AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene68403

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68403.t1 MTR_1g045470 91.489 188 16 0 1 188 1 188 1.66e-129 367
MS.gene68403.t1 MTR_7g116460 62.564 195 61 2 1 183 1 195 5.14e-82 242
MS.gene68403.t1 MTR_1g053575 65.263 190 47 5 1 187 1 174 3.00e-75 229
MS.gene68403.t1 MTR_1g019820 54.167 96 30 2 95 177 2 96 2.50e-23 92.8
MS.gene68403.t1 MTR_7g100990 34.194 155 83 6 13 157 19 164 3.58e-16 75.1
MS.gene68403.t1 MTR_7g005280 32.639 144 85 4 13 154 23 156 8.08e-16 73.6
MS.gene68403.t1 MTR_2g093810 30.726 179 101 8 13 180 22 188 1.17e-12 65.5
MS.gene68403.t1 MTR_4g089135 33.858 127 75 4 13 137 23 142 1.55e-11 62.4
MS.gene68403.t1 MTR_8g063550 30.065 153 93 8 11 157 12 156 1.89e-11 62.4
MS.gene68403.t1 MTR_8g063550 30.065 153 93 8 11 157 12 156 2.06e-11 62.0
MS.gene68403.t1 MTR_8g063550 30.065 153 93 8 11 157 12 156 2.45e-11 62.0
MS.gene68403.t1 MTR_8g093580 30.065 153 93 8 11 157 12 156 4.44e-11 61.2
MS.gene68403.t1 MTR_5g041940 30.719 153 89 6 13 157 11 154 6.13e-11 60.1
MS.gene68403.t1 MTR_4g101680 31.126 151 95 6 13 160 15 159 6.86e-11 60.5
MS.gene68403.t1 MTR_1g069805 27.374 179 115 7 13 188 18 184 7.23e-11 60.1
MS.gene68403.t1 MTR_7g097090 29.167 144 91 5 13 154 18 152 7.71e-11 60.1
MS.gene68403.t1 MTR_3g064580 32.258 155 89 7 13 160 14 159 8.69e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68403.t1 AT5G13180 33.793 145 83 5 13 154 22 156 1.51e-14 70.1
MS.gene68403.t1 AT5G62380 32.026 153 95 6 13 162 15 161 2.68e-13 67.4
MS.gene68403.t1 AT5G62380 32.026 153 95 6 13 162 15 161 2.68e-13 67.4
MS.gene68403.t1 AT3G10480 32.895 152 88 8 13 158 35 178 4.37e-13 67.0
MS.gene68403.t1 AT2G24430 30.201 149 93 6 13 157 24 165 1.80e-12 64.7
MS.gene68403.t1 AT2G24430 30.201 149 93 6 13 157 24 165 1.80e-12 64.7
MS.gene68403.t1 AT5G08790 32.275 189 105 8 3 181 5 180 1.93e-12 64.7
MS.gene68403.t1 AT3G10480 32.680 153 88 8 13 158 35 179 2.84e-12 64.7
MS.gene68403.t1 AT2G33480 31.507 146 84 6 13 154 23 156 9.83e-12 62.4
MS.gene68403.t1 AT3G15510 32.468 154 89 6 13 162 25 167 1.25e-11 62.8
MS.gene68403.t1 AT1G56010 27.957 186 107 11 13 188 27 195 1.68e-11 62.0
MS.gene68403.t1 AT3G17730 29.448 163 101 8 13 168 14 169 2.15e-11 61.2
MS.gene68403.t1 AT5G63790 32.919 161 89 6 3 154 48 198 2.38e-11 61.6
MS.gene68403.t1 AT5G63790 32.919 161 89 6 3 154 58 208 2.79e-11 61.6
MS.gene68403.t1 AT5G66300 29.936 157 101 6 13 166 20 170 4.44e-11 60.8
MS.gene68403.t1 AT3G10490 30.380 158 95 8 13 163 35 184 6.87e-11 59.7
MS.gene68403.t1 AT1G69490 32.258 155 84 7 13 157 17 160 9.61e-11 59.7

Find 42 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGGCAGATTTCTTCTTTA+AGG 0.216337 1.3:+27031010 None:intergenic
CAAAGAATCCATGGGAGATT+TGG 0.252767 1.3:-27031088 MS.gene68403:CDS
TCTGCATAGAACATAATTAT+TGG 0.253885 1.3:+27030699 None:intergenic
CCTCAACTCTTCTTCCAATA+AGG 0.285996 1.3:-27031222 MS.gene68403:CDS
AATGGGTGCGATAACCTTAT+TGG 0.291794 1.3:+27031208 None:intergenic
GCACCATTGGACTTGGTAGA+TGG 0.309802 1.3:-27030971 MS.gene68403:CDS
ACAGTGACTGCGGCAGGTTC+AGG 0.347861 1.3:+27030601 None:intergenic
TCAGGAACGACTGTCTTTCT+TGG 0.364568 1.3:+27030619 None:intergenic
AAAGAATCCATGGGAGATTT+GGG 0.379921 1.3:-27031087 MS.gene68403:CDS
TTCATTGATAAGCAATCCTT+TGG 0.384426 1.3:-27030811 MS.gene68403:intron
TTCAAGAATGGTGATATGAT+TGG 0.399692 1.3:+27031130 None:intergenic
TTGTAGAAGTTCATTATCAA+TGG 0.404907 1.3:+27031190 None:intergenic
GCAAGATCCATCCACCATCT+TGG 0.430936 1.3:+27030853 None:intergenic
CAAGATCCATCCACCATCTT+GGG 0.431083 1.3:+27030854 None:intergenic
ATTCTTGAATATGATTTGTT+CGG 0.434843 1.3:-27031116 MS.gene68403:CDS
TCAAGAATGGTGATATGATT+GGG 0.471621 1.3:+27031131 None:intergenic
TGGGAGATTTGGGAAGAGTT+CGG 0.477611 1.3:-27031077 MS.gene68403:CDS
CTTATTGGAAGAAGAGTTGA+GGG 0.477892 1.3:+27031223 None:intergenic
TGTAGAAGTTCATTATCAAT+GGG 0.485791 1.3:+27031191 None:intergenic
AATCTCCCATGGATTCTTTG+CGG 0.489258 1.3:+27031091 None:intergenic
CACCATTGGACTTGGTAGAT+GGG 0.507896 1.3:-27030970 MS.gene68403:CDS
GAACAAATCATATTCAAGAA+TGG 0.524428 1.3:+27031118 None:intergenic
AACTCTTCCCAAATCTCCCA+TGG 0.530624 1.3:+27031080 None:intergenic
TCGGCACCGCAAAGAATCCA+TGG 0.544845 1.3:-27031097 MS.gene68403:CDS
ACAGGTACAGTGACTGCGGC+AGG 0.546185 1.3:+27030595 None:intergenic
AAGAGTGACACTTCCCAAGA+TGG 0.562341 1.3:-27030867 MS.gene68403:CDS
GATTGCTTATCAATGAATTG+TGG 0.566276 1.3:+27030817 None:intergenic
TCACGCGTAGCTCGCACCAT+TGG 0.571107 1.3:-27030984 MS.gene68403:CDS
ACACTTCCCAAGATGGTGGA+TGG 0.575047 1.3:-27030860 MS.gene68403:CDS
GCGAGCTACGCGTGAGCTAG+TGG 0.575601 1.3:+27030992 None:intergenic
GTAGCTCGCACCATTGGACT+TGG 0.575679 1.3:-27030978 MS.gene68403:CDS
TGCTTATCAATGAATTGTGG+AGG 0.585480 1.3:+27030820 None:intergenic
CCTTATTGGAAGAAGAGTTG+AGG 0.596076 1.3:+27031222 None:intergenic
ATTGGACTTGGTAGATGGGA+AGG 0.601702 1.3:-27030966 MS.gene68403:CDS
AAAGACAAGAACCAAATCCT+CGG 0.605189 1.3:-27030915 MS.gene68403:CDS
TTCCCATCTACCAAGTCCAA+TGG 0.611326 1.3:+27030968 None:intergenic
ATGGTGATATGATTGGGCAA+AGG 0.612759 1.3:+27031137 None:intergenic
CGGCACCGCAAAGAATCCAT+GGG 0.621679 1.3:-27031096 MS.gene68403:CDS
AGATGGGAAGGTGAAGACGC+TGG 0.631377 1.3:-27030954 MS.gene68403:CDS
AGTGACACTTCCCAAGATGG+TGG 0.639769 1.3:-27030864 MS.gene68403:CDS
GGAACTTCCTACTCGTATCG+TGG 0.641732 1.3:-27031056 MS.gene68403:CDS
ACTTACAGGTACAGTGACTG+CGG 0.729652 1.3:+27030591 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCTTGAATATGATTTGTT+CGG - chr1.3:27030708-27030727 MS.gene68403:intron 20.0%
! GAACAAATCATATTCAAGAA+TGG + chr1.3:27030709-27030728 None:intergenic 25.0%
! TCTGCATAGAACATAATTAT+TGG + chr1.3:27031128-27031147 None:intergenic 25.0%
! TGTAGAAGTTCATTATCAAT+GGG + chr1.3:27030636-27030655 None:intergenic 25.0%
! TTGTAGAAGTTCATTATCAA+TGG + chr1.3:27030637-27030656 None:intergenic 25.0%
!! ATCTTGTGCAACAATATTTT+TGG + chr1.3:27031182-27031201 None:intergenic 25.0%
!!! TTTTGTATCTTGTTTTTTGC+AGG - chr1.3:27031102-27031121 MS.gene68403:CDS 25.0%
AAATCATGCACCAAATAACT+AGG + chr1.3:27031080-27031099 None:intergenic 30.0%
AATCATGCACCAAATAACTA+GGG + chr1.3:27031079-27031098 None:intergenic 30.0%
GATTGCTTATCAATGAATTG+TGG + chr1.3:27031010-27031029 None:intergenic 30.0%
TCAAGAATGGTGATATGATT+GGG + chr1.3:27030696-27030715 None:intergenic 30.0%
TTCAAGAATGGTGATATGAT+TGG + chr1.3:27030697-27030716 None:intergenic 30.0%
TTCATTGATAAGCAATCCTT+TGG - chr1.3:27031013-27031032 MS.gene68403:CDS 30.0%
!! TGTTGTGAATTTTGTTGTAG+AGG + chr1.3:27030665-27030684 None:intergenic 30.0%
!!! GCAACAATATTTTTGGTTAC+AGG + chr1.3:27031175-27031194 None:intergenic 30.0%
AAAGAATCCATGGGAGATTT+GGG - chr1.3:27030737-27030756 MS.gene68403:intron 35.0%
AAAGACAAGAACCAAATCCT+CGG - chr1.3:27030909-27030928 MS.gene68403:CDS 35.0%
AGTGGCAGATTTCTTCTTTA+AGG + chr1.3:27030817-27030836 None:intergenic 35.0%
CTTATTGGAAGAAGAGTTGA+GGG + chr1.3:27030604-27030623 None:intergenic 35.0%
GAATCAAACGCTACAGATAT+TGG + chr1.3:27031052-27031071 None:intergenic 35.0%
GATTCTTAGCCCTAGTTATT+TGG - chr1.3:27031067-27031086 MS.gene68403:CDS 35.0%
TGCTTATCAATGAATTGTGG+AGG + chr1.3:27031007-27031026 None:intergenic 35.0%
AATCTCCCATGGATTCTTTG+CGG + chr1.3:27030736-27030755 None:intergenic 40.0%
AATGGGTGCGATAACCTTAT+TGG + chr1.3:27030619-27030638 None:intergenic 40.0%
ATGGTGATATGATTGGGCAA+AGG + chr1.3:27030690-27030709 None:intergenic 40.0%
CAAAGAATCCATGGGAGATT+TGG - chr1.3:27030736-27030755 MS.gene68403:intron 40.0%
CCTCAACTCTTCTTCCAATA+AGG - chr1.3:27030602-27030621 MS.gene68403:CDS 40.0%
CCTTATTGGAAGAAGAGTTG+AGG + chr1.3:27030605-27030624 None:intergenic 40.0%
GCTACAGATATTGGAACCTA+GGG + chr1.3:27031043-27031062 None:intergenic 40.0%
!!! GAAAACGTTTTTTCATGCCG+AGG + chr1.3:27030929-27030948 None:intergenic 40.0%
!!! GTTTTTTCATGCCGAGGATT+TGG + chr1.3:27030923-27030942 None:intergenic 40.0%
AACTCTTCCCAAATCTCCCA+TGG + chr1.3:27030747-27030766 None:intergenic 45.0%
AAGAGTGACACTTCCCAAGA+TGG - chr1.3:27030957-27030976 MS.gene68403:CDS 45.0%
CAAGATCCATCCACCATCTT+GGG + chr1.3:27030973-27030992 None:intergenic 45.0%
CGCTACAGATATTGGAACCT+AGG + chr1.3:27031044-27031063 None:intergenic 45.0%
TCAGGAACGACTGTCTTTCT+TGG + chr1.3:27031208-27031227 None:intergenic 45.0%
TGGGAGATTTGGGAAGAGTT+CGG - chr1.3:27030747-27030766 MS.gene68403:intron 45.0%
TTCCCATCTACCAAGTCCAA+TGG + chr1.3:27030859-27030878 None:intergenic 45.0%
! ATTGGACTTGGTAGATGGGA+AGG - chr1.3:27030858-27030877 MS.gene68403:CDS 45.0%
! CACCATTGGACTTGGTAGAT+GGG - chr1.3:27030854-27030873 MS.gene68403:CDS 45.0%
! GTCTTTTCCACGATACGAGT+AGG + chr1.3:27030778-27030797 None:intergenic 45.0%
AGTGACACTTCCCAAGATGG+TGG - chr1.3:27030960-27030979 MS.gene68403:CDS 50.0%
GAAGAAGAGTTGAGGGCCAT+AGG + chr1.3:27030597-27030616 None:intergenic 50.0%
GCAAGATCCATCCACCATCT+TGG + chr1.3:27030974-27030993 None:intergenic 50.0%
GCAATCCTTTGGTAAGCCCT+AGG - chr1.3:27031024-27031043 MS.gene68403:CDS 50.0%
GGAACTTCCTACTCGTATCG+TGG - chr1.3:27030768-27030787 MS.gene68403:intron 50.0%
TGGAACCTAGGGCTTACCAA+AGG + chr1.3:27031032-27031051 None:intergenic 50.0%
! GCACCATTGGACTTGGTAGA+TGG - chr1.3:27030853-27030872 MS.gene68403:CDS 50.0%
!! ACACTTCCCAAGATGGTGGA+TGG - chr1.3:27030964-27030983 MS.gene68403:CDS 50.0%
AGATGGGAAGGTGAAGACGC+TGG - chr1.3:27030870-27030889 MS.gene68403:CDS 55.0%
CGGCACCGCAAAGAATCCAT+GGG - chr1.3:27030728-27030747 MS.gene68403:intron 55.0%
GTAGCTCGCACCATTGGACT+TGG - chr1.3:27030846-27030865 MS.gene68403:CDS 55.0%
TCGGCACCGCAAAGAATCCA+TGG - chr1.3:27030727-27030746 MS.gene68403:intron 55.0%
ACAGTGACTGCGGCAGGTTC+AGG + chr1.3:27031226-27031245 None:intergenic 60.0%
TCACGCGTAGCTCGCACCAT+TGG - chr1.3:27030840-27030859 MS.gene68403:CDS 60.0%
GCGAGCTACGCGTGAGCTAG+TGG + chr1.3:27030835-27030854 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 27030597 27031249 27030597 ID=MS.gene68403
chr1.3 mRNA 27030597 27031249 27030597 ID=MS.gene68403.t1;Parent=MS.gene68403
chr1.3 exon 27030812 27031249 27030812 ID=MS.gene68403.t1.exon1;Parent=MS.gene68403.t1
chr1.3 CDS 27030812 27031249 27030812 ID=cds.MS.gene68403.t1;Parent=MS.gene68403.t1
chr1.3 exon 27030597 27030722 27030597 ID=MS.gene68403.t1.exon2;Parent=MS.gene68403.t1
chr1.3 CDS 27030597 27030722 27030597 ID=cds.MS.gene68403.t1;Parent=MS.gene68403.t1
Gene Sequence

>MS.gene68403

ATGGCCCTCAACTCTTCTTCCAATAAGGTTATCGCACCCATTGATAATGAACTTCTACAACAATTCCTCTACAACAAAATTCACAACAAACCTTTGCCCAATCATATCACCATTCTTGAATATGATTTGTTCGGCACCGCAAAGAATCCATGGGAGATTTGGGAAGAGTTCGGAACTTCCTACTCGTATCGTGGAAAAGACTTATACTTCTTTACAACCTTAAAGAAGAAATCTGCCACTAGCTCACGCGTAGCTCGCACCATTGGACTTGGTAGATGGGAAGGTGAAGACGCTGGAAAAAATATATTGAGCAAAGACAAGAACCAAATCCTCGGCATGAAAAAACGTTTTCGCTTTGAGAAGAGTGACACTTCCCAAGATGGTGGATGGATCTTGCATGAATATAGCCTCCACAATTCATTGATAAGCAATCCTTTGGTAAGCCCTAGGTTCCAATATCTGTAGCGTTTGATTCTTAGCCCTAGTTATTTGGTGCATGATTTGATTTTGTATCTTGTTTTTTGCAGGCCAATAATTATGTTCTATGCAGATTTAGAAAGAATTGCACTCACTTACCTGTAACCAAAAATATTGTTGCACAAGATAAACCAAGAAAGACAGTCGTTCCTGAACCTGCCGCAGTCACTGTACCT
Protein sequence

>MS.gene68403.t1

MALNSSSNKVIAPIDNELLQQFLYNKIHNKPLPNHITILEYDLFGTAKNPWEIWEEFGTSYSYRGKDLYFFTTLKKKSATSSRVARTIGLGRWEGEDAGKNILSKDKNQILGMKKRFRFEKSDTSQDGGWILHEYSLHNSLISNPLANNYVLCRFRKNCTHLPVTKNIVAQDKPRKTVVPEPAAVTVP