AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010504

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010504.t1 MTR_5g020230 90.377 239 12 5 1 232 1 235 1.42e-147 410
MS.gene010504.t1 MTR_8g077510 55.556 243 82 8 1 232 1 228 4.16e-59 186
MS.gene010504.t1 MTR_1g016170 38.889 90 52 2 89 177 155 242 3.17e-14 70.9
MS.gene010504.t1 MTR_7g112330 56.250 48 19 1 119 166 18 63 3.56e-13 64.7
MS.gene010504.t1 MTR_2g094600 40.000 60 36 0 96 155 189 248 1.07e-12 66.6
MS.gene010504.t1 MTR_4g121110 67.568 37 12 0 123 159 30 66 1.37e-12 63.5
MS.gene010504.t1 MTR_4g126350 69.048 42 12 1 111 152 175 215 1.77e-12 65.9
MS.gene010504.t1 MTR_4g058910 32.143 84 52 1 72 155 268 346 1.79e-11 63.2
MS.gene010504.t1 MTR_1g116010 62.857 35 13 0 121 155 162 196 2.43e-11 62.0
MS.gene010504.t1 MTR_1g094930 62.162 37 14 0 119 155 143 179 4.52e-11 61.2
MS.gene010504.t1 MTR_5g021340 38.571 70 41 1 88 155 263 332 7.46e-11 61.6
MS.gene010504.t1 MTR_1g094930 62.162 37 14 0 119 155 238 274 8.30e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010504.t1 AT3G50870 41.281 281 104 10 5 232 9 281 1.61e-48 161
MS.gene010504.t1 AT4G36620 43.891 221 83 10 27 232 3 197 6.99e-39 134
MS.gene010504.t1 AT2G18380 41.304 230 93 8 19 230 2 207 1.64e-36 128
MS.gene010504.t1 AT5G56860 49.462 93 33 3 64 156 185 263 5.65e-17 79.3
MS.gene010504.t1 AT5G49300 53.731 67 27 2 98 162 11 75 4.41e-15 70.1
MS.gene010504.t1 AT4G26150 63.830 47 16 1 107 153 184 229 1.14e-13 69.7
MS.gene010504.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene010504.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene010504.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene010504.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene010504.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene010504.t1 AT5G26930 67.568 37 12 0 123 159 26 62 4.32e-12 61.6
MS.gene010504.t1 AT3G06740 71.429 35 10 0 125 159 43 77 7.06e-12 61.6
MS.gene010504.t1 AT3G20750 70.588 34 10 0 127 160 163 196 1.63e-11 62.0
MS.gene010504.t1 AT2G45050 36.585 82 45 2 74 155 137 211 6.99e-11 60.8
MS.gene010504.t1 AT4G34680 50.980 51 23 1 107 155 162 212 7.93e-11 60.8
MS.gene010504.t1 AT4G34680 50.980 51 23 1 107 155 162 212 7.93e-11 60.8

Find 48 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAATCATGATTCTGAAAA+TGG 0.202815 5.2:+11595584 MS.gene010504:CDS
GGAGTGAAACAATAGGTTTC+AGG 0.229794 5.2:-11594961 None:intergenic
GTTGGAGTTGTTGTTATTAT+TGG 0.243633 5.2:-11595175 None:intergenic
GAAGAAGAAGATGAAGAATT+AGG 0.286532 5.2:-11594982 None:intergenic
ATGGCATTCCATTTCTCTCT+TGG 0.336081 5.2:+11595603 MS.gene010504:CDS
GAGAGAAACACTGCATCTTC+TGG 0.356763 5.2:-11595526 None:intergenic
AACGCCATCTATCGGCATAA+TGG 0.385803 5.2:+11595442 MS.gene010504:CDS
CGGAACTCGTTAGTCATTGC+TGG 0.406108 5.2:-11595548 None:intergenic
TGTTCATGTGGTATGTTTCA+TGG 0.414708 5.2:+11594892 MS.gene010504:CDS
CCACCTCCACACCGCTTTGG+AGG 0.424846 5.2:+11595238 MS.gene010504:CDS
TAGGTTTCAGGTTCATCATA+AGG 0.424993 5.2:-11594949 None:intergenic
ATGCCGATAGATGGCGTTGC+CGG 0.430815 5.2:-11595437 None:intergenic
TAGAGTCTCCAAGAGAGAAA+TGG 0.442835 5.2:-11595611 None:intergenic
AGAATTAGGAGTGAAACAAT+AGG 0.458450 5.2:-11594968 None:intergenic
AGAAGAGCAACTGCTGCAGC+CGG 0.462808 5.2:+11595410 MS.gene010504:CDS
ACACCACCTCCACACCGCTT+TGG 0.463073 5.2:+11595235 MS.gene010504:CDS
GATTCCATTATGCCGATAGA+TGG 0.464364 5.2:-11595446 None:intergenic
CCTCCAAAGCGGTGTGGAGG+TGG 0.470303 5.2:-11595238 None:intergenic
TGAGTACTGTTGTACTGTTT+AGG 0.483115 5.2:-11595123 None:intergenic
CACTGCATCTTCTGGTTCTG+TGG 0.485352 5.2:-11595518 None:intergenic
AGCAAGAAGAGAATCATTGT+TGG 0.486549 5.2:-11595193 None:intergenic
GATTGGTTTCATCAATGAAA+CGG 0.487226 5.2:-11595568 None:intergenic
AACTGCTGCAGCCGGCACAC+CGG 0.491074 5.2:+11595418 MS.gene010504:CDS
AGATGGCGTTGCCGGTGTGC+CGG 0.497703 5.2:-11595429 None:intergenic
ATCTCAAGGGCAACACGTGA+TGG 0.509206 5.2:+11594864 MS.gene010504:CDS
TCCACACCGCTTTGGAGGAA+CGG 0.515774 5.2:+11595243 MS.gene010504:CDS
GTTGATTGTACTCTTTCACT+TGG 0.527724 5.2:+11595006 MS.gene010504:CDS
ATGATGCATCGTTCATCTCA+AGG 0.533388 5.2:+11594850 MS.gene010504:CDS
CAGAACGACGTTCATGATGT+CGG 0.540322 5.2:-11595071 None:intergenic
ACACCGGCAACGCCATCTAT+CGG 0.547655 5.2:+11595434 MS.gene010504:CDS
TCTCAAGGGCAACACGTGAT+GGG 0.577571 5.2:+11594865 MS.gene010504:CDS
CAGTCACTATGCAATGCATG+TGG 0.582954 5.2:+11595365 MS.gene010504:intron
ACCACCATCACAACAACTCA+TGG 0.584082 5.2:+11595486 MS.gene010504:CDS
CAGTACTCAGTCTCAAACAA+AGG 0.584934 5.2:+11595137 MS.gene010504:CDS
TCTTCAGTGAAACGAGTGGA+TGG 0.587900 5.2:-11595033 None:intergenic
ATGAGTTGTTGTGATGGTGG+TGG 0.588375 5.2:-11595484 None:intergenic
TGATGCATCGTTCATCTCAA+GGG 0.590177 5.2:+11594851 MS.gene010504:CDS
GTTCCTCCAAAGCGGTGTGG+AGG 0.595180 5.2:-11595241 None:intergenic
GAACGGTCCACGAGGCCCAA+AGG 0.609147 5.2:+11595260 MS.gene010504:CDS
ACCGTTCCTCCAAAGCGGTG+TGG 0.617219 5.2:-11595244 None:intergenic
TTCATCTTCAGTGAAACGAG+TGG 0.627984 5.2:-11595037 None:intergenic
ATGTGGGATCAGATTCAAGA+AGG 0.634149 5.2:+11595382 MS.gene010504:CDS
ACCATGAGTTGTTGTGATGG+TGG 0.656581 5.2:-11595487 None:intergenic
AGTCACTATGCAATGCATGT+GGG 0.668102 5.2:+11595366 MS.gene010504:intron
CGTACCATGAGTTGTTGTGA+TGG 0.677789 5.2:-11595490 None:intergenic
CGTGGACCGTTCCTCCAAAG+CGG 0.688334 5.2:-11595249 None:intergenic
CTTTGGAGGAACGGTCCACG+AGG 0.702547 5.2:+11595252 MS.gene010504:CDS
GTGATGGGACACTGTTCATG+TGG 0.723745 5.2:+11594880 MS.gene010504:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATGTTATATTTCATGT+TGG - chr5.2:11595330-11595349 None:intergenic 15.0%
!!! ATATAACATTTTATGTTGAA+TGG + chr5.2:11595337-11595356 MS.gene010504:intron 15.0%
!! TTATATTTCATGTTGGTATT+TGG - chr5.2:11595323-11595342 None:intergenic 20.0%
!!! ATGTAGAGTATTTTTACCTT+TGG - chr5.2:11595279-11595298 None:intergenic 25.0%
!!! TGTAGAGTATTTTTACCTTT+GGG - chr5.2:11595278-11595297 None:intergenic 25.0%
AGAATTAGGAGTGAAACAAT+AGG - chr5.2:11594971-11594990 None:intergenic 30.0%
GAAGAAGAAGATGAAGAATT+AGG - chr5.2:11594985-11595004 None:intergenic 30.0%
TTCTGTCAAAAACTTCTGTT+GGG + chr5.2:11595089-11595108 MS.gene010504:CDS 30.0%
! ACCAATCATGATTCTGAAAA+TGG + chr5.2:11595584-11595603 MS.gene010504:CDS 30.0%
! GTTGGAGTTGTTGTTATTAT+TGG - chr5.2:11595178-11595197 None:intergenic 30.0%
!! GATTGGTTTCATCAATGAAA+CGG - chr5.2:11595571-11595590 None:intergenic 30.0%
AGCAAGAAGAGAATCATTGT+TGG - chr5.2:11595196-11595215 None:intergenic 35.0%
GTTCTGTCAAAAACTTCTGT+TGG + chr5.2:11595088-11595107 MS.gene010504:CDS 35.0%
GTTGATTGTACTCTTTCACT+TGG + chr5.2:11595006-11595025 MS.gene010504:CDS 35.0%
TGTTCATGTGGTATGTTTCA+TGG + chr5.2:11594892-11594911 MS.gene010504:CDS 35.0%
! TGAGTACTGTTGTACTGTTT+AGG - chr5.2:11595126-11595145 None:intergenic 35.0%
!! GCCATTTTCAGAATCATGAT+TGG - chr5.2:11595588-11595607 None:intergenic 35.0%
!! TAGGTTTCAGGTTCATCATA+AGG - chr5.2:11594952-11594971 None:intergenic 35.0%
AGTCACTATGCAATGCATGT+GGG + chr5.2:11595366-11595385 MS.gene010504:intron 40.0%
ATGATGCATCGTTCATCTCA+AGG + chr5.2:11594850-11594869 MS.gene010504:CDS 40.0%
ATGGCATTCCATTTCTCTCT+TGG + chr5.2:11595603-11595622 MS.gene010504:CDS 40.0%
ATGTGGGATCAGATTCAAGA+AGG + chr5.2:11595382-11595401 MS.gene010504:CDS 40.0%
CAGTACTCAGTCTCAAACAA+AGG + chr5.2:11595137-11595156 MS.gene010504:CDS 40.0%
GATTCCATTATGCCGATAGA+TGG - chr5.2:11595449-11595468 None:intergenic 40.0%
GGAGTGAAACAATAGGTTTC+AGG - chr5.2:11594964-11594983 None:intergenic 40.0%
TAGAGTCTCCAAGAGAGAAA+TGG - chr5.2:11595614-11595633 None:intergenic 40.0%
TGATGCATCGTTCATCTCAA+GGG + chr5.2:11594851-11594870 MS.gene010504:CDS 40.0%
TTCATCTTCAGTGAAACGAG+TGG - chr5.2:11595040-11595059 None:intergenic 40.0%
AACGCCATCTATCGGCATAA+TGG + chr5.2:11595442-11595461 MS.gene010504:CDS 45.0%
ACCACCATCACAACAACTCA+TGG + chr5.2:11595486-11595505 MS.gene010504:CDS 45.0%
ACCATGAGTTGTTGTGATGG+TGG - chr5.2:11595490-11595509 None:intergenic 45.0%
CAGAACGACGTTCATGATGT+CGG - chr5.2:11595074-11595093 None:intergenic 45.0%
CAGTCACTATGCAATGCATG+TGG + chr5.2:11595365-11595384 MS.gene010504:intron 45.0%
CGTACCATGAGTTGTTGTGA+TGG - chr5.2:11595493-11595512 None:intergenic 45.0%
GAGAGAAACACTGCATCTTC+TGG - chr5.2:11595529-11595548 None:intergenic 45.0%
TCTTCAGTGAAACGAGTGGA+TGG - chr5.2:11595036-11595055 None:intergenic 45.0%
! ATTTTTACCTTTGGGCCTCG+TGG - chr5.2:11595270-11595289 None:intergenic 45.0%
!! ATGAGTTGTTGTGATGGTGG+TGG - chr5.2:11595487-11595506 None:intergenic 45.0%
ATCTCAAGGGCAACACGTGA+TGG + chr5.2:11594864-11594883 MS.gene010504:CDS 50.0%
CGGAACTCGTTAGTCATTGC+TGG - chr5.2:11595551-11595570 None:intergenic 50.0%
TCTCAAGGGCAACACGTGAT+GGG + chr5.2:11594865-11594884 MS.gene010504:CDS 50.0%
! GTGATGGGACACTGTTCATG+TGG + chr5.2:11594880-11594899 MS.gene010504:CDS 50.0%
!! CACTGCATCTTCTGGTTCTG+TGG - chr5.2:11595521-11595540 None:intergenic 50.0%
ACACCGGCAACGCCATCTAT+CGG + chr5.2:11595434-11595453 MS.gene010504:CDS 55.0%
AGAAGAGCAACTGCTGCAGC+CGG + chr5.2:11595410-11595429 MS.gene010504:CDS 55.0%
ATGCCGATAGATGGCGTTGC+CGG - chr5.2:11595440-11595459 None:intergenic 55.0%
!! TCCACACCGCTTTGGAGGAA+CGG + chr5.2:11595243-11595262 MS.gene010504:CDS 55.0%
ACACCACCTCCACACCGCTT+TGG + chr5.2:11595235-11595254 MS.gene010504:CDS 60.0%
ACCGTTCCTCCAAAGCGGTG+TGG - chr5.2:11595247-11595266 None:intergenic 60.0%
CGTGGACCGTTCCTCCAAAG+CGG - chr5.2:11595252-11595271 None:intergenic 60.0%
GTTCCTCCAAAGCGGTGTGG+AGG - chr5.2:11595244-11595263 None:intergenic 60.0%
! CTTTGGAGGAACGGTCCACG+AGG + chr5.2:11595252-11595271 MS.gene010504:CDS 60.0%
AACTGCTGCAGCCGGCACAC+CGG + chr5.2:11595418-11595437 MS.gene010504:CDS 65.0%
AGATGGCGTTGCCGGTGTGC+CGG - chr5.2:11595432-11595451 None:intergenic 65.0%
CCACCTCCACACCGCTTTGG+AGG + chr5.2:11595238-11595257 MS.gene010504:CDS 65.0%
CCTCCAAAGCGGTGTGGAGG+TGG - chr5.2:11595241-11595260 None:intergenic 65.0%
GAACGGTCCACGAGGCCCAA+AGG + chr5.2:11595260-11595279 MS.gene010504:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 11594850 11595634 11594850 ID=MS.gene010504
chr5.2 mRNA 11594850 11595634 11594850 ID=MS.gene010504.t1;Parent=MS.gene010504
chr5.2 exon 11594850 11595281 11594850 ID=MS.gene010504.t1.exon1;Parent=MS.gene010504.t1
chr5.2 CDS 11594850 11595281 11594850 ID=cds.MS.gene010504.t1;Parent=MS.gene010504.t1
chr5.2 exon 11595368 11595634 11595368 ID=MS.gene010504.t1.exon2;Parent=MS.gene010504.t1
chr5.2 CDS 11595368 11595634 11595368 ID=cds.MS.gene010504.t1;Parent=MS.gene010504.t1
Gene Sequence

>MS.gene010504

ATGATGCATCGTTCATCTCAAGGGCAACACGTGATGGGACACTGTTCATGTGGTATGTTTCATGGACAAAACAACTCATTCTCAATGTTATTCTCTACACCTTATGATGAACCTGAAACCTATTGTTTCACTCCTAATTCTTCATCTTCTTCTTCTGTTGATTGTACTCTTTCACTTGGAACACCATCCACTCGTTTCACTGAAGATGAAGAGAAAAGAAGCCGACATCATGAACGTCGTTCTGTCAAAAACTTCTGTTGGGATTTGTTAACACCTAAACAGTACAACAGTACTCAGTCTCAAACAAAGGCAACACGTGCAAATACCAATAATAACAACAACTCCAACAATGATTCTCTTCTTGCTCGTAGATGTGCAAACTGTGACACCACCTCCACACCGCTTTGGAGGAACGGTCCACGAGGCCCAAAGGTAAAAATACTCTACATATATATATAACTATATGCATTCCAAATACCAACATGAAATATAACATTTTATGTTGAATGGAATTACAGTCACTATGCAATGCATGTGGGATCAGATTCAAGAAGGAAGAGAGAAGAGCAACTGCTGCAGCCGGCACACCGGCAACGCCATCTATCGGCATAATGGAATCAGCTTCGATGTATAACCACCACCATCACAACAACTCATGGTACGTACAACCACAGAACCAGAAGATGCAGTGTTTCTCTCCAGCAATGACTAACGAGTTCCGTTTCATTGATGAAACCAATCATGATTCTGAAAATGGCATTCCATTTCTCTCTTGGAGACTCTAA
Protein sequence

>MS.gene010504.t1

MMHRSSQGQHVMGHCSCGMFHGQNNSFSMLFSTPYDEPETYCFTPNSSSSSSVDCTLSLGTPSTRFTEDEEKRSRHHERRSVKNFCWDLLTPKQYNSTQSQTKATRANTNNNNNSNNDSLLARRCANCDTTSTPLWRNGPRGPKSLCNACGIRFKKEERRATAAAGTPATPSIGIMESASMYNHHHHNNSWYVQPQNQKMQCFSPAMTNEFRFIDETNHDSENGIPFLSWRL