AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048593

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048593.t1 MTR_3g031100 90.826 218 18 1 1 218 29 244 6.10e-134 376
MS.gene048593.t1 MTR_2g016210 41.121 214 117 3 1 209 29 238 6.34e-49 160
MS.gene048593.t1 MTR_3g031240 48.889 135 69 0 1 135 29 163 1.08e-37 129
MS.gene048593.t1 MTR_3g467080 46.512 129 69 0 1 129 29 157 2.21e-33 118
MS.gene048593.t1 MTR_3g466980 41.447 152 78 3 1 148 29 173 1.20e-31 115
MS.gene048593.t1 MTR_4g063790 42.446 139 80 0 1 139 29 167 5.11e-31 112
MS.gene048593.t1 MTR_3g465410 41.135 141 83 0 1 141 1 141 1.05e-29 108
MS.gene048593.t1 MTR_3g065100 31.527 203 131 3 4 200 32 232 3.74e-28 106
MS.gene048593.t1 MTR_4g032620 39.683 126 76 0 1 126 29 154 3.06e-26 101
MS.gene048593.t1 MTR_4g032290 39.837 123 74 0 6 128 34 156 6.26e-25 98.2
MS.gene048593.t1 MTR_4g031910 38.211 123 76 0 6 128 34 156 1.84e-23 94.4
MS.gene048593.t1 MTR_4g032260 35.772 123 79 0 6 128 34 156 1.10e-21 87.8
MS.gene048593.t1 MTR_2g035610 43.333 90 51 0 4 93 32 121 5.21e-21 84.7
MS.gene048593.t1 MTR_8g036130 35.714 140 88 1 1 138 29 168 1.11e-20 87.4
MS.gene048593.t1 MTR_5g075380 34.921 126 81 1 1 126 29 153 2.35e-19 81.6
MS.gene048593.t1 MTR_3g466900 32.031 128 86 1 4 131 2 128 2.86e-19 80.5
MS.gene048593.t1 MTR_3g466930 32.031 128 86 1 4 131 2 128 1.96e-18 78.6
MS.gene048593.t1 MTR_3g466830 34.586 133 86 1 1 133 28 159 2.21e-18 79.0
MS.gene048593.t1 MTR_2g035580 40.769 130 76 1 2 131 30 158 2.51e-18 79.0
MS.gene048593.t1 MTR_3g466890 31.538 130 88 1 2 131 29 157 8.56e-17 75.1
MS.gene048593.t1 MTR_1g077300 33.333 126 74 3 4 126 32 150 5.68e-15 70.1
MS.gene048593.t1 MTR_5g047580 31.008 129 87 2 1 129 29 155 1.39e-14 68.9
MS.gene048593.t1 MTR_1g084950 30.952 126 85 2 4 129 32 155 3.38e-14 67.8
MS.gene048593.t1 MTR_1g077390 31.343 134 80 4 1 129 29 155 1.49e-12 63.5
MS.gene048593.t1 MTR_1g077320 31.200 125 82 3 6 129 34 155 1.58e-12 63.5
MS.gene048593.t1 MTR_7g011950 31.452 124 83 2 6 129 34 155 4.01e-12 62.4
MS.gene048593.t1 MTR_1g090710 28.682 129 91 1 1 129 29 156 4.88e-12 62.0
MS.gene048593.t1 MTR_1g090697 29.771 131 86 4 1 129 29 155 9.71e-12 61.2
MS.gene048593.t1 MTR_1g090783 30.075 133 87 4 1 131 28 156 3.62e-11 59.7
MS.gene048593.t1 MTR_4g028720 29.032 124 86 2 6 129 34 155 5.80e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048593.t1 AT5G48670 36.585 123 77 1 5 127 33 154 6.67e-19 83.6
MS.gene048593.t1 AT5G27810 43.820 89 50 0 1 89 1 89 3.78e-18 77.4
MS.gene048593.t1 AT1G65300 30.928 194 121 5 2 183 29 221 2.04e-16 76.3
MS.gene048593.t1 AT3G05860 30.061 163 99 4 1 161 29 178 2.10e-14 70.5
MS.gene048593.t1 AT3G05860 30.061 163 99 4 1 161 29 178 2.35e-14 70.5
MS.gene048593.t1 AT3G05860 30.061 163 99 4 1 161 29 178 2.61e-14 69.3
MS.gene048593.t1 AT1G65330 40.449 89 53 0 1 89 28 116 3.00e-14 70.5
MS.gene048593.t1 AT5G26630 30.159 126 83 2 4 127 32 154 3.76e-13 66.2
MS.gene048593.t1 AT5G26650 36.364 88 56 0 2 89 28 115 8.79e-13 66.6
MS.gene048593.t1 AT5G27960 36.364 88 56 0 2 89 28 115 2.18e-12 65.5

Find 48 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGAGACTAACATGAATTA+TGG 0.238809 3.3:+53691531 MS.gene048593:CDS
TGCTTTCTCATACTTCTCTT+TGG 0.254440 3.3:-53691205 None:intergenic
GATTTCGACCAAAATGGATT+TGG 0.277929 3.3:+53691624 MS.gene048593:CDS
GCCTATGAGCAGGTTGTAAA+TGG 0.282566 3.3:+53691396 MS.gene048593:CDS
AGATAGATCCAAATCCATTT+TGG 0.313676 3.3:-53691632 None:intergenic
TATAAAGGATGGAGATTTGT+TGG 0.354629 3.3:+53691428 MS.gene048593:CDS
ATCATGGTCAAGCAGAAGTT+TGG 0.397626 3.3:+53691067 MS.gene048593:CDS
TTCAATAGGTATAATGAAGA+AGG 0.408359 3.3:+53690987 None:intergenic
TCCATTTACAACCTGCTCAT+AGG 0.410839 3.3:-53691397 None:intergenic
TACAACCTGCTCATAGGCTT+GGG 0.417911 3.3:-53691391 None:intergenic
AAATGGAGCTGAAGTTATAA+AGG 0.419655 3.3:+53691413 MS.gene048593:CDS
GAAGTATGAGAAAGCAATGA+TGG 0.430824 3.3:+53691212 MS.gene048593:CDS
GAGGTAGGTGTAATAATCTA+TGG 0.450650 3.3:+53691039 MS.gene048593:CDS
CGATCAGAGGTTGGATTCAA+TGG 0.450987 3.3:+53691365 MS.gene048593:CDS
TTACAACCTGCTCATAGGCT+TGG 0.477059 3.3:-53691392 None:intergenic
AATGAATTGAGCACCCTTTG+TGG 0.480151 3.3:+53691012 MS.gene048593:CDS
ATGAATTGAGCACCCTTTGT+GGG 0.482929 3.3:+53691013 MS.gene048593:CDS
AAGTGATGAGCAACTACCTA+TGG 0.489610 3.3:+53691560 MS.gene048593:CDS
TCAAAATCAAAATCATCAAA+TGG 0.490798 3.3:-53691597 None:intergenic
GAGCACCCTTTGTGGGGTAG+AGG 0.494310 3.3:+53691020 MS.gene048593:CDS
GGAGCTGAAGTTATAAAGGA+TGG 0.504690 3.3:+53691417 MS.gene048593:CDS
ATAATCTATGGTGAAAATCA+TGG 0.511237 3.3:+53691051 MS.gene048593:CDS
AGGAGATACGCGGGATAACA+TGG 0.519105 3.3:+53691485 MS.gene048593:CDS
ACCTACCTCTACCCCACAAA+GGG 0.522550 3.3:-53691025 None:intergenic
CCTACTCGTAACTATAATGT+TGG 0.540983 3.3:+53691279 MS.gene048593:CDS
ACCCTTTGTGGGGTAGAGGT+AGG 0.548601 3.3:+53691024 MS.gene048593:CDS
GAAGTTTGGCCACCCGCGAT+AGG 0.561174 3.3:+53691081 MS.gene048593:CDS
GAAGAAAGTCGATCAGAGGT+TGG 0.574938 3.3:+53691356 MS.gene048593:CDS
TCATGTTAGTCTCATAACCA+TGG 0.584822 3.3:-53691524 None:intergenic
GGTAACCCAAGCCTATGAGC+AGG 0.588115 3.3:+53691386 MS.gene048593:CDS
CATGTTAGTCTCATAACCAT+GGG 0.600840 3.3:-53691523 None:intergenic
GCTCAAGTGCCGCTGAGTGG+AGG 0.602451 3.3:+53691465 MS.gene048593:CDS
TACGCGGGATAACATGGATG+AGG 0.607587 3.3:+53691491 MS.gene048593:CDS
AATCATCAAATGGTGGCATG+AGG 0.619303 3.3:-53691587 None:intergenic
CACCTACCTCTACCCCACAA+AGG 0.621156 3.3:-53691026 None:intergenic
ATTGCTCAAGTGCCGCTGAG+TGG 0.623375 3.3:+53691462 MS.gene048593:CDS
AAATCAAAATCATCAAATGG+TGG 0.629108 3.3:-53691594 None:intergenic
TGAATTGAGCACCCTTTGTG+GGG 0.632793 3.3:+53691014 MS.gene048593:CDS
CCAACATTATAGTTACGAGT+AGG 0.633928 3.3:-53691279 None:intergenic
CGCTGAGTGGAGGAGATACG+CGG 0.636983 3.3:+53691475 MS.gene048593:CDS
ATATGAAGAAAGTCGATCAG+AGG 0.644108 3.3:+53691352 MS.gene048593:CDS
CACACGTTCTAGTCCTATCG+CGG 0.645712 3.3:-53691094 None:intergenic
ACACGTTCTAGTCCTATCGC+GGG 0.647206 3.3:-53691093 None:intergenic
GGTGGCATGAGGAAGTCCAT+AGG 0.659527 3.3:-53691576 None:intergenic
CGTTCTAGTCCTATCGCGGG+TGG 0.679992 3.3:-53691090 None:intergenic
GATGAGGTTGCTGATACCCA+TGG 0.682185 3.3:+53691507 MS.gene048593:CDS
GCTGAGTGGAGGAGATACGC+GGG 0.694950 3.3:+53691476 MS.gene048593:CDS
CGCGTATCTCCTCCACTCAG+CGG 0.703078 3.3:-53691474 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTTAAAAGAAACAAAAATA+TGG + chr3.3:53691143-53691162 MS.gene048593:CDS 15.0%
!! TAAAAGAAACAAAAATATGG+TGG + chr3.3:53691146-53691165 MS.gene048593:CDS 20.0%
!! TCAAAATCAAAATCATCAAA+TGG - chr3.3:53691600-53691619 None:intergenic 20.0%
!!! CTTCATATTTTCATCAATTA+AGG - chr3.3:53691340-53691359 None:intergenic 20.0%
! AAATCAAAATCATCAAATGG+TGG - chr3.3:53691597-53691616 None:intergenic 25.0%
! ATAATCTATGGTGAAAATCA+TGG + chr3.3:53691051-53691070 MS.gene048593:CDS 25.0%
! TATGAGACTAACATGAATTA+TGG + chr3.3:53691531-53691550 MS.gene048593:CDS 25.0%
AAATGGAGCTGAAGTTATAA+AGG + chr3.3:53691413-53691432 MS.gene048593:CDS 30.0%
TATAAAGGATGGAGATTTGT+TGG + chr3.3:53691428-53691447 MS.gene048593:CDS 30.0%
! AGATAGATCCAAATCCATTT+TGG - chr3.3:53691635-53691654 None:intergenic 30.0%
!! TATATAGCTTTTTGGTGCAA+AGG + chr3.3:53691172-53691191 MS.gene048593:CDS 30.0%
!!! GATTTTGATTTCGACCAAAA+TGG + chr3.3:53691618-53691637 MS.gene048593:CDS 30.0%
ATATGAAGAAAGTCGATCAG+AGG + chr3.3:53691352-53691371 MS.gene048593:CDS 35.0%
CCAACATTATAGTTACGAGT+AGG - chr3.3:53691282-53691301 None:intergenic 35.0%
CCTACTCGTAACTATAATGT+TGG + chr3.3:53691279-53691298 MS.gene048593:CDS 35.0%
GAAGTATGAGAAAGCAATGA+TGG + chr3.3:53691212-53691231 MS.gene048593:CDS 35.0%
GAGGTAGGTGTAATAATCTA+TGG + chr3.3:53691039-53691058 MS.gene048593:CDS 35.0%
TGCTTTCTCATACTTCTCTT+TGG - chr3.3:53691208-53691227 None:intergenic 35.0%
! CATGTTAGTCTCATAACCAT+GGG - chr3.3:53691526-53691545 None:intergenic 35.0%
! GATTTCGACCAAAATGGATT+TGG + chr3.3:53691624-53691643 MS.gene048593:CDS 35.0%
! GGTGGATCTATATAGCTTTT+TGG + chr3.3:53691164-53691183 MS.gene048593:CDS 35.0%
! TCATGTTAGTCTCATAACCA+TGG - chr3.3:53691527-53691546 None:intergenic 35.0%
AAGTGATGAGCAACTACCTA+TGG + chr3.3:53691560-53691579 MS.gene048593:CDS 40.0%
AATCATCAAATGGTGGCATG+AGG - chr3.3:53691590-53691609 None:intergenic 40.0%
AATGAATTGAGCACCCTTTG+TGG + chr3.3:53691012-53691031 MS.gene048593:CDS 40.0%
ATCATGGTCAAGCAGAAGTT+TGG + chr3.3:53691067-53691086 MS.gene048593:CDS 40.0%
ATGAATTGAGCACCCTTTGT+GGG + chr3.3:53691013-53691032 MS.gene048593:CDS 40.0%
GGAGCTGAAGTTATAAAGGA+TGG + chr3.3:53691417-53691436 MS.gene048593:CDS 40.0%
TCCATTTACAACCTGCTCAT+AGG - chr3.3:53691400-53691419 None:intergenic 40.0%
CGATCAGAGGTTGGATTCAA+TGG + chr3.3:53691365-53691384 MS.gene048593:CDS 45.0%
GAAGAAAGTCGATCAGAGGT+TGG + chr3.3:53691356-53691375 MS.gene048593:CDS 45.0%
GCCTATGAGCAGGTTGTAAA+TGG + chr3.3:53691396-53691415 MS.gene048593:CDS 45.0%
TACAACCTGCTCATAGGCTT+GGG - chr3.3:53691394-53691413 None:intergenic 45.0%
TGAATTGAGCACCCTTTGTG+GGG + chr3.3:53691014-53691033 MS.gene048593:CDS 45.0%
TTACAACCTGCTCATAGGCT+TGG - chr3.3:53691395-53691414 None:intergenic 45.0%
ACACGTTCTAGTCCTATCGC+GGG - chr3.3:53691096-53691115 None:intergenic 50.0%
ACCTACCTCTACCCCACAAA+GGG - chr3.3:53691028-53691047 None:intergenic 50.0%
AGGAGATACGCGGGATAACA+TGG + chr3.3:53691485-53691504 MS.gene048593:CDS 50.0%
CACACGTTCTAGTCCTATCG+CGG - chr3.3:53691097-53691116 None:intergenic 50.0%
GATGAGGTTGCTGATACCCA+TGG + chr3.3:53691507-53691526 MS.gene048593:CDS 50.0%
TACGCGGGATAACATGGATG+AGG + chr3.3:53691491-53691510 MS.gene048593:CDS 50.0%
ACCCTTTGTGGGGTAGAGGT+AGG + chr3.3:53691024-53691043 MS.gene048593:CDS 55.0%
CACCTACCTCTACCCCACAA+AGG - chr3.3:53691029-53691048 None:intergenic 55.0%
GGTAACCCAAGCCTATGAGC+AGG + chr3.3:53691386-53691405 MS.gene048593:CDS 55.0%
GGTGGCATGAGGAAGTCCAT+AGG - chr3.3:53691579-53691598 None:intergenic 55.0%
! ATTGCTCAAGTGCCGCTGAG+TGG + chr3.3:53691462-53691481 MS.gene048593:CDS 55.0%
CGCGTATCTCCTCCACTCAG+CGG - chr3.3:53691477-53691496 None:intergenic 60.0%
CGCTGAGTGGAGGAGATACG+CGG + chr3.3:53691475-53691494 MS.gene048593:CDS 60.0%
CGTTCTAGTCCTATCGCGGG+TGG - chr3.3:53691093-53691112 None:intergenic 60.0%
GAAGTTTGGCCACCCGCGAT+AGG + chr3.3:53691081-53691100 MS.gene048593:CDS 60.0%
GAGCACCCTTTGTGGGGTAG+AGG + chr3.3:53691020-53691039 MS.gene048593:CDS 60.0%
GCTGAGTGGAGGAGATACGC+GGG + chr3.3:53691476-53691495 MS.gene048593:CDS 60.0%
! GCTCAAGTGCCGCTGAGTGG+AGG + chr3.3:53691465-53691484 MS.gene048593:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 53691000 53691656 53691000 ID=MS.gene048593
chr3.3 mRNA 53691000 53691656 53691000 ID=MS.gene048593.t1;Parent=MS.gene048593
chr3.3 exon 53691000 53691656 53691000 ID=MS.gene048593.t1.exon1;Parent=MS.gene048593.t1
chr3.3 CDS 53691000 53691656 53691000 ID=cds.MS.gene048593.t1;Parent=MS.gene048593.t1
Gene Sequence

>MS.gene048593

ATGAAGAAGGCTAATGAATTGAGCACCCTTTGTGGGGTAGAGGTAGGTGTAATAATCTATGGTGAAAATCATGGTCAAGCAGAAGTTTGGCCACCCGCGATAGGACTAGAACGTGTGTTGCACAAGTTTGAGAGTTTGTCTGAACTTAAAAGAAACAAAAATATGGTGGATCTATATAGCTTTTTGGTGCAAAGGATTGAAAAAGCCAAAGAGAAGTATGAGAAAGCAATGATGGAAAATAAGAAGAAAGAAATGACTAATTTTATACGTCAATTTATTCCTACTCGTAACTATAATGTTGGTGATCTGAGCTTAAATGATATCAATTATCTGACGACCTTAATTGATGAAAATATGAAGAAAGTCGATCAGAGGTTGGATTCAATGGTAACCCAAGCCTATGAGCAGGTTGTAAATGGAGCTGAAGTTATAAAGGATGGAGATTTGTTGGCTAGTACAAACATTGCTCAAGTGCCGCTGAGTGGAGGAGATACGCGGGATAACATGGATGAGGTTGCTGATACCCATGGTTATGAGACTAACATGAATTATGGTTTGCAAAGTGATGAGCAACTACCTATGGACTTCCTCATGCCACCATTTGATGATTTTGATTTTGATTTTGATTTCGACCAAAATGGATTTGGATCTATCTAG
Protein sequence

>MS.gene048593.t1

MKKANELSTLCGVEVGVIIYGENHGQAEVWPPAIGLERVLHKFESLSELKRNKNMVDLYSFLVQRIEKAKEKYEKAMMENKKKEMTNFIRQFIPTRNYNVGDLSLNDINYLTTLIDENMKKVDQRLDSMVTQAYEQVVNGAEVIKDGDLLASTNIAQVPLSGGDTRDNMDEVADTHGYETNMNYGLQSDEQLPMDFLMPPFDDFDFDFDFDQNGFGSI