6
MS.gene47253.t1 AT5G52170 33.582 134 88 1 29 162 61 193 2.10e-16 76.3
MS.gene47253.t1 AT5G52170 33.582 134 88 1 29 162 61 193 2.10e-16 76.3
MS.gene47253.t1 AT4G00730 28.966 145 93 3 17 156 125 264 3.60e-16 75.9
MS.gene47253.t1 AT4G00730 28.966 145 93 3 17 156 125 264 6.65e-16 74.7
MS.gene47253.t1 AT1G79840 29.371 143 89 2 15 155 120 252 7.35e-16 74.7
MS.gene47253.t1 AT1G79840 29.371 143 89 2 15 155 33 165 8.40e-16 74.7
MS.gene47253.t1 AT1G79840 29.371 143 89 2 15 155 33 165 8.40e-16 74.7
MS.gene47253.t1 AT1G79840 29.371 143 89 2 15 155 91 223 1.08e-15 74.3
MS.gene47253.t1 AT1G34650 32.331 133 89 1 33 165 24 155 1.89e-15 73.6
MS.gene47253.t1 AT1G79840 28.859 149 89 3 9 155 90 223 2.58e-14 70.1
MS.gene47253.t1 AT1G79840 28.859 149 89 3 9 155 90 223 2.61e-14 70.5
MS.gene47253.t1 AT4G17710 27.559 127 79 1 28 154 91 204 6.21e-14 69.3
MS.gene47253.t1 AT2G32370 26.797 153 103 2 10 158 53 200 7.24e-11 60.5

Find 34 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATTTCGTTGGGCTTCATT+TGG 0.279004 6.3:+18636167 None:intergenic
GAACCAAGATTTGATTTGTT+TGG 0.287062 6.3:+18636118 None:intergenic
AACCAAGATTTGATTTGTTT+GGG 0.304941 6.3:+18636119 None:intergenic
ATGGGAGGCGTCGGTGGGTC+TGG 0.334236 6.3:-18636738 MS.gene47253:CDS
AGCCCAAACAAATCAAATCT+TGG 0.386306 6.3:-18636121 MS.gene47253:CDS
GATTTCGTTGGGCTTCATTT+GGG 0.397275 6.3:+18636168 None:intergenic
CTTAGCTAATTGATTTCGTT+GGG 0.409743 6.3:+18636157 None:intergenic
ATCAATTAGCTAAGGAGGTT+GGG 0.412482 6.3:-18636148 MS.gene47253:CDS
AATCTTGGTTCGATAATAAG+AGG 0.416511 6.3:-18636106 MS.gene47253:CDS
CCTTAGCTAATTGATTTCGT+TGG 0.420498 6.3:+18636156 None:intergenic
AACGTTCATGCTCATGCATT+GGG 0.431887 6.3:+18635836 None:intergenic
TCTGTTCGTACTTTGCTAGC+AGG 0.432332 6.3:+18635642 None:intergenic
CTGTTCGTACTTTGCTAGCA+GGG 0.445221 6.3:+18635643 None:intergenic
TATTCGATGGGAGGCGTCGG+TGG 0.460383 6.3:-18636744 MS.gene47253:CDS
ATCTGAGACTGAGTTATCAA+TGG 0.465187 6.3:+18636707 None:intergenic
AATCAATTAGCTAAGGAGGT+TGG 0.482913 6.3:-18636149 MS.gene47253:CDS
TTTGAATAAAGATTCATGGC+AGG 0.493133 6.3:-18636200 MS.gene47253:intron
AAACGTTCATGCTCATGCAT+TGG 0.496436 6.3:+18635835 None:intergenic
TTTCATGCAAAAGATGAGAA+TGG 0.506914 6.3:-18635815 MS.gene47253:CDS
TTGAATAAAGATTCATGGCA+GGG 0.511003 6.3:-18636199 MS.gene47253:intron
CCACTAAAACCTTTGTATTG+TGG 0.519309 6.3:+18636672 None:intergenic
ATTCGATGGGAGGCGTCGGT+GGG 0.547865 6.3:-18636743 MS.gene47253:CDS
TGCTCATGCATTGGGAAAGG+AGG 0.551665 6.3:+18635844 None:intergenic
TAATAAGAGGGCTACACTGA+AGG 0.581057 6.3:-18636093 MS.gene47253:intron
ACGAAATCAATTAGCTAAGG+AGG 0.581875 6.3:-18636153 MS.gene47253:CDS
GAATGACATGCTGAAAGAGA+AGG 0.584443 6.3:-18635791 MS.gene47253:intron
TCATGCTCATGCATTGGGAA+AGG 0.590182 6.3:+18635841 None:intergenic
GTTTATTCGATGGGAGGCGT+CGG 0.591995 6.3:-18636747 MS.gene47253:CDS
CCAACGAAATCAATTAGCTA+AGG 0.600046 6.3:-18636156 MS.gene47253:CDS
GCTAGCAAAGTACGAACAGA+AGG 0.603167 6.3:-18635639 MS.gene47253:CDS
AAAATGGTTTATTCGATGGG+AGG 0.608024 6.3:-18636753 MS.gene47253:CDS
ATCTTGGTTCGATAATAAGA+GGG 0.641146 6.3:-18636105 MS.gene47253:CDS
TTCGTACTTTGCTAGCAGGG+TGG 0.642156 6.3:+18635646 None:intergenic
CAAAGCAGACCACAATACAA+AGG 0.659814 6.3:-18636681 MS.gene47253:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATACTTAGTTATTTTTT+AGG + chr6.3:18636627-18636646 None:intergenic 10.0%
!!! TAATACTTAGTTATTTTTTA+GGG + chr6.3:18636626-18636645 None:intergenic 10.0%
!!! TCTTTTATTACTTGATTTAT+TGG - chr6.3:18635801-18635820 MS.gene47253:CDS 15.0%
!!! TTATTTTGAATAAAGATTCA+TGG - chr6.3:18636132-18636151 MS.gene47253:CDS 15.0%
!!! ACTTGATTTATTGGTTTTAT+GGG - chr6.3:18635810-18635829 MS.gene47253:CDS 20.0%
!!! CAATCATATTTTTTTTTTGG+TGG - chr6.3:18636076-18636095 MS.gene47253:intron 20.0%
!!! GCTCAATCATATTTTTTTTT+TGG - chr6.3:18636073-18636092 MS.gene47253:intron 20.0%
!!! TACTTGATTTATTGGTTTTA+TGG - chr6.3:18635809-18635828 MS.gene47253:CDS 20.0%
!!! TATGTGTTGTTTCAATTTAT+TGG - chr6.3:18635777-18635796 MS.gene47253:intron 20.0%
! ATTGAAACAACACATACAAA+TGG + chr6.3:18635773-18635792 None:intergenic 25.0%
! CTACAAAATTGATGTATGTA+TGG + chr6.3:18635837-18635856 None:intergenic 25.0%
! GCTTAAGTAACAATAAATCA+TGG + chr6.3:18636055-18636074 None:intergenic 25.0%
!! CATACATACATCAATTTTGT+AGG - chr6.3:18635835-18635854 MS.gene47253:CDS 25.0%
!!! AACCAAGATTTGATTTGTTT+GGG + chr6.3:18636220-18636239 None:intergenic 25.0%
!!! TATATTTTAAACCACCAAAC+TGG - chr6.3:18635877-18635896 MS.gene47253:CDS 25.0%
!!! TTTATTTTTTCAGATCGAGA+AGG - chr6.3:18636664-18636683 MS.gene47253:CDS 25.0%
ACAATAAATCATGGCTTCAA+AGG + chr6.3:18636046-18636065 None:intergenic 30.0%
CAATAAATCATGGCTTCAAA+GGG + chr6.3:18636045-18636064 None:intergenic 30.0%
TTGAATAAAGATTCATGGCA+GGG - chr6.3:18636137-18636156 MS.gene47253:CDS 30.0%
TTTCATGCAAAAGATGAGAA+TGG - chr6.3:18636521-18636540 MS.gene47253:intron 30.0%
TTTGAATAAAGATTCATGGC+AGG - chr6.3:18636136-18636155 MS.gene47253:CDS 30.0%
! AATCTTGGTTCGATAATAAG+AGG - chr6.3:18636230-18636249 MS.gene47253:intron 30.0%
! ATCTTGGTTCGATAATAAGA+GGG - chr6.3:18636231-18636250 MS.gene47253:intron 30.0%
! CTTAGCTAATTGATTTCGTT+GGG + chr6.3:18636182-18636201 None:intergenic 30.0%
!! GAACCAAGATTTGATTTGTT+TGG + chr6.3:18636221-18636240 None:intergenic 30.0%
!!! ACTTTTGAAGTATACTTCTC+TGG + chr6.3:18635693-18635712 None:intergenic 30.0%
AATCAATTAGCTAAGGAGGT+TGG - chr6.3:18636187-18636206 MS.gene47253:CDS 35.0%
ACGAAATCAATTAGCTAAGG+AGG - chr6.3:18636183-18636202 MS.gene47253:CDS 35.0%
AGCCCAAACAAATCAAATCT+TGG - chr6.3:18636215-18636234 MS.gene47253:intron 35.0%
ATCAATTAGCTAAGGAGGTT+GGG - chr6.3:18636188-18636207 MS.gene47253:CDS 35.0%
CCAACGAAATCAATTAGCTA+AGG - chr6.3:18636180-18636199 MS.gene47253:CDS 35.0%
CCACTAAAACCTTTGTATTG+TGG + chr6.3:18635667-18635686 None:intergenic 35.0%
! ATCTGAGACTGAGTTATCAA+TGG + chr6.3:18635632-18635651 None:intergenic 35.0%
! ATGACATTTTGCGAAAGTTG+TGG - chr6.3:18636465-18636484 MS.gene47253:intron 35.0%
! CCTTAGCTAATTGATTTCGT+TGG + chr6.3:18636183-18636202 None:intergenic 35.0%
! TGACATTTTGCGAAAGTTGT+GGG - chr6.3:18636466-18636485 MS.gene47253:intron 35.0%
! TGTTATCGATTAGACCAGTT+TGG + chr6.3:18635894-18635913 None:intergenic 35.0%
!! CCACAATACAAAGGTTTTAG+TGG - chr6.3:18635664-18635683 MS.gene47253:intron 35.0%
AAACGTTCATGCTCATGCAT+TGG + chr6.3:18636504-18636523 None:intergenic 40.0%
AAATCATGGCTTCAAAGGGA+TGG + chr6.3:18636041-18636060 None:intergenic 40.0%
AACGTTCATGCTCATGCATT+GGG + chr6.3:18636503-18636522 None:intergenic 40.0%
CAAAGCAGACCACAATACAA+AGG - chr6.3:18635655-18635674 MS.gene47253:CDS 40.0%
GAATGACATGCTGAAAGAGA+AGG - chr6.3:18636545-18636564 MS.gene47253:intron 40.0%
GATTTCGTTGGGCTTCATTT+GGG + chr6.3:18636171-18636190 None:intergenic 40.0%
TAATAAGAGGGCTACACTGA+AGG - chr6.3:18636243-18636262 MS.gene47253:intron 40.0%
TGATTTCGTTGGGCTTCATT+TGG + chr6.3:18636172-18636191 None:intergenic 40.0%
! ACATTTTGCGAAAGTTGTGG+GGG - chr6.3:18636468-18636487 MS.gene47253:intron 40.0%
! GACATTTTGCGAAAGTTGTG+GGG - chr6.3:18636467-18636486 MS.gene47253:intron 40.0%
! TATCGATTAGACCAGTTTGG+TGG + chr6.3:18635891-18635910 None:intergenic 40.0%
CTGTTCGTACTTTGCTAGCA+GGG + chr6.3:18636696-18636715 None:intergenic 45.0%
GCTAGCAAAGTACGAACAGA+AGG - chr6.3:18636697-18636716 MS.gene47253:CDS 45.0%
TCATGCTCATGCATTGGGAA+AGG + chr6.3:18636498-18636517 None:intergenic 45.0%
TCTGTTCGTACTTTGCTAGC+AGG + chr6.3:18636697-18636716 None:intergenic 45.0%
TGCTCATGCATTGGGAAAGG+AGG + chr6.3:18636495-18636514 None:intergenic 50.0%
TTCGTACTTTGCTAGCAGGG+TGG + chr6.3:18636693-18636712 None:intergenic 50.0%
! GTTTATTCGATGGGAGGCGT+CGG - chr6.3:18635589-18635608 MS.gene47253:CDS 50.0%
!! ATTCGATGGGAGGCGTCGGT+GGG - chr6.3:18635593-18635612 MS.gene47253:CDS 60.0%
!! TATTCGATGGGAGGCGTCGG+TGG - chr6.3:18635592-18635611 MS.gene47253:CDS 60.0%
!! ATGGGAGGCGTCGGTGGGTC+TGG - chr6.3:18635598-18635617 MS.gene47253:CDS 70.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 18635586 18636772 18635586 ID=MS.gene47253
chr6.3 mRNA 18635586 18636772 18635586 ID=MS.gene47253.t1;Parent=MS.gene47253
chr6.3 exon 18636648 18636772 18636648 ID=MS.gene47253.t1.exon1;Parent=MS.gene47253.t1
chr6.3 CDS 18636648 18636772 18636648 ID=cds.MS.gene47253.t1;Parent=MS.gene47253.t1
chr6.3 exon 18636094 18636211 18636094 ID=MS.gene47253.t1.exon2;Parent=MS.gene47253.t1
chr6.3 CDS 18636094 18636211 18636094 ID=cds.MS.gene47253.t1;Parent=MS.gene47253.t1
chr6.3 exon 18635792 18635983 18635792 ID=MS.gene47253.t1.exon3;Parent=MS.gene47253.t1
chr6.3 CDS 18635792 18635983 18635792 ID=cds.MS.gene47253.t1;Parent=MS.gene47253.t1
chr6.3 exon 18635586 18635681 18635586 ID=MS.gene47253.t1.exon4;Parent=MS.gene47253.t1
chr6.3 CDS 18635586 18635681 18635586 ID=cds.MS.gene47253.t1;Parent=MS.gene47253.t1
Gene Sequence

>MS.gene47253

ATGGTTTATTCGATGGGAGGCGTCGGTGGGTCTGGAGATAAAGCCATTGATAACTCAGTCTCAGATAATCAAAGCAGACCACAATACAAAGGTTTTAGTGGTTACCAGAGAAGTATACTTCAAAAGTAAGATGAACTTTTTTTTTTTGTTAAGAATATTTTCTTTTCATTTTTATTATTTGTAACCATTTGTATGTGTTGTTTCAATTTATTGGTTCTTTTATTACTTGATTTATTGGTTTTATGGGACCATACATACATCAATTTTGTAGGAAAGCATACAAAAAATGTTTATATTTTAAACCACCAAACTGGTCTAATCGATAACAGACACACATGATTACAAAACTTTCTGTGTCTAATTAAGTTTTTTTAGATGTTATGTTTAATTAAGTTATACACATATCTTTTCATTGATTATGAATCAAGTATCTTAGTTTTTGTTTGTTTTGACCATCCCTTTGAAGCCATGATTTATTGTTACTTAAGCTCAATCATATTTTTTTTTTGGTGGTGTTAAGCTCAATCATTTGATTACTTAATTAATTTATTTTGAATAAAGATTCATGGCAGGGAACTCTAACCCAAATGAAGCCCAACGAAATCAATTAGCTAAGGAGGTTGGGCTTGAGCCCAAACAAATCAAATCTTGGTTCGATAATAAGAGGGCTACACTGAAGGTAATTGTCTTCAAAATATCACTGCTCTTTTTCTTTTCACTAACTCATATCACATGCTTTCATATAACTAGTACTAATTATTTATATATATTTTTTACATTATTATTAAGAAAAAACACATGAGAGAAGATAACAAAGCTCTTCATGCTGCAAGAAAAGAGCTCATTACTGAAAATATCGTTGTGAAAAAGATATTCAAGATGACATTTTGCGAAAGTTGTGGGGGTCCTCCTTTCCCAATGCATGAGCATGAACGTTTCATGCAAAAGATGAGAATGGAGAATGACATGCTGAAAGAGAAGGTTAGTGAATATTTTAATTTTATCAAATATCGATGATAATTTTTTAATTAAATATTCCCTAAAAAATAACTAAGTATTATTTATTCATGAATCAAGTTTTATTTTTTCAGATCGAGAAGGTGTCCACCCTGCTAGCAAAGTACGAACAGAAGGAAATCTCACAGTTTGATTTTGAATACACTTTTGCTCGTTTAAATGCATTTTGA
Protein sequence

>MS.gene47253.t1

MVYSMGGVGGSGDKAIDNSVSDNQSRPQYKGFSGYQRSILQKFMAGNSNPNEAQRNQLAKEVGLEPKQIKSWFDNKRATLKKKHMREDNKALHAARKELITENIVVKKIFKMTFCESCGGPPFPMHEHERFMQKMRMENDMLKEKIEKVSTLLAKYEQKEISQFDFEYTFARLNAF