AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88088

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88088.t1 MTR_4g032290 80.751 213 28 1 7 219 32 231 1.89e-124 352
MS.gene88088.t1 MTR_4g031910 79.812 213 28 1 7 219 32 229 5.95e-119 337
MS.gene88088.t1 MTR_4g032620 58.257 218 78 2 2 219 27 231 1.34e-85 253
MS.gene88088.t1 MTR_8g036130 59.471 227 77 4 2 219 27 247 7.32e-84 249
MS.gene88088.t1 MTR_4g032260 82.400 125 22 0 7 131 32 156 1.17e-74 223
MS.gene88088.t1 MTR_3g065100 44.811 212 110 3 7 216 32 238 3.94e-53 171
MS.gene88088.t1 MTR_4g032270 74.545 110 14 1 110 219 36 131 5.73e-52 164
MS.gene88088.t1 MTR_3g466980 55.039 129 57 1 2 130 27 154 3.32e-48 157
MS.gene88088.t1 MTR_2g035610 74.725 91 23 0 7 97 32 122 3.73e-42 139
MS.gene88088.t1 MTR_3g466830 41.606 137 79 1 2 138 26 161 1.77e-34 120
MS.gene88088.t1 MTR_4g063790 39.568 139 84 0 2 140 27 165 8.75e-33 117
MS.gene88088.t1 MTR_3g465410 39.416 137 83 0 4 140 1 137 9.60e-33 115
MS.gene88088.t1 MTR_3g466900 40.000 130 77 1 7 136 2 130 1.72e-31 112
MS.gene88088.t1 MTR_3g467080 39.231 130 79 0 2 131 27 156 3.60e-29 107
MS.gene88088.t1 MTR_3g466890 38.519 135 82 1 2 136 26 159 3.64e-29 107
MS.gene88088.t1 MTR_5g075380 39.062 128 77 1 2 129 27 153 1.07e-28 105
MS.gene88088.t1 MTR_3g466930 37.692 130 80 1 7 136 2 130 1.32e-28 104
MS.gene88088.t1 MTR_7g055800 57.303 89 23 1 6 94 18 91 2.57e-28 102
MS.gene88088.t1 MTR_3g031100 39.231 130 79 0 2 131 27 156 4.15e-28 106
MS.gene88088.t1 MTR_2g016210 36.154 130 83 0 2 131 27 156 6.01e-26 101
MS.gene88088.t1 MTR_5g047580 36.923 130 80 2 2 131 27 154 9.93e-24 93.2
MS.gene88088.t1 MTR_2g035590 57.732 97 40 1 49 144 1 97 1.03e-23 91.3
MS.gene88088.t1 MTR_4g028800 86.364 44 6 0 2 45 25 68 6.58e-23 88.2
MS.gene88088.t1 MTR_7g055940 56.579 76 18 1 6 81 18 78 3.83e-22 86.7
MS.gene88088.t1 MTR_1g084950 35.200 125 79 2 7 131 32 154 1.04e-21 87.8
MS.gene88088.t1 MTR_1g077320 34.400 125 80 2 7 131 32 154 3.49e-21 86.3
MS.gene88088.t1 MTR_1g077300 35.385 130 80 2 7 136 32 157 3.90e-21 86.3
MS.gene88088.t1 MTR_1g090697 33.333 132 86 2 2 133 27 156 8.06e-21 85.5
MS.gene88088.t1 MTR_1g077390 34.615 130 83 2 2 131 27 154 9.69e-21 85.1
MS.gene88088.t1 MTR_3g093900 34.746 118 77 0 2 119 30 147 1.46e-20 89.7
MS.gene88088.t1 MTR_7g011950 34.400 125 80 2 7 131 32 154 2.32e-20 84.3
MS.gene88088.t1 MTR_3g031240 31.818 132 90 0 2 133 27 158 3.68e-20 84.3
MS.gene88088.t1 MTR_4g028720 33.600 125 81 2 7 131 32 154 4.71e-20 83.6
MS.gene88088.t1 MTR_1g090710 30.303 132 91 1 2 133 27 157 1.88e-19 82.0
MS.gene88088.t1 MTR_4g019670 41.584 101 59 0 2 102 30 130 1.99e-19 86.3
MS.gene88088.t1 MTR_1g090783 31.538 130 87 2 2 131 26 153 2.37e-19 81.6
MS.gene88088.t1 MTR_7g106510 39.806 103 62 0 2 104 30 132 1.76e-18 83.6
MS.gene88088.t1 MTR_2g035580 34.615 130 84 1 2 131 27 155 8.69e-18 77.4
MS.gene88088.t1 MTR_7g055790 49.412 85 25 1 2 86 85 151 5.65e-15 69.7
MS.gene88088.t1 MTR_5g047560 39.474 76 45 1 17 92 26 100 1.90e-12 62.8
MS.gene88088.t1 MTR_4g084780 57.692 52 22 0 49 100 1 52 4.46e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88088.t1 AT5G48670 49.612 129 64 1 7 135 32 159 3.21e-36 129
MS.gene88088.t1 AT1G65300 45.736 129 69 1 2 130 26 153 1.53e-33 122
MS.gene88088.t1 AT5G27810 56.989 93 40 0 4 96 1 93 4.79e-32 113
MS.gene88088.t1 AT1G65330 40.127 157 80 2 2 158 26 168 1.09e-31 117
MS.gene88088.t1 AT5G26630 35.326 184 106 2 9 192 34 204 1.43e-29 110
MS.gene88088.t1 AT5G26650 38.028 142 87 1 2 143 25 165 4.26e-29 112
MS.gene88088.t1 AT5G27960 37.324 142 88 1 2 143 25 165 2.23e-28 109
MS.gene88088.t1 AT1G31640 40.157 127 74 2 2 128 26 150 1.50e-26 106
MS.gene88088.t1 AT1G31630 34.395 157 88 3 2 158 26 167 1.77e-26 104
MS.gene88088.t1 AT3G05860 40.496 121 71 1 2 122 27 146 2.28e-22 90.9
MS.gene88088.t1 AT3G05860 40.496 121 71 1 2 122 27 146 7.62e-22 90.5
MS.gene88088.t1 AT3G05860 40.496 121 71 1 2 122 27 146 7.69e-22 90.5
MS.gene88088.t1 AT2G28700 36.508 126 75 2 2 125 27 149 1.48e-19 85.5
MS.gene88088.t1 AT5G26580 34.109 129 70 2 2 130 27 140 2.04e-17 79.7
MS.gene88088.t1 AT1G22590 28.462 130 89 1 2 131 27 152 1.41e-16 74.3
MS.gene88088.t1 AT5G06500 36.458 96 61 0 2 97 27 122 2.52e-13 67.4
MS.gene88088.t1 AT2G40210 34.862 109 71 0 1 109 26 134 1.25e-12 66.2
MS.gene88088.t1 AT2G15660 23.926 163 102 4 13 173 31 173 1.04e-11 62.8

Find 57 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGTGAAGAAATGGCAATTA+TGG 0.233693 4.3:-68654818 MS.gene88088:CDS
TGAAACAAAGAAAAGATAAT+AGG 0.275750 4.3:-68655080 MS.gene88088:CDS
GTGAGGTCAATTCTGAAGTT+TGG 0.316605 4.3:-68654690 MS.gene88088:CDS
AACGATGGGTCTATTGAAAA+AGG 0.323964 4.3:-68655313 None:intergenic
TTCCTTCAAGGTAATAAATC+AGG 0.333441 4.3:+68654667 None:intergenic
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.3:-68655233 MS.gene88088:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.373927 4.3:+68655237 None:intergenic
ATAATGTCATCATCATTAAT+AGG 0.375800 4.3:+68654775 None:intergenic
CCGCCATTTCAAGTTGGACT+TGG 0.376976 4.3:+68654875 None:intergenic
GGCCTGATTTATTACCTTGA+AGG 0.402135 4.3:-68654669 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.408286 4.3:-68654755 MS.gene88088:CDS
GAAACAAAGAAAAGATAATA+GGG 0.419680 4.3:-68655079 MS.gene88088:CDS
AGTGAAGAAATGGCAATTAT+GGG 0.424565 4.3:-68654817 MS.gene88088:CDS
GAATCACGTTGGTAGACGTT+TGG 0.432671 4.3:-68654944 MS.gene88088:CDS
AAACCAAGTCCAACTTGAAA+TGG 0.439012 4.3:-68654878 MS.gene88088:CDS
CTCCTAGATGCTGCTGGAGG+TGG 0.449911 4.3:+68654838 None:intergenic
AGCATCTAGGAGTGAAGAAA+TGG 0.457574 4.3:-68654827 MS.gene88088:CDS
TCTGGTGAAGGCCAAATCTC+AGG 0.467267 4.3:+68655222 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4.3:+68655251 None:intergenic
CTAGATGCTGCTGGAGGTGG+TGG 0.469667 4.3:+68654841 None:intergenic
TCTTCACTCCTAGATGCTGC+TGG 0.474575 4.3:+68654832 None:intergenic
TTATGGGTCATGGCCATGTT+GGG 0.476409 4.3:-68654801 MS.gene88088:CDS
TTGGTAGACGTTTGGAAGCA+TGG 0.476773 4.3:-68654936 MS.gene88088:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4.3:-68654746 MS.gene88088:CDS
CACCACCTCCAGCAGCATCT+AGG 0.503861 4.3:-68654840 MS.gene88088:CDS
TGGATATGAGTTATCTTGCT+TGG 0.509186 4.3:-68654984 MS.gene88088:CDS
AGAGACTTTCTTGACACAAA+GGG 0.517022 4.3:-68655127 MS.gene88088:CDS
TCAGAATTGACCTCACCAAA+TGG 0.518052 4.3:+68654697 None:intergenic
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4.3:+68655130 None:intergenic
GATGCTGCTGGAGGTGGTGG+CGG 0.531345 4.3:+68654844 None:intergenic
TCTCAGGTTGAGGCTCATAA+GGG 0.533923 4.3:+68655238 None:intergenic
GTGCAAGAGACAGTGCCATT+TGG 0.542398 4.3:-68654712 MS.gene88088:CDS
GAAATGGCAATTATGGGTCA+TGG 0.549964 4.3:-68654811 MS.gene88088:CDS
TGGTAGACGTTTGGAAGCAT+GGG 0.550080 4.3:-68654935 MS.gene88088:CDS
ATGGCTCAATGTCTTAATGA+AGG 0.551341 4.3:-68655036 MS.gene88088:CDS
GAAGCTTGTGCCATAGTGTA+TGG 0.557418 4.3:-68655261 MS.gene88088:CDS
TACCAACGTGATTCAAATTG+TGG 0.563911 4.3:+68654953 None:intergenic
ATTATGGGTCATGGCCATGT+TGG 0.565284 4.3:-68654802 MS.gene88088:CDS
GAGATTTGGCCTTCACCAGA+GGG 0.565461 4.3:-68655219 MS.gene88088:CDS
GATTTGGCCTTCACCAGAGG+GGG 0.573799 4.3:-68655217 MS.gene88088:CDS
CATTAATAGGTATCCCAACA+TGG 0.589301 4.3:+68654788 None:intergenic
GAAGGCCAAATCTCAGGTTG+AGG 0.598100 4.3:+68655228 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.3:-68654739 MS.gene88088:CDS
AAGAGACTTTCTTGACACAA+AGG 0.607804 4.3:-68655128 MS.gene88088:CDS
GCACAACAATATGTCAACAA+TGG 0.611524 4.3:-68655004 MS.gene88088:CDS
TGAGATTTGGCCTTCACCAG+AGG 0.614269 4.3:-68655220 MS.gene88088:CDS
CCAAGTCCAACTTGAAATGG+CGG 0.616407 4.3:-68654875 MS.gene88088:CDS
ACAAGCTTCAATGCCACAGA+GGG 0.623111 4.3:+68655275 None:intergenic
TTGTTGCCGCCATTTCAAGT+TGG 0.623247 4.3:+68654869 None:intergenic
GCAAGAGATGACAATACTCA+TGG 0.625488 4.3:-68655055 MS.gene88088:CDS
AGAGACAGTGCCATTTGGTG+AGG 0.639188 4.3:-68654707 MS.gene88088:CDS
CACAAGCTTCAATGCCACAG+AGG 0.641156 4.3:+68655274 None:intergenic
TCACTCCTAGATGCTGCTGG+AGG 0.645942 4.3:+68654835 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.650878 4.3:-68655218 MS.gene88088:CDS
GACCACAATTTGAATCACGT+TGG 0.659174 4.3:-68654955 MS.gene88088:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4.3:-68654743 MS.gene88088:CDS
GATGAACTTAGCACCCTCTG+TGG 0.718700 4.3:-68655288 MS.gene88088:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATGTCATCATCATTAAT+AGG + chr4.3:68655209-68655228 None:intergenic 20.0%
!! GAAACAAAGAAAAGATAATA+GGG - chr4.3:68654902-68654921 MS.gene88088:CDS 20.0%
!! TGAAACAAAGAAAAGATAAT+AGG - chr4.3:68654901-68654920 MS.gene88088:CDS 20.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.3:68655226-68655245 MS.gene88088:CDS 25.0%
AGTGAAGAAATGGCAATTAT+GGG - chr4.3:68655164-68655183 MS.gene88088:CDS 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.3:68655235-68655254 MS.gene88088:CDS 30.0%
AAACCAAGTCCAACTTGAAA+TGG - chr4.3:68655103-68655122 MS.gene88088:CDS 35.0%
AAGAGACTTTCTTGACACAA+AGG - chr4.3:68654853-68654872 MS.gene88088:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG - chr4.3:68654854-68654873 MS.gene88088:CDS 35.0%
ATGGCTCAATGTCTTAATGA+AGG - chr4.3:68654945-68654964 MS.gene88088:CDS 35.0%
CATTAATAGGTATCCCAACA+TGG + chr4.3:68655196-68655215 None:intergenic 35.0%
GAGTGAAGAAATGGCAATTA+TGG - chr4.3:68655163-68655182 MS.gene88088:CDS 35.0%
GCACAACAATATGTCAACAA+TGG - chr4.3:68654977-68654996 MS.gene88088:CDS 35.0%
TACCAACGTGATTCAAATTG+TGG + chr4.3:68655031-68655050 None:intergenic 35.0%
TGGATATGAGTTATCTTGCT+TGG - chr4.3:68654997-68655016 MS.gene88088:CDS 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4.3:68654854-68654873 None:intergenic 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.3:68655238-68655257 MS.gene88088:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG + chr4.3:68654791-68654810 None:intergenic 35.0%
AGCATCTAGGAGTGAAGAAA+TGG - chr4.3:68655154-68655173 MS.gene88088:CDS 40.0%
GAAATGGCAATTATGGGTCA+TGG - chr4.3:68655170-68655189 MS.gene88088:CDS 40.0%
GACCACAATTTGAATCACGT+TGG - chr4.3:68655026-68655045 MS.gene88088:CDS 40.0%
GCAAGAGATGACAATACTCA+TGG - chr4.3:68654926-68654945 MS.gene88088:CDS 40.0%
TCAGAATTGACCTCACCAAA+TGG + chr4.3:68655287-68655306 None:intergenic 40.0%
!! GTGAGGTCAATTCTGAAGTT+TGG - chr4.3:68655291-68655310 MS.gene88088:CDS 40.0%
ACAAGCTTCAATGCCACAGA+GGG + chr4.3:68654709-68654728 None:intergenic 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.3:68654748-68654767 MS.gene88088:CDS 45.0%
ATTATGGGTCATGGCCATGT+TGG - chr4.3:68655179-68655198 MS.gene88088:CDS 45.0%
CCAAGTCCAACTTGAAATGG+CGG - chr4.3:68655106-68655125 MS.gene88088:CDS 45.0%
CTCATAAGGGCCATACACTA+TGG + chr4.3:68654733-68654752 None:intergenic 45.0%
GAAGCTTGTGCCATAGTGTA+TGG - chr4.3:68654720-68654739 MS.gene88088:CDS 45.0%
TTATGGGTCATGGCCATGTT+GGG - chr4.3:68655180-68655199 MS.gene88088:CDS 45.0%
TTGGTAGACGTTTGGAAGCA+TGG - chr4.3:68655045-68655064 MS.gene88088:CDS 45.0%
! GAATCACGTTGGTAGACGTT+TGG - chr4.3:68655037-68655056 MS.gene88088:CDS 45.0%
! TGGTAGACGTTTGGAAGCAT+GGG - chr4.3:68655046-68655065 MS.gene88088:CDS 45.0%
! TTGTTGCCGCCATTTCAAGT+TGG + chr4.3:68655115-68655134 None:intergenic 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG + chr4.3:68654747-68654766 None:intergenic 45.0%
!! TCTCAGGTTGAGGCTCATAA+GGG + chr4.3:68654746-68654765 None:intergenic 45.0%
CACAAGCTTCAATGCCACAG+AGG + chr4.3:68654710-68654729 None:intergenic 50.0%
GATGAACTTAGCACCCTCTG+TGG - chr4.3:68654693-68654712 MS.gene88088:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+AGG + chr4.3:68654762-68654781 None:intergenic 50.0%
TCTTCACTCCTAGATGCTGC+TGG + chr4.3:68655152-68655171 None:intergenic 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4.3:68654763-68654782 MS.gene88088:CDS 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG + chr4.3:68654756-68654775 None:intergenic 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4.3:68654762-68654781 MS.gene88088:CDS 50.0%
! GTGCAAGAGACAGTGCCATT+TGG - chr4.3:68655269-68655288 MS.gene88088:CDS 50.0%
! TGAGATTTGGCCTTCACCAG+AGG - chr4.3:68654761-68654780 MS.gene88088:CDS 50.0%
!! AGAGACAGTGCCATTTGGTG+AGG - chr4.3:68655274-68655293 MS.gene88088:CDS 50.0%
!! CCGCCATTTCAAGTTGGACT+TGG + chr4.3:68655109-68655128 None:intergenic 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.3:68655242-68655261 MS.gene88088:CDS 50.0%
TCACTCCTAGATGCTGCTGG+AGG + chr4.3:68655149-68655168 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4.3:68654764-68654783 MS.gene88088:CDS 55.0%
AGCACAGATTGGACCCCCTC+TGG + chr4.3:68654780-68654799 None:intergenic 60.0%
CACCACCTCCAGCAGCATCT+AGG - chr4.3:68655141-68655160 MS.gene88088:CDS 60.0%
CTAGATGCTGCTGGAGGTGG+TGG + chr4.3:68655143-68655162 None:intergenic 60.0%
CTCCTAGATGCTGCTGGAGG+TGG + chr4.3:68655146-68655165 None:intergenic 60.0%
GATTGGACCCCCTCTGGTGA+AGG + chr4.3:68654774-68654793 None:intergenic 60.0%
! GATGCTGCTGGAGGTGGTGG+CGG + chr4.3:68655140-68655159 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 68654672 68655331 68654672 ID=MS.gene88088
chr4.3 mRNA 68654672 68655331 68654672 ID=MS.gene88088.t1;Parent=MS.gene88088
chr4.3 exon 68654672 68655331 68654672 ID=MS.gene88088.t1.exon1;Parent=MS.gene88088.t1
chr4.3 CDS 68654672 68655331 68654672 ID=cds.MS.gene88088.t1;Parent=MS.gene88088.t1
Gene Sequence

>MS.gene88088

ATGGGTCTATTGAAAAAGGTTGATGAACTTAGCACCCTCTGTGGCATTGAAGCTTGTGCCATAGTGTATGGCCCTTATGAGCCTCAACCTGAGATTTGGCCTTCACCAGAGGGGGTCCAATCTGTGCTCTCAAAATTCATGACGATGCATGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTTCTGAAGACTGAAGAGAAATTGATGAAACAAAGAAAAGATAATAGGGAGCAAGAGATGACAATACTCATGGCTCAATGTCTTAATGAAGGCAAAGTTGTGCACAACAATATGTCAACAATGGATATGAGTTATCTTGCTTGGTTGATCGACCACAATTTGAATCACGTTGGTAGACGTTTGGAAGCATGGGATAACAATGATCAAAATCAAATCATTGCTATTCAAAACCAAGTCCAACTTGAAATGGCGGCAACAATACCGCCACCACCTCCAGCAGCATCTAGGAGTGAAGAAATGGCAATTATGGGTCATGGCCATGTTGGGATACCTATTAATGATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCATTTGGTGAGGTCAATTCTGAAGTTTGGCCTGATTTATTACCTTGA
Protein sequence

>MS.gene88088.t1

MGLLKKVDELSTLCGIEACAIVYGPYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKTEEKLMKQRKDNREQEMTILMAQCLNEGKVVHNNMSTMDMSYLAWLIDHNLNHVGRRLEAWDNNDQNQIIAIQNQVQLEMAATIPPPPPAASRSEEMAIMGHGHVGIPINDDDIMQSQLLMDSMVAGNVQETVPFGEVNSEVWPDLLP