AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88159

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88159.t1 MTR_4g031910 82.231 242 28 1 4 245 3 229 2.58e-135 380
MS.gene88159.t1 MTR_4g032290 79.752 242 36 1 4 245 3 231 1.06e-130 369
MS.gene88159.t1 MTR_8g036130 61.753 251 81 5 4 245 3 247 3.83e-98 286
MS.gene88159.t1 MTR_4g032620 58.367 245 88 4 1 245 1 231 3.32e-94 276
MS.gene88159.t1 MTR_4g032260 81.169 154 29 0 4 157 3 156 2.86e-80 238
MS.gene88159.t1 MTR_3g065100 48.548 241 117 4 4 242 3 238 1.61e-62 196
MS.gene88159.t1 MTR_3g466980 54.248 153 69 1 4 156 3 154 1.03e-56 180
MS.gene88159.t1 MTR_4g032270 55.629 151 46 2 95 245 2 131 7.95e-51 162
MS.gene88159.t1 MTR_2g035610 72.500 120 33 0 4 123 3 122 7.90e-49 157
MS.gene88159.t1 MTR_3g466830 44.099 161 89 1 4 164 2 161 1.43e-42 142
MS.gene88159.t1 MTR_5g075380 44.667 150 82 1 6 155 5 153 1.34e-40 137
MS.gene88159.t1 MTR_4g063790 40.491 163 97 0 4 166 3 165 3.06e-40 137
MS.gene88159.t1 MTR_3g466890 41.509 159 92 1 4 162 2 159 3.41e-38 131
MS.gene88159.t1 MTR_3g467080 40.260 154 92 0 4 157 3 156 5.72e-38 130
MS.gene88159.t1 MTR_5g047580 44.156 154 84 2 4 157 3 154 3.16e-37 128
MS.gene88159.t1 MTR_3g031100 41.401 157 91 1 1 157 1 156 4.33e-37 130
MS.gene88159.t1 MTR_2g016210 40.789 152 90 0 6 157 5 156 1.19e-36 129
MS.gene88159.t1 MTR_1g077390 40.260 154 90 2 4 157 3 154 7.20e-33 117
MS.gene88159.t1 MTR_1g090783 38.961 154 92 2 4 157 2 153 7.87e-33 117
MS.gene88159.t1 MTR_1g090710 38.994 159 95 2 1 159 1 157 2.34e-32 116
MS.gene88159.t1 MTR_1g090697 39.103 156 93 2 4 159 3 156 7.18e-32 114
MS.gene88159.t1 MTR_3g465410 39.416 137 83 0 30 166 1 137 3.18e-31 112
MS.gene88159.t1 MTR_7g011950 42.208 154 87 2 4 157 3 154 2.36e-30 110
MS.gene88159.t1 MTR_1g077320 42.208 154 87 2 4 157 3 154 2.38e-30 110
MS.gene88159.t1 MTR_1g084950 42.857 154 86 2 4 157 3 154 2.77e-30 110
MS.gene88159.t1 MTR_4g028800 77.273 66 13 1 6 71 5 68 8.39e-29 104
MS.gene88159.t1 MTR_4g028720 40.909 154 89 2 4 157 3 154 9.12e-29 107
MS.gene88159.t1 MTR_1g077300 42.208 154 85 2 4 157 3 152 2.10e-27 103
MS.gene88159.t1 MTR_3g466900 37.692 130 80 1 33 162 2 130 2.43e-27 102
MS.gene88159.t1 MTR_3g031240 32.704 159 106 1 1 159 1 158 4.62e-27 103
MS.gene88159.t1 MTR_7g055800 49.573 117 31 2 4 120 3 91 1.00e-26 99.4
MS.gene88159.t1 MTR_3g466930 35.385 130 83 1 33 162 2 130 4.10e-25 96.7
MS.gene88159.t1 MTR_4g019670 38.462 156 80 2 3 158 5 144 6.21e-25 102
MS.gene88159.t1 MTR_7g106510 37.821 156 81 2 3 158 5 144 7.78e-25 102
MS.gene88159.t1 MTR_2g035590 59.794 97 38 1 75 170 1 97 1.08e-24 94.4
MS.gene88159.t1 MTR_7g055790 53.211 109 33 1 4 112 61 151 1.16e-24 95.9
MS.gene88159.t1 MTR_3g093900 29.016 193 126 2 3 195 5 186 2.18e-24 101
MS.gene88159.t1 MTR_2g035580 34.437 151 98 1 7 157 6 155 5.92e-22 89.0
MS.gene88159.t1 MTR_7g055940 48.077 104 26 2 4 107 3 78 4.54e-21 84.3
MS.gene88159.t1 MTR_5g047560 40.870 115 51 2 4 118 3 100 4.91e-19 80.9
MS.gene88159.t1 MTR_4g084780 57.692 52 22 0 75 126 1 52 1.39e-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.gene88159.t1 AT5G48670 53.165 158 73 1 4 161 3 159 4.33e-44 151
MS.gene88159.t1 AT1G65300 44.444 153 84 1 4 156 2 153 2.38e-39 137
MS.gene88159.t1 AT5G26630 41.872 203 101 3 4 204 3 190 7.42e-39 134
MS.gene88159.t1 AT1G65330 40.000 185 97 2 4 188 2 172 2.13e-38 135
MS.gene88159.t1 AT5G26650 40.244 164 97 1 6 169 3 165 2.76e-35 129
MS.gene88159.t1 AT5G27960 39.634 164 98 1 6 169 3 165 1.58e-34 126
MS.gene88159.t1 AT1G31630 34.615 182 104 3 4 185 2 168 4.35e-33 122
MS.gene88159.t1 AT1G31640 38.411 151 91 2 4 154 2 150 4.19e-30 117
MS.gene88159.t1 AT5G27810 53.763 93 43 0 30 122 1 93 5.85e-29 106
MS.gene88159.t1 AT3G05860 38.514 148 90 1 4 151 3 149 2.63e-28 107
MS.gene88159.t1 AT3G05860 38.514 148 90 1 4 151 3 149 1.05e-27 106
MS.gene88159.t1 AT3G05860 38.514 148 90 1 4 151 3 149 1.07e-27 107
MS.gene88159.t1 AT2G28700 35.758 165 101 2 4 166 3 164 4.71e-26 103
MS.gene88159.t1 AT5G26580 35.762 151 82 2 6 156 5 140 2.70e-24 99.8
MS.gene88159.t1 AT1G22590 31.210 157 103 2 1 157 1 152 3.94e-23 92.4
MS.gene88159.t1 AT5G06500 34.868 152 97 2 4 155 3 152 4.78e-19 83.6
MS.gene88159.t1 AT2G40210 39.098 133 79 2 4 135 3 134 2.91e-17 80.5
MS.gene88159.t1 AT5G58890 37.795 127 68 5 7 124 6 130 1.99e-14 71.6
MS.gene88159.t1 AT5G55690 41.772 79 38 3 1 72 1 78 6.62e-11 61.2
MS.gene88159.t1 AT5G55690 41.772 79 38 3 1 72 1 78 6.62e-11 61.2

Find 60 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4.3:-68799963 MS.gene88159:CDS
GAGTGAAGAAATGGCAATTA+TGG 0.233693 4.3:-68799701 MS.gene88159:CDS
CCATTTGGTGAGGTCAATTC+TGG 0.238528 4.3:-68799580 MS.gene88159:CDS
TCAATTTCTCTTCAGCCTTC+AGG 0.259829 4.3:+68799986 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4.3:-68800196 MS.gene88159:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.3:-68800116 MS.gene88159:CDS
AAACCAAGTCCAACTCAAAA+TGG 0.356752 4.3:-68799761 MS.gene88159:CDS
ATAATGTCATCATCATTAAT+AGG 0.375800 4.3:+68799658 None:intergenic
GAAGCCTTTGCCATAGTGTA+TGG 0.388094 4.3:-68800144 MS.gene88159:CDS
TATGCAAAGTCAATTATTGA+TGG 0.408286 4.3:-68799638 MS.gene88159:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.418788 4.3:+68800120 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4.3:-68799962 MS.gene88159:CDS
GTGAGGTCAATTCTGGACTT+TGG 0.420430 4.3:-68799573 MS.gene88159:CDS
AGTGAAGAAATGGCAATTAT+GGG 0.424565 4.3:-68799700 MS.gene88159:CDS
GGTCTGATTTACTACCTTGA+AGG 0.436579 4.3:-68799552 None:intergenic
GAAGGATGTTAGCAGACGTT+TGG 0.439330 4.3:-68799827 MS.gene88159:CDS
AGCATCTAGGAGTGAAGAAA+TGG 0.457574 4.3:-68799710 MS.gene88159:CDS
AACCTTACTTCTTCTACCCA+TGG 0.464315 4.3:+68800272 None:intergenic
CTCATAAGGTCCATACACTA+TGG 0.467279 4.3:+68800134 None:intergenic
TTATGGGTCATGGCCATGTT+GGG 0.476409 4.3:-68799684 MS.gene88159:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4.3:-68799629 MS.gene88159:CDS
GTTGATTGACCACAATTTGA+AGG 0.487410 4.3:-68799845 MS.gene88159:CDS
TCTGGTAAAGGCCAAATCTC+AGG 0.493519 4.3:+68800105 None:intergenic
AACCATGGGTAGAAGAAGTA+AGG 0.501192 4.3:-68800274 None:intergenic
CCAGAATTGACCTCACCAAA+TGG 0.507378 4.3:+68799580 None:intergenic
TGGATATGAGTTATCTTGCT+TGG 0.509186 4.3:-68799867 MS.gene88159:CDS
GATTGGACACCCTCTGGTAA+AGG 0.514238 4.3:+68800093 None:intergenic
TTAGCAGACGTTTGGAAGCA+TGG 0.514834 4.3:-68799819 MS.gene88159:CDS
TGCAACATCATTGACAATGA+AGG 0.517037 4.3:+68800242 None:intergenic
ATGAGTCAATGTCTTAATGA+AGG 0.517500 4.3:-68799919 MS.gene88159:CDS
CAATGATCAAAATCAAATCA+TGG 0.521352 4.3:-68799791 MS.gene88159:CDS
AGCACAGATTGGACACCCTC+TGG 0.522070 4.3:+68800087 None:intergenic
CACCACTTCTAGCAGCATCT+AGG 0.525777 4.3:-68799723 MS.gene88159:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4.3:+68800013 None:intergenic
AGAGACTTTCTTGACACAAA+GGG 0.533444 4.3:-68800010 MS.gene88159:CDS
GTGCAAGAGACAGTGCCATT+TGG 0.542398 4.3:-68799595 MS.gene88159:CDS
GAAATGGCAATTATGGGTCA+TGG 0.549964 4.3:-68799694 MS.gene88159:CDS
TGCTAACATCCTTCAAATTG+TGG 0.552324 4.3:+68799836 None:intergenic
TAGCAGACGTTTGGAAGCAT+GGG 0.557068 4.3:-68799818 MS.gene88159:CDS
GAGATTTGGCCTTTACCAGA+GGG 0.563951 4.3:-68800102 MS.gene88159:CDS
ATTATGGGTCATGGCCATGT+TGG 0.565284 4.3:-68799685 MS.gene88159:CDS
CTTGACACAAAGGGTCCTGA+AGG 0.570745 4.3:-68800001 MS.gene88159:CDS
CTCCTAGATGCTGCTAGAAG+TGG 0.571630 4.3:+68799721 None:intergenic
CATTAATAGGTATCCCAACA+TGG 0.589301 4.3:+68799671 None:intergenic
TCATTGTCAATGATGTTGCA+AGG 0.595963 4.3:-68800239 MS.gene88159:CDS
AAAGGCCAAATCTCAGGTTG+AGG 0.605277 4.3:+68800111 None:intergenic
CTAGATGCTGCTAGAAGTGG+TGG 0.605478 4.3:+68799724 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.3:-68799622 MS.gene88159:CDS
AAAGGCTTCAATGCCACAGA+GGG 0.618725 4.3:+68800158 None:intergenic
ATCATACAAGAAAAGAACGA+AGG 0.618898 4.3:-68800211 MS.gene88159:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4.3:-68800210 MS.gene88159:CDS
AAGAGACTTTCTTGACACAA+AGG 0.620991 4.3:-68800011 MS.gene88159:CDS
TGAGATTTGGCCTTTACCAG+AGG 0.625137 4.3:-68800103 MS.gene88159:CDS
GATGCTGCTAGAAGTGGTGG+TGG 0.633563 4.3:+68799727 None:intergenic
AGGTCCATACACTATGGCAA+AGG 0.638234 4.3:+68800140 None:intergenic
AGAGACAGTGCCATTTGGTG+AGG 0.639188 4.3:-68799590 MS.gene88159:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4.3:-68799626 MS.gene88159:CDS
GCATGACAATATGTCAACAA+TGG 0.671130 4.3:-68799887 MS.gene88159:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4.3:-68800171 MS.gene88159:CDS
CAAAGGCTTCAATGCCACAG+AGG 0.706392 4.3:+68800157 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG - chr4.3:68799862-68799881 MS.gene88159:CDS 20.0%
!! ATAATGTCATCATCATTAAT+AGG + chr4.3:68800170-68800189 None:intergenic 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG - chr4.3:68799863-68799882 MS.gene88159:CDS 20.0%
! CAATGATCAAAATCAAATCA+TGG - chr4.3:68800034-68800053 MS.gene88159:CDS 25.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.3:68800187-68800206 MS.gene88159:CDS 25.0%
AGTGAAGAAATGGCAATTAT+GGG - chr4.3:68800125-68800144 MS.gene88159:CDS 30.0%
ATCATACAAGAAAAGAACGA+AGG - chr4.3:68799614-68799633 MS.gene88159:CDS 30.0%
ATGAGTCAATGTCTTAATGA+AGG - chr4.3:68799906-68799925 MS.gene88159:CDS 30.0%
TCATACAAGAAAAGAACGAA+GGG - chr4.3:68799615-68799634 MS.gene88159:CDS 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.3:68800196-68800215 MS.gene88159:CDS 30.0%
AAACCAAGTCCAACTCAAAA+TGG - chr4.3:68800064-68800083 MS.gene88159:CDS 35.0%
AACGAAGGGTCTATTGAAAA+AGG - chr4.3:68799629-68799648 MS.gene88159:CDS 35.0%
AAGAGACTTTCTTGACACAA+AGG - chr4.3:68799814-68799833 MS.gene88159:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG - chr4.3:68799815-68799834 MS.gene88159:CDS 35.0%
CATTAATAGGTATCCCAACA+TGG + chr4.3:68800157-68800176 None:intergenic 35.0%
GAGTGAAGAAATGGCAATTA+TGG - chr4.3:68800124-68800143 MS.gene88159:CDS 35.0%
GCATGACAATATGTCAACAA+TGG - chr4.3:68799938-68799957 MS.gene88159:CDS 35.0%
GTTGATTGACCACAATTTGA+AGG - chr4.3:68799980-68799999 MS.gene88159:CDS 35.0%
TCATTGTCAATGATGTTGCA+AGG - chr4.3:68799586-68799605 MS.gene88159:CDS 35.0%
TGCAACATCATTGACAATGA+AGG + chr4.3:68799586-68799605 None:intergenic 35.0%
TGCTAACATCCTTCAAATTG+TGG + chr4.3:68799992-68800011 None:intergenic 35.0%
TGGATATGAGTTATCTTGCT+TGG - chr4.3:68799958-68799977 MS.gene88159:CDS 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4.3:68799815-68799834 None:intergenic 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.3:68800199-68800218 MS.gene88159:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG + chr4.3:68799752-68799771 None:intergenic 35.0%
AGCATCTAGGAGTGAAGAAA+TGG - chr4.3:68800115-68800134 MS.gene88159:CDS 40.0%
CTCATAAGGTCCATACACTA+TGG + chr4.3:68799694-68799713 None:intergenic 40.0%
GAAATGGCAATTATGGGTCA+TGG - chr4.3:68800131-68800150 MS.gene88159:CDS 40.0%
TCAATTTCTCTTCAGCCTTC+AGG + chr4.3:68799842-68799861 None:intergenic 40.0%
!! TTGTTGTCGCCATTTTGAGT+TGG + chr4.3:68800076-68800095 None:intergenic 40.0%
AAAGGCTTCAATGCCACAGA+GGG + chr4.3:68799670-68799689 None:intergenic 45.0%
AGGTCCATACACTATGGCAA+AGG + chr4.3:68799688-68799707 None:intergenic 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.3:68799709-68799728 MS.gene88159:CDS 45.0%
ATTATGGGTCATGGCCATGT+TGG - chr4.3:68800140-68800159 MS.gene88159:CDS 45.0%
CCAGAATTGACCTCACCAAA+TGG + chr4.3:68800248-68800267 None:intergenic 45.0%
GAAGCCTTTGCCATAGTGTA+TGG - chr4.3:68799681-68799700 MS.gene88159:CDS 45.0%
GAAGGATGTTAGCAGACGTT+TGG - chr4.3:68799998-68800017 MS.gene88159:CDS 45.0%
GTGAGGTCAATTCTGGACTT+TGG - chr4.3:68800252-68800271 MS.gene88159:CDS 45.0%
TCTGGTAAAGGCCAAATCTC+AGG + chr4.3:68799723-68799742 None:intergenic 45.0%
TTAGCAGACGTTTGGAAGCA+TGG - chr4.3:68800006-68800025 MS.gene88159:CDS 45.0%
TTATGGGTCATGGCCATGTT+GGG - chr4.3:68800141-68800160 MS.gene88159:CDS 45.0%
! AAAGGCCAAATCTCAGGTTG+AGG + chr4.3:68799717-68799736 None:intergenic 45.0%
! CCATTTGGTGAGGTCAATTC+TGG - chr4.3:68800245-68800264 MS.gene88159:CDS 45.0%
! GAGATTTGGCCTTTACCAGA+GGG - chr4.3:68799723-68799742 MS.gene88159:CDS 45.0%
! TAGCAGACGTTTGGAAGCAT+GGG - chr4.3:68800007-68800026 MS.gene88159:CDS 45.0%
! TGAGATTTGGCCTTTACCAG+AGG - chr4.3:68799722-68799741 MS.gene88159:CDS 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG + chr4.3:68799708-68799727 None:intergenic 45.0%
!!! TCGCCATTTTGAGTTGGACT+TGG + chr4.3:68800070-68800089 None:intergenic 45.0%
CAAAGGCTTCAATGCCACAG+AGG + chr4.3:68799671-68799690 None:intergenic 50.0%
CACCACTTCTAGCAGCATCT+AGG - chr4.3:68800102-68800121 MS.gene88159:CDS 50.0%
CTAGATGCTGCTAGAAGTGG+TGG + chr4.3:68800104-68800123 None:intergenic 50.0%
CTCCTAGATGCTGCTAGAAG+TGG + chr4.3:68800107-68800126 None:intergenic 50.0%
CTTGACACAAAGGGTCCTGA+AGG - chr4.3:68799824-68799843 MS.gene88159:CDS 50.0%
GATTGGACACCCTCTGGTAA+AGG + chr4.3:68799735-68799754 None:intergenic 50.0%
! GTGCAAGAGACAGTGCCATT+TGG - chr4.3:68800230-68800249 MS.gene88159:CDS 50.0%
!! AGAGACAGTGCCATTTGGTG+AGG - chr4.3:68800235-68800254 MS.gene88159:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.3:68800203-68800222 MS.gene88159:CDS 50.0%
AGCACAGATTGGACACCCTC+TGG + chr4.3:68799741-68799760 None:intergenic 55.0%
GATGCTGCTAGAAGTGGTGG+TGG + chr4.3:68800101-68800120 None:intergenic 55.0%
GCTGAACTTAGCACCCTCTG+TGG - chr4.3:68799654-68799673 MS.gene88159:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 68799555 68800292 68799555 ID=MS.gene88159
chr4.3 mRNA 68799555 68800292 68799555 ID=MS.gene88159.t1;Parent=MS.gene88159
chr4.3 exon 68799555 68800292 68799555 ID=MS.gene88159.t1.exon1;Parent=MS.gene88159.t1
chr4.3 CDS 68799555 68800292 68799555 ID=cds.MS.gene88159.t1;Parent=MS.gene88159.t1
Gene Sequence

>MS.gene88159

ATGGGTAGAAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGTTGCAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTTTGCCATAGTGTATGGACCTTATGAGCCTCAACCTGAGATTTGGCCTTTACCAGAGGGTGTCCAATCTGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTCCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGAGTCAATGTCTTAATGAAGGTAAAGTTGTGCATGACAATATGTCAACAATGGATATGAGTTATCTTGCTTGGTTGATTGACCACAATTTGAAGGATGTTAGCAGACGTTTGGAAGCATGGGATAACAATGATCAAAATCAAATCATGGCTATTCAAAACCAAGTCCAACTCAAAATGGCGACAACAATACCACCACCACTTCTAGCAGCATCTAGGAGTGAAGAAATGGCAATTATGGGTCATGGCCATGTTGGGATACCTATTAATGATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCATTTGGTGAGGTCAATTCTGGACTTTGGTCTGATTTACTACCTTGA
Protein sequence

>MS.gene88159.t1

MGRRSKVKLAFIVNDVARKASYKKRTKGLLKKVAELSTLCGIEAFAIVYGPYEPQPEIWPLPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLKKQRKENREQEMTILMSQCLNEGKVVHDNMSTMDMSYLAWLIDHNLKDVSRRLEAWDNNDQNQIMAIQNQVQLKMATTIPPPLLAASRSEEMAIMGHGHVGIPINDDDIMQSQLLMDSMVAGNVQETVPFGEVNSGLWSDLLP