AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene037375


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037375.t1 MTR_1g114640 83.410 217 27 1 1 208 1 217 2.75e-130 366
MS.gene037375.t1 MTR_1g033750 62.385 218 70 3 5 210 4 221 4.45e-90 264
MS.gene037375.t1 MTR_1g114640 80.000 165 24 1 1 156 1 165 2.36e-88 258
MS.gene037375.t1 MTR_1g114690 50.218 229 86 4 1 212 1 218 1.03e-68 210
MS.gene037375.t1 MTR_1g114690 48.649 222 102 3 1 213 1 219 3.19e-67 206
MS.gene037375.t1 MTR_1g114750 46.256 227 109 3 1 216 1 225 5.14e-65 201
MS.gene037375.t1 MTR_1g115130 47.926 217 95 3 1 217 1 199 3.16e-63 195
MS.gene037375.t1 MTR_1g114690 44.106 263 85 5 1 212 1 252 1.07e-61 193
MS.gene037375.t1 MTR_1g114680 84.956 113 17 0 102 214 53 165 7.46e-58 181
MS.gene037375.t1 MTR_6g077990 55.629 151 67 0 64 214 8 158 5.87e-57 178
MS.gene037375.t1 MTR_6g077990 55.629 151 67 0 64 214 50 200 2.59e-56 177
MS.gene037375.t1 MTR_6g077990 55.629 151 67 0 64 214 51 201 2.79e-56 177
MS.gene037375.t1 MTR_8g100065 57.333 150 63 1 64 212 36 185 6.54e-56 176
MS.gene037375.t1 MTR_8g100065 57.333 150 63 1 64 212 58 207 2.10e-55 176
MS.gene037375.t1 MTR_1g114690 48.810 168 70 4 1 157 1 163 5.20e-41 139
MS.gene037375.t1 MTR_7g083570 35.450 189 113 1 28 207 84 272 1.86e-38 134
MS.gene037375.t1 MTR_8g069110 38.621 145 88 1 64 208 123 266 5.60e-35 125
MS.gene037375.t1 MTR_3g100750 39.726 146 85 2 64 208 111 254 6.52e-35 124
MS.gene037375.t1 MTR_8g100065 61.702 94 35 1 64 156 36 129 1.29e-33 117
MS.gene037375.t1 MTR_6g077990 58.763 97 40 0 64 160 50 146 2.02e-33 117
MS.gene037375.t1 MTR_8g100065 61.702 94 35 1 64 156 58 151 4.12e-33 117
MS.gene037375.t1 MTR_5g015750 85.714 63 9 0 1 63 1 63 9.05e-31 109
MS.gene037375.t1 MTR_2g076350 40.000 145 86 1 64 207 79 223 4.91e-27 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037375.t1 AT5G08350 56.701 194 74 3 28 212 23 215 1.34e-70 215
MS.gene037375.t1 AT5G23370 52.018 223 93 3 1 214 1 218 1.65e-70 214
MS.gene037375.t1 AT5G23350 56.842 190 73 3 28 208 23 212 5.30e-68 208
MS.gene037375.t1 AT5G23360 51.196 209 96 2 1 208 1 204 1.83e-66 204
MS.gene037375.t1 AT4G01600 42.384 151 86 1 59 208 34 184 2.99e-38 131
MS.gene037375.t1 AT5G13200 38.889 162 97 1 46 205 95 256 3.37e-38 133
MS.gene037375.t1 AT4G01600 36.585 205 117 3 16 208 15 218 4.55e-38 132
MS.gene037375.t1 AT4G01600 42.384 151 86 1 59 208 73 223 1.00e-37 131
MS.gene037375.t1 AT1G28200 41.096 146 83 2 64 208 110 253 1.44e-35 126
MS.gene037375.t1 AT1G28200 41.096 146 83 2 64 208 110 253 1.44e-35 126
MS.gene037375.t1 AT2G22475 39.041 146 86 2 64 208 147 290 9.17e-33 120
MS.gene037375.t1 AT5G13200 36.842 114 70 1 46 157 95 208 1.25e-20 86.3
MS.gene037375.t1 AT4G40100 32.824 131 59 1 76 206 112 213 4.21e-20 85.1
MS.gene037375.t1 AT2G22475 37.662 77 48 0 64 140 147 223 3.80e-14 69.7

Find 42 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACTCACAAAGTTGCTTTC+TGG 0.165974 1.3:-77693502 MS.gene037375:CDS
TTCCTTCATGAGCTACTTAA+TGG 0.213634 1.3:-77694165 MS.gene037375:CDS
GCGTAGATGGTTTCGACTTC+TGG 0.218018 1.3:-77693247 MS.gene037375:CDS
AAGATAACAGATACAGTAAA+AGG 0.228633 1.3:-77693680 MS.gene037375:CDS
TTTACTGTATCTGTTATCTT+TGG 0.247894 1.3:+77693683 None:intergenic
TCCTCCAACTTGAATAATTC+TGG 0.255353 1.3:+77693640 None:intergenic
AGATACTTGGCTGATTCTTC+TGG 0.277973 1.3:-77694099 MS.gene037375:CDS
ACTCTAATCAATTCTCCTTT+TGG 0.287784 1.3:+77693452 None:intergenic
ATACAGTAAAAGGGAAATTA+AGG 0.314014 1.3:-77693670 MS.gene037375:CDS
CTGACTAAGATGAACATGTT+TGG 0.338683 1.3:-77693928 MS.gene037375:CDS
TGTTACTTATCAACCACATT+AGG 0.368586 1.3:-77693551 MS.gene037375:CDS
AGGCTACTACCCTAGCTCAT+AGG 0.375066 1.3:-77693178 MS.gene037375:CDS
TGACTAAGATGAACATGTTT+GGG 0.379362 1.3:-77693927 MS.gene037375:CDS
GATGAACATGTTTGGGAGAA+AGG 0.393124 1.3:-77693920 MS.gene037375:CDS
ATTGATTAGAGTTCTCTATA+AGG 0.399862 1.3:-77693441 MS.gene037375:intron
GGCTACTACCCTAGCTCATA+GGG 0.422187 1.3:-77693177 MS.gene037375:CDS
AGTAAAAGGGAAATTAAGGT+TGG 0.443877 1.3:-77693666 MS.gene037375:CDS
ATGAACATGTTTGGGAGAAA+GGG 0.454867 1.3:-77693919 MS.gene037375:CDS
ATCACCTCAACTCATTCAGT+TGG 0.473136 1.3:-77694135 MS.gene037375:CDS
ATAGAAATAGTCAGCGTAGA+TGG 0.474979 1.3:-77693260 MS.gene037375:CDS
ATGAAGAGGAGGCCAGCTAT+AGG 0.476519 1.3:+77693527 None:intergenic
CTGTAACCTGCAGTGAGACT+TGG 0.489945 1.3:-77693707 MS.gene037375:intron
AGAATTCTCCCCTATGAGCT+AGG 0.495167 1.3:+77693168 None:intergenic
GGAGCCAGAATTATTCAAGT+TGG 0.504215 1.3:-77693644 MS.gene037375:CDS
GTAAAAGGGAAATTAAGGTT+GGG 0.509520 1.3:-77693665 MS.gene037375:CDS
AGCTTTAAGATATCTTCAGC+AGG 0.515990 1.3:-77693198 MS.gene037375:CDS
ATCAAGATCTCGTCACCAAA+AGG 0.523407 1.3:-77693467 MS.gene037375:CDS
GCCAGAATTATTCAAGTTGG+AGG 0.527943 1.3:-77693641 MS.gene037375:CDS
TCACCTCAACTCATTCAGTT+GGG 0.537734 1.3:-77694134 MS.gene037375:CDS
AGATAACAGATACAGTAAAA+GGG 0.540258 1.3:-77693679 MS.gene037375:CDS
ATGTTTGGGAGAAAGGGTGA+TGG 0.565214 1.3:-77693913 MS.gene037375:intron
GAATTCTCCCCTATGAGCTA+GGG 0.581089 1.3:+77693169 None:intergenic
TCCATTACAAAATCAAAGCA+AGG 0.583726 1.3:-77694063 MS.gene037375:intron
TTCCATTAAGTAGCTCATGA+AGG 0.584791 1.3:+77694163 None:intergenic
ACCACATTAGGTCCTATAGC+TGG 0.588201 1.3:-77693539 MS.gene037375:CDS
GAAGTCATCAAAGAGATACT+TGG 0.597294 1.3:-77694112 MS.gene037375:CDS
CCAGAAAGCAACTTTGTGAG+TGG 0.608051 1.3:+77693502 None:intergenic
CTTTGTGAGTGGATATGAAG+AGG 0.608902 1.3:+77693513 None:intergenic
GCCAGCTATAGGACCTAATG+TGG 0.654715 1.3:+77693538 None:intergenic
TGTGAGTGGATATGAAGAGG+AGG 0.670894 1.3:+77693516 None:intergenic
CTTCCCAACTGAATGAGTTG+AGG 0.692685 1.3:+77694131 None:intergenic
GCTACTACCCTAGCTCATAG+GGG 0.696994 1.3:-77693176 MS.gene037375:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATAATTTAATTCATCA+TGG - chr1.3:77693357-77693376 MS.gene037375:intron 10.0%
!! ATGATGTATAATTTGAACTT+TGG - chr1.3:77693561-77693580 MS.gene037375:CDS 20.0%
!!! AAATACAGTTTTGTTAATGT+AGG + chr1.3:77693316-77693335 None:intergenic 20.0%
!!! AATGAAGTTTTAACTGATAA+TGG - chr1.3:77693600-77693619 MS.gene037375:CDS 20.0%
!!! ATGGTCATTTTTATATTTTC+AGG - chr1.3:77693376-77693395 MS.gene037375:intron 20.0%
!!! CTTAATTTGTTTACTATTTC+AGG - chr1.3:77693989-77694008 MS.gene037375:intron 20.0%
! AAGATAACAGATACAGTAAA+AGG - chr1.3:77693663-77693682 MS.gene037375:CDS 25.0%
! AAGTGTGAAGAAAAGATAAA+AGG + chr1.3:77693972-77693991 None:intergenic 25.0%
! AATTATACATCATAGCAGTT+TGG + chr1.3:77693554-77693573 None:intergenic 25.0%
! AGATAACAGATACAGTAAAA+GGG - chr1.3:77693664-77693683 MS.gene037375:CDS 25.0%
! ATACAGTAAAAGGGAAATTA+AGG - chr1.3:77693673-77693692 MS.gene037375:CDS 25.0%
! ATCAATGAAAAATTGAAGGT+TGG + chr1.3:77693507-77693526 None:intergenic 25.0%
! ATTGATTAGAGTTCTCTATA+AGG - chr1.3:77693902-77693921 MS.gene037375:intron 25.0%
! TGGAATCAATGAAAAATTGA+AGG + chr1.3:77693511-77693530 None:intergenic 25.0%
! TTTACTGTATCTGTTATCTT+TGG + chr1.3:77693663-77693682 None:intergenic 25.0%
!! ATTTCTATGTACTTTTCTGA+AGG + chr1.3:77694071-77694090 None:intergenic 25.0%
AAACTACTATACAATGCTCT+TGG + chr1.3:77693531-77693550 None:intergenic 30.0%
AGTAAAAGGGAAATTAAGGT+TGG - chr1.3:77693677-77693696 MS.gene037375:CDS 30.0%
GTAAAAGGGAAATTAAGGTT+GGG - chr1.3:77693678-77693697 MS.gene037375:CDS 30.0%
TCCATTACAAAATCAAAGCA+AGG - chr1.3:77693280-77693299 MS.gene037375:CDS 30.0%
TGACTAAGATGAACATGTTT+GGG - chr1.3:77693416-77693435 MS.gene037375:intron 30.0%
! ACTCTAATCAATTCTCCTTT+TGG + chr1.3:77693894-77693913 None:intergenic 30.0%
! TGTTACTTATCAACCACATT+AGG - chr1.3:77693792-77693811 MS.gene037375:intron 30.0%
!! ACCTTGCTTTGATTTTGTAA+TGG + chr1.3:77693284-77693303 None:intergenic 30.0%
AATTTGAACTTTGGCGTGAT+TGG - chr1.3:77693570-77693589 MS.gene037375:CDS 35.0%
ATAGAAATAGTCAGCGTAGA+TGG - chr1.3:77694083-77694102 MS.gene037375:CDS 35.0%
ATGAACATGTTTGGGAGAAA+GGG - chr1.3:77693424-77693443 MS.gene037375:intron 35.0%
CTGACTAAGATGAACATGTT+TGG - chr1.3:77693415-77693434 MS.gene037375:intron 35.0%
GAAGTCATCAAAGAGATACT+TGG - chr1.3:77693231-77693250 MS.gene037375:CDS 35.0%
TCCTCCAACTTGAATAATTC+TGG + chr1.3:77693706-77693725 None:intergenic 35.0%
TTCCATTAAGTAGCTCATGA+AGG + chr1.3:77693183-77693202 None:intergenic 35.0%
TTCCTTCATGAGCTACTTAA+TGG - chr1.3:77693178-77693197 MS.gene037375:CDS 35.0%
! ACATGCTGTATCTTTTCATG+TGG + chr1.3:77694023-77694042 None:intergenic 35.0%
!! AAGGAATGAGAGCATTTACA+TGG + chr1.3:77693953-77693972 None:intergenic 35.0%
!! AGCTTTAAGATATCTTCAGC+AGG - chr1.3:77694145-77694164 MS.gene037375:CDS 35.0%
!!! GCTTCTTCACATTTTGACTT+TGG + chr1.3:77694049-77694068 None:intergenic 35.0%
ATCAAGATCTCGTCACCAAA+AGG - chr1.3:77693876-77693895 MS.gene037375:intron 40.0%
ATCACCTCAACTCATTCAGT+TGG - chr1.3:77693208-77693227 MS.gene037375:CDS 40.0%
CTTTGTGAGTGGATATGAAG+AGG + chr1.3:77693833-77693852 None:intergenic 40.0%
GATGAACATGTTTGGGAGAA+AGG - chr1.3:77693423-77693442 MS.gene037375:intron 40.0%
GGAGCCAGAATTATTCAAGT+TGG - chr1.3:77693699-77693718 MS.gene037375:intron 40.0%
TCACCTCAACTCATTCAGTT+GGG - chr1.3:77693209-77693228 MS.gene037375:CDS 40.0%
! AACTTTTCAGCGTACAAGAC+GGG - chr1.3:77693745-77693764 MS.gene037375:intron 40.0%
! AGATACTTGGCTGATTCTTC+TGG - chr1.3:77693244-77693263 MS.gene037375:CDS 40.0%
! CAACTTTTCAGCGTACAAGA+CGG - chr1.3:77693744-77693763 MS.gene037375:intron 40.0%
!! GCCAGAATTATTCAAGTTGG+AGG - chr1.3:77693702-77693721 MS.gene037375:intron 40.0%
!!! GGTTTCGACTTCTGGTTTTT+GGG - chr1.3:77694104-77694123 MS.gene037375:CDS 40.0%
!!! TGGTTTCGACTTCTGGTTTT+TGG - chr1.3:77694103-77694122 MS.gene037375:CDS 40.0%
!!! TTTTGGTGACGAGATCTTGA+TGG + chr1.3:77693877-77693896 None:intergenic 40.0%
ACCACATTAGGTCCTATAGC+TGG - chr1.3:77693804-77693823 MS.gene037375:intron 45.0%
AGAATTCTCCCCTATGAGCT+AGG + chr1.3:77694178-77694197 None:intergenic 45.0%
ATGTTTGGGAGAAAGGGTGA+TGG - chr1.3:77693430-77693449 MS.gene037375:intron 45.0%
CCAGAAAGCAACTTTGTGAG+TGG + chr1.3:77693844-77693863 None:intergenic 45.0%
CTTCCCAACTGAATGAGTTG+AGG + chr1.3:77693215-77693234 None:intergenic 45.0%
GAATTCTCCCCTATGAGCTA+GGG + chr1.3:77694177-77694196 None:intergenic 45.0%
TGTGAGTGGATATGAAGAGG+AGG + chr1.3:77693830-77693849 None:intergenic 45.0%
! ACTTTTCAGCGTACAAGACG+GGG - chr1.3:77693746-77693765 MS.gene037375:intron 45.0%
! CCACTCACAAAGTTGCTTTC+TGG - chr1.3:77693841-77693860 MS.gene037375:intron 45.0%
!! TGAATTAAATTATATTAAAT+TGG + chr1.3:77693354-77693373 None:intergenic 5.0%
AGGCTACTACCCTAGCTCAT+AGG - chr1.3:77694165-77694184 MS.gene037375:CDS 50.0%
ATGAAGAGGAGGCCAGCTAT+AGG + chr1.3:77693819-77693838 None:intergenic 50.0%
CTGTAACCTGCAGTGAGACT+TGG - chr1.3:77693636-77693655 MS.gene037375:CDS 50.0%
GCCAGCTATAGGACCTAATG+TGG + chr1.3:77693808-77693827 None:intergenic 50.0%
GCGTAGATGGTTTCGACTTC+TGG - chr1.3:77694096-77694115 MS.gene037375:CDS 50.0%
GCTACTACCCTAGCTCATAG+GGG - chr1.3:77694167-77694186 MS.gene037375:CDS 50.0%
GGCTACTACCCTAGCTCATA+GGG - chr1.3:77694166-77694185 MS.gene037375:CDS 50.0%
TTTGGTCCAAGTCTCACTGC+AGG + chr1.3:77693645-77693664 None:intergenic 50.0%
GTGCATGCAGTCTGAGAGCA+TGG - chr1.3:77693457-77693476 MS.gene037375:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 77693166 77694199 77693166 ID=MS.gene037375
chr1.3 mRNA 77693166 77694199 77693166 ID=MS.gene037375.t1;Parent=MS.gene037375
chr1.3 exon 77694064 77694199 77694064 ID=MS.gene037375.t1.exon1;Parent=MS.gene037375.t1
chr1.3 CDS 77694064 77694199 77694064 ID=cds.MS.gene037375.t1;Parent=MS.gene037375.t1
chr1.3 exon 77693914 77693967 77693914 ID=MS.gene037375.t1.exon2;Parent=MS.gene037375.t1
chr1.3 CDS 77693914 77693967 77693914 ID=cds.MS.gene037375.t1;Parent=MS.gene037375.t1
chr1.3 exon 77693442 77693716 77693442 ID=MS.gene037375.t1.exon3;Parent=MS.gene037375.t1
chr1.3 CDS 77693442 77693716 77693442 ID=cds.MS.gene037375.t1;Parent=MS.gene037375.t1
chr1.3 exon 77693166 77693354 77693166 ID=MS.gene037375.t1.exon4;Parent=MS.gene037375.t1
chr1.3 CDS 77693166 77693354 77693166 ID=cds.MS.gene037375.t1;Parent=MS.gene037375.t1
Gene Sequence

>MS.gene037375

ATGAAGACGTCATTCCTTCATGAGCTACTTAATGGAATTTCTATCACCTCAACTCATTCAGTTGGGAAGTCATCAAAGAGATACTTGGCTGATTCTTCTGGCATATACAACAAATCCATTACAAAATCAAAGCAAGGTATGCACAAACCTACATTAACAAAACTGTATTTCATAAATACTTCATTCCAATTTAATATAATTTAATTCATCATGGTCATTTTTATATTTTCAGGTAAATTTAATTCAGTTCTGACTAAGATGAACATGTTTGGGAGAAAGGGTGATGGTTTTGTGCATGCAGTCTGAGAGCATGGTATGTAATCAGTAATCTTTAAACACCAACCTTCAATTTTTCATTGATTCCAAGAGCATTGTATAGTAGTTTCCAAACTGCTATGATGTATAATTTGAACTTTGGCGTGATTGGAAAATCGAATGAAGTTTTAACTGATAATGGCTTAAAACTGTTACTGTAACCTGCAGTGAGACTTGGACCAAAGATAACAGATACAGTAAAAGGGAAATTAAGGTTGGGAGCCAGAATTATTCAAGTTGGAGGAATAGAGAAAGTGTTTATGCAACTTTTCAGCGTACAAGACGGGGAGAAGCTGTTGAAAGCGTCACAATGTTACTTATCAACCACATTAGGTCCTATAGCTGGCCTCCTCTTCATATCCACTCACAAAGTTGCTTTCTGGAGTGACAAATCCATCAAGATCTCGTCACCAAAAGGAGAATTGATTAGAGTTCTCTATAAGGTGATTTTCTTACTTTTTTATAATGTCCATGTAAATGCTCTCATTCCTTTTATCTTTTCTTCACACTTAATTTGTTTACTATTTCAGGTCTCTATTCCACATGAAAAGATACAGCATGTCAACCAAAGTCAAAATGTGAAGAAGCCTTCAGAAAAGTACATAGAAATAGTCAGCGTAGATGGTTTCGACTTCTGGTTTTTGGGTTTCTTTAATTATAAGAAAGCTTTAAGATATCTTCAGCAGGCTACTACCCTAGCTCATAGGGGAGAATTCTAG

Protein sequence

>MS.gene037375.t1

MKTSFLHELLNGISITSTHSVGKSSKRYLADSSGIYNKSITKSKQGKFNSVLTKMNMFGRKGDVRLGPKITDTVKGKLRLGARIIQVGGIEKVFMQLFSVQDGEKLLKASQCYLSTTLGPIAGLLFISTHKVAFWSDKSIKISSPKGELIRVLYKVSIPHEKIQHVNQSQNVKKPSEKYIEIVSVDGFDFWFLGFFNYKKALRYLQQATTLAHRGEF