AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene019352

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene019352.t1 MTR_8g036130 86.853 251 27 2 1 249 1 247 7.25e-152 423
MS.gene019352.t1 MTR_4g032620 59.839 249 82 2 1 249 1 231 1.53e-105 305
MS.gene019352.t1 MTR_4g031910 58.233 249 84 4 1 249 1 229 7.18e-90 265
MS.gene019352.t1 MTR_4g032290 56.471 255 81 5 1 249 1 231 8.64e-81 242
MS.gene019352.t1 MTR_3g065100 57.895 247 94 5 1 246 1 238 1.35e-79 239
MS.gene019352.t1 MTR_3g466980 52.549 255 77 9 1 245 1 221 1.87e-76 231
MS.gene019352.t1 MTR_4g032260 70.513 156 46 0 1 156 1 156 8.06e-67 204
MS.gene019352.t1 MTR_2g035610 77.049 122 28 0 1 122 1 122 1.03e-60 187
MS.gene019352.t1 MTR_3g466830 50.314 159 78 1 3 161 2 159 1.33e-54 173
MS.gene019352.t1 MTR_4g063790 44.379 169 94 0 1 169 1 169 9.62e-49 158
MS.gene019352.t1 MTR_3g466890 46.203 158 84 1 3 160 2 158 5.65e-47 154
MS.gene019352.t1 MTR_2g016210 45.238 168 88 1 1 168 1 164 1.24e-45 153
MS.gene019352.t1 MTR_3g467080 43.312 157 89 0 1 157 1 157 2.79e-45 149
MS.gene019352.t1 MTR_5g047580 45.860 157 83 2 1 157 1 155 2.71e-44 147
MS.gene019352.t1 MTR_3g031100 42.675 157 90 0 1 157 1 157 1.35e-42 145
MS.gene019352.t1 MTR_5g075380 40.909 154 90 1 1 154 1 153 3.59e-41 139
MS.gene019352.t1 MTR_3g031240 39.506 162 98 0 1 162 1 162 1.61e-38 132
MS.gene019352.t1 MTR_1g090783 40.385 156 91 2 3 158 2 155 5.06e-37 128
MS.gene019352.t1 MTR_7g011950 44.586 157 85 2 1 157 1 155 2.21e-36 126
MS.gene019352.t1 MTR_1g090697 37.975 158 96 2 1 158 1 156 5.29e-36 125
MS.gene019352.t1 MTR_1g084950 43.949 157 86 2 1 157 1 155 7.47e-36 125
MS.gene019352.t1 MTR_1g077390 39.490 157 93 2 1 157 1 155 1.22e-35 124
MS.gene019352.t1 MTR_1g090710 36.709 158 99 1 1 158 1 157 3.05e-35 123
MS.gene019352.t1 MTR_7g055800 56.303 119 24 2 1 119 1 91 2.80e-34 119
MS.gene019352.t1 MTR_1g077320 42.675 157 88 2 1 157 1 155 6.00e-34 120
MS.gene019352.t1 MTR_3g466900 41.085 129 75 1 32 160 2 129 6.49e-34 119
MS.gene019352.t1 MTR_4g028720 42.675 157 88 2 1 157 1 155 1.59e-33 119
MS.gene019352.t1 MTR_3g466930 41.860 129 74 1 32 160 2 129 9.24e-33 116
MS.gene019352.t1 MTR_3g465410 42.857 126 72 0 29 154 1 126 1.15e-32 116
MS.gene019352.t1 MTR_1g077300 43.949 157 84 2 1 157 1 153 6.94e-32 115
MS.gene019352.t1 MTR_2g035580 41.667 156 90 1 1 156 1 155 2.47e-31 113
MS.gene019352.t1 MTR_7g055790 55.856 111 31 1 1 111 59 151 1.34e-30 111
MS.gene019352.t1 MTR_4g028800 73.611 72 17 1 1 72 1 70 1.82e-30 108
MS.gene019352.t1 MTR_7g055940 55.660 106 19 2 1 106 1 78 3.47e-28 102
MS.gene019352.t1 MTR_2g035590 59.406 101 38 1 74 174 1 98 1.65e-27 102
MS.gene019352.t1 MTR_5g047560 36.306 157 82 3 1 157 1 139 7.76e-26 99.0
MS.gene019352.t1 MTR_4g019670 39.716 141 76 2 1 138 1 135 1.04e-25 105
MS.gene019352.t1 MTR_7g106510 38.298 141 78 2 1 138 1 135 1.78e-25 104
MS.gene019352.t1 MTR_3g093900 33.566 143 95 0 3 145 6 148 5.97e-24 100
MS.gene019352.t1 MTR_4g032270 41.739 115 48 2 135 249 36 131 4.61e-22 88.6
MS.gene019352.t1 MTR_4g084780 69.231 52 16 0 74 125 1 52 7.82e-18 78.2
MS.gene019352.t1 MTR_6g018920 28.125 160 100 6 1 154 1 151 9.76e-14 70.1
MS.gene019352.t1 MTR_1g114730 28.319 113 74 3 1 107 1 112 3.31e-12 65.9
MS.gene019352.t1 MTR_6g005450 31.858 113 70 4 1 107 1 112 5.07e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene019352.t1 AT5G48670 53.977 176 79 2 1 175 1 175 3.23e-58 187
MS.gene019352.t1 AT1G65300 44.172 163 90 1 3 165 2 163 3.80e-44 150
MS.gene019352.t1 AT5G26650 43.396 159 89 1 4 162 2 159 4.58e-42 147
MS.gene019352.t1 AT3G05860 44.512 164 90 1 1 164 1 163 7.58e-42 142
MS.gene019352.t1 AT5G26630 46.629 178 94 1 1 178 1 177 1.13e-41 142
MS.gene019352.t1 AT3G05860 40.500 200 109 3 1 199 1 191 1.53e-41 142
MS.gene019352.t1 AT3G05860 44.512 164 90 1 1 164 1 163 2.45e-41 142
MS.gene019352.t1 AT5G27960 42.767 159 90 1 4 162 2 159 2.86e-41 144
MS.gene019352.t1 AT1G65330 41.379 174 99 2 3 174 2 174 5.15e-40 139
MS.gene019352.t1 AT5G27810 59.140 93 38 0 29 121 1 93 8.35e-37 126
MS.gene019352.t1 AT1G31630 36.810 163 101 2 3 165 2 162 2.44e-36 131
MS.gene019352.t1 AT1G31640 37.423 163 100 2 3 165 2 162 6.79e-34 127
MS.gene019352.t1 AT2G28700 37.037 162 97 2 1 160 1 159 1.06e-33 124
MS.gene019352.t1 AT1G22590 33.742 163 104 1 1 163 1 159 4.87e-29 107
MS.gene019352.t1 AT5G26580 36.646 161 87 2 1 161 1 146 7.74e-29 112
MS.gene019352.t1 AT2G40210 40.152 132 79 0 1 132 1 132 5.26e-22 93.6
MS.gene019352.t1 AT5G06500 29.870 154 106 1 1 154 1 152 8.63e-20 85.5
MS.gene019352.t1 AT5G58890 41.964 112 56 4 1 105 1 110 6.90e-16 75.9
MS.gene019352.t1 AT5G55690 35.484 124 71 3 1 115 1 124 3.70e-15 73.6
MS.gene019352.t1 AT5G55690 35.484 124 71 3 1 115 1 124 3.70e-15 73.6
MS.gene019352.t1 AT2G15660 25.000 164 105 4 38 201 31 176 1.42e-12 65.9

Find 56 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGCTTTGTTCCATTTC+AGG 0.136228 8.3:+59557087 None:intergenic
TCCCAATGTCCTTCAAATTT+TGG 0.150964 8.3:+59556878 None:intergenic
GAAGCTTGTGCTATAATTTA+CGG 0.231910 8.3:-59557186 MS.gene019352:CDS
GACTAATCATGATTTGATTC+TGG 0.234615 8.3:+59556815 None:intergenic
ATGATGAGTCGTGACCATTT+TGG 0.256307 8.3:-59556727 MS.gene019352:CDS
CTAGTCTTCAAAGTGGATTT+TGG 0.265657 8.3:-59556600 MS.gene019352:CDS
TTTGGGATAGTTATGAATAA+TGG 0.329950 8.3:-59556709 MS.gene019352:CDS
TCAGACATTGAAACATTAGA+AGG 0.343484 8.3:+59556968 None:intergenic
ATGAACCACAACCTGAGATT+TGG 0.352882 8.3:-59557158 MS.gene019352:CDS
CTTTAGCCTTCATCACCCTT+TGG 0.360586 8.3:+59557037 None:intergenic
ACCAAAATTTGAAGGACATT+GGG 0.367874 8.3:-59556879 MS.gene019352:CDS
ATTCAAGACAATGCCTGAAA+TGG 0.391921 8.3:-59557100 MS.gene019352:CDS
TGAGATTTGGCCATCCCCTT+GGG 0.393251 8.3:-59557145 MS.gene019352:CDS
ATCTCAGGTTGTGGTTCATA+AGG 0.415912 8.3:+59557162 None:intergenic
TATTCATAACTATCCCAAAA+TGG 0.424398 8.3:+59556713 None:intergenic
GACCAAAATTTGAAGGACAT+TGG 0.425243 8.3:-59556880 MS.gene019352:CDS
GCGTCATGGGGATGACCAAA+TGG 0.428494 8.3:+59556622 None:intergenic
GGAAAGCAACATACAAGAAA+AGG 0.431751 8.3:-59557260 MS.gene019352:CDS
CTCATTCAAGGTAGTAGATT+AGG 0.433236 8.3:+59556577 None:intergenic
CATGTGATGGTGGTGCCATT+TGG 0.434827 8.3:+59556770 None:intergenic
AATTTGATGATGAATGATAA+TGG 0.435040 8.3:-59556658 MS.gene019352:CDS
GTTGATTGACCAAAATTTGA+AGG 0.435105 8.3:-59556887 MS.gene019352:CDS
GACGAACTAAGCACACTTTG+TGG 0.444181 8.3:-59557213 MS.gene019352:CDS
CAAGGGGATGGCCAAATCTC+AGG 0.453389 8.3:+59557147 None:intergenic
AATTGAACTTCTCTCTGAGT+TGG 0.458967 8.3:+59556793 None:intergenic
CTGAGATTTGGCCATCCCCT+TGG 0.462588 8.3:-59557146 MS.gene019352:CDS
TTTCACCTTTCTTCTAGTCA+TGG 0.469195 8.3:+59557311 None:intergenic
GAAGGACATTGGGAGAAGGT+TGG 0.475154 8.3:-59556869 MS.gene019352:CDS
TTGGAAGCAGTGGACAATAA+TGG 0.490759 8.3:-59556850 MS.gene019352:CDS
AACATACAAGAAAAGGAAGA+AGG 0.492306 8.3:-59557253 MS.gene019352:CDS
GGAGATGAGAAAGTCCCATT+TGG 0.495533 8.3:-59556637 MS.gene019352:CDS
ATGTTTCAATGTCTGAATGC+AGG 0.499753 8.3:-59556961 MS.gene019352:CDS
TCTTCATTCTTGACATGTGA+TGG 0.500207 8.3:+59556757 None:intergenic
TTGATGTGAATCATCTTACT+TGG 0.506323 8.3:-59556909 MS.gene019352:CDS
CATGAACCAAAGGGTGATGA+AGG 0.509359 8.3:-59557043 MS.gene019352:CDS
CGTCATGGGGATGACCAAAT+GGG 0.512246 8.3:+59556623 None:intergenic
TGGGAGAAGGTTGGAAGCAG+TGG 0.521549 8.3:-59556860 MS.gene019352:CDS
GAGAGAAGTTCAATTCCAAA+TGG 0.524320 8.3:-59556785 MS.gene019352:CDS
ACTTTGAAGACTAGCGTCAT+GGG 0.524361 8.3:+59556609 None:intergenic
CAAAACCATGACTAGAAGAA+AGG 0.529842 8.3:-59557316 None:intergenic
CACTTTGAAGACTAGCGTCA+TGG 0.544123 8.3:+59556608 None:intergenic
TGTTTCAATGTCTGAATGCA+GGG 0.544428 8.3:-59556960 MS.gene019352:CDS
ATTTGAAGGACATTGGGAGA+AGG 0.551499 8.3:-59556873 MS.gene019352:CDS
TGCAGCGTCATTGACAATGA+AGG 0.552900 8.3:+59557284 None:intergenic
AAGAGACTTTCATGAACCAA+AGG 0.569196 8.3:-59557053 MS.gene019352:CDS
GATGGCCAAATCTCAGGTTG+TGG 0.572435 8.3:+59557153 None:intergenic
GGTGATGAAGGCTAAAGAGC+AGG 0.574380 8.3:-59557031 MS.gene019352:CDS
TCATTCTTGACATGTGATGG+TGG 0.582023 8.3:+59556760 None:intergenic
GAGATTTGGCCATCCCCTTG+GGG 0.591825 8.3:-59557144 MS.gene019352:CDS
AGAGACTTTCATGAACCAAA+GGG 0.592104 8.3:-59557052 MS.gene019352:CDS
ACATACAAGAAAAGGAAGAA+GGG 0.593121 8.3:-59557252 MS.gene019352:CDS
TCATTGTCAATGACGCTGCA+AGG 0.601167 8.3:-59557281 MS.gene019352:CDS
CAGACATTGAAACATTAGAA+GGG 0.603894 8.3:+59556969 None:intergenic
CATGACGCTAGTCTTCAAAG+TGG 0.634478 8.3:-59556607 MS.gene019352:CDS
CTTTGAAGACTAGCGTCATG+GGG 0.666640 8.3:+59556610 None:intergenic
TGTGCAGAACAATATGTCAG+TGG 0.716818 8.3:-59556932 MS.gene019352:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTGATGATGAATGATAA+TGG - chr8.3:59557233-59557252 MS.gene019352:CDS 20.0%
! AAAACAACAAAAAGACAACA+AGG - chr8.3:59556887-59556906 MS.gene019352:CDS 25.0%
! TATTCATAACTATCCCAAAA+TGG + chr8.3:59557181-59557200 None:intergenic 25.0%
!! TTTGGGATAGTTATGAATAA+TGG - chr8.3:59557182-59557201 MS.gene019352:CDS 25.0%
AACATACAAGAAAAGGAAGA+AGG - chr8.3:59556638-59556657 MS.gene019352:CDS 30.0%
ACATACAAGAAAAGGAAGAA+GGG - chr8.3:59556639-59556658 MS.gene019352:CDS 30.0%
ACCAAAATTTGAAGGACATT+GGG - chr8.3:59557012-59557031 MS.gene019352:CDS 30.0%
CAGACATTGAAACATTAGAA+GGG + chr8.3:59556925-59556944 None:intergenic 30.0%
GAAGCTTGTGCTATAATTTA+CGG - chr8.3:59556705-59556724 MS.gene019352:CDS 30.0%
GACTAATCATGATTTGATTC+TGG + chr8.3:59557079-59557098 None:intergenic 30.0%
GTTGATTGACCAAAATTTGA+AGG - chr8.3:59557004-59557023 MS.gene019352:CDS 30.0%
TCAGACATTGAAACATTAGA+AGG + chr8.3:59556926-59556945 None:intergenic 30.0%
TTGATGTGAATCATCTTACT+TGG - chr8.3:59556982-59557001 MS.gene019352:CDS 30.0%
!! TGAATTTTGAGAGCACATTT+TGG + chr8.3:59556776-59556795 None:intergenic 30.0%
AAGAGACTTTCATGAACCAA+AGG - chr8.3:59556838-59556857 MS.gene019352:CDS 35.0%
AATTGAACTTCTCTCTGAGT+TGG + chr8.3:59557101-59557120 None:intergenic 35.0%
AGAGACTTTCATGAACCAAA+GGG - chr8.3:59556839-59556858 MS.gene019352:CDS 35.0%
ATGTTTCAATGTCTGAATGC+AGG - chr8.3:59556930-59556949 MS.gene019352:CDS 35.0%
ATTCAAGACAATGCCTGAAA+TGG - chr8.3:59556791-59556810 MS.gene019352:CDS 35.0%
GACCAAAATTTGAAGGACAT+TGG - chr8.3:59557011-59557030 MS.gene019352:CDS 35.0%
GAGAGAAGTTCAATTCCAAA+TGG - chr8.3:59557106-59557125 MS.gene019352:CDS 35.0%
GGAAAGCAACATACAAGAAA+AGG - chr8.3:59556631-59556650 MS.gene019352:CDS 35.0%
TCTTCATTCTTGACATGTGA+TGG + chr8.3:59557137-59557156 None:intergenic 35.0%
TGTTTCAATGTCTGAATGCA+GGG - chr8.3:59556931-59556950 MS.gene019352:CDS 35.0%
! TCCCAATGTCCTTCAAATTT+TGG + chr8.3:59557016-59557035 None:intergenic 35.0%
! TTCTTGCTTTGTTCCATTTC+AGG + chr8.3:59556807-59556826 None:intergenic 35.0%
!! CTAGTCTTCAAAGTGGATTT+TGG - chr8.3:59557291-59557310 MS.gene019352:CDS 35.0%
ATGAACCACAACCTGAGATT+TGG - chr8.3:59556733-59556752 MS.gene019352:CDS 40.0%
ATTTGAAGGACATTGGGAGA+AGG - chr8.3:59557018-59557037 MS.gene019352:CDS 40.0%
TCATTCTTGACATGTGATGG+TGG + chr8.3:59557134-59557153 None:intergenic 40.0%
TGTGCAGAACAATATGTCAG+TGG - chr8.3:59556959-59556978 MS.gene019352:CDS 40.0%
TTGGAAGCAGTGGACAATAA+TGG - chr8.3:59557041-59557060 MS.gene019352:CDS 40.0%
! ACTTTGAAGACTAGCGTCAT+GGG + chr8.3:59557285-59557304 None:intergenic 40.0%
! ATCTCAGGTTGTGGTTCATA+AGG + chr8.3:59556732-59556751 None:intergenic 40.0%
! ATGATGAGTCGTGACCATTT+TGG - chr8.3:59557164-59557183 MS.gene019352:CDS 40.0%
! TGATGAGTCGTGACCATTTT+GGG - chr8.3:59557165-59557184 MS.gene019352:CDS 40.0%
CATGAACCAAAGGGTGATGA+AGG - chr8.3:59556848-59556867 MS.gene019352:CDS 45.0%
GACGAACTAAGCACACTTTG+TGG - chr8.3:59556678-59556697 MS.gene019352:CDS 45.0%
GGAGATGAGAAAGTCCCATT+TGG - chr8.3:59557254-59557273 MS.gene019352:CDS 45.0%
TCATTGTCAATGACGCTGCA+AGG - chr8.3:59556610-59556629 MS.gene019352:CDS 45.0%
TGCAGCGTCATTGACAATGA+AGG + chr8.3:59556610-59556629 None:intergenic 45.0%
! CACTTTGAAGACTAGCGTCA+TGG + chr8.3:59557286-59557305 None:intergenic 45.0%
! CTTTAGCCTTCATCACCCTT+TGG + chr8.3:59556857-59556876 None:intergenic 45.0%
! CTTTGAAGACTAGCGTCATG+GGG + chr8.3:59557284-59557303 None:intergenic 45.0%
!! CATGACGCTAGTCTTCAAAG+TGG - chr8.3:59557284-59557303 MS.gene019352:CDS 45.0%
CGTCATGGGGATGACCAAAT+GGG + chr8.3:59557271-59557290 None:intergenic 50.0%
GAAGGACATTGGGAGAAGGT+TGG - chr8.3:59557022-59557041 MS.gene019352:CDS 50.0%
GGTGATGAAGGCTAAAGAGC+AGG - chr8.3:59556860-59556879 MS.gene019352:CDS 50.0%
TGAGATTTGGCCATCCCCTT+GGG - chr8.3:59556746-59556765 MS.gene019352:CDS 50.0%
! AGCACATTTTGGACTCCCCA+AGG + chr8.3:59556765-59556784 None:intergenic 50.0%
! CACATTTTGGACTCCCCAAG+GGG + chr8.3:59556763-59556782 None:intergenic 50.0%
! GATGGCCAAATCTCAGGTTG+TGG + chr8.3:59556741-59556760 None:intergenic 50.0%
! GCACATTTTGGACTCCCCAA+GGG + chr8.3:59556764-59556783 None:intergenic 50.0%
!! CATGTGATGGTGGTGCCATT+TGG + chr8.3:59557124-59557143 None:intergenic 50.0%
CAAGGGGATGGCCAAATCTC+AGG + chr8.3:59556747-59556766 None:intergenic 55.0%
CTGAGATTTGGCCATCCCCT+TGG - chr8.3:59556745-59556764 MS.gene019352:CDS 55.0%
GAGATTTGGCCATCCCCTTG+GGG - chr8.3:59556747-59556766 MS.gene019352:CDS 55.0%
GCGTCATGGGGATGACCAAA+TGG + chr8.3:59557272-59557291 None:intergenic 55.0%
TGGGAGAAGGTTGGAAGCAG+TGG - chr8.3:59557031-59557050 MS.gene019352:CDS 55.0%
! TTTTGGACTCCCCAAGGGGA+TGG + chr8.3:59556759-59556778 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 59556582 59557331 59556582 ID=MS.gene019352
chr8.3 mRNA 59556582 59557331 59556582 ID=MS.gene019352.t1;Parent=MS.gene019352
chr8.3 exon 59556582 59557331 59556582 ID=MS.gene019352.t1.exon1;Parent=MS.gene019352.t1
chr8.3 CDS 59556582 59557331 59556582 ID=cds.MS.gene019352.t1;Parent=MS.gene019352.t1
Gene Sequence

>MS.gene019352

ATGACTAGAAGAAAGGTGAAACTTGCCTTCATTGTCAATGACGCTGCAAGGAAAGCAACATACAAGAAAAGGAAGAAGGGTTTATTGAAGAAGATCGACGAACTAAGCACACTTTGTGGAATTGAAGCTTGTGCTATAATTTACGGTCCTTATGAACCACAACCTGAGATTTGGCCATCCCCTTGGGGAGTCCAAAATGTGCTCTCAAAATTCAAGACAATGCCTGAAATGGAACAAAGCAAGAAAATGATGAATCAAGAGACTTTCATGAACCAAAGGGTGATGAAGGCTAAAGAGCAGGTGAAAAAACAACAAAAAGACAACAAGGAGAAAGAGATGACCCTTCTAATGTTTCAATGTCTGAATGCAGGGAAAATTGTGCAGAACAATATGTCAGTGGTTGATGTGAATCATCTTACTTGGTTGATTGACCAAAATTTGAAGGACATTGGGAGAAGGTTGGAAGCAGTGGACAATAATGGTCAAATTCAAAGCCAGAATCAAATCATGATTAGTCCAACTCAGAGAGAAGTTCAATTCCAAATGGCACCACCATCACATGTCAAGAATGAAGAAATGTCGATGATGAGTCGTGACCATTTTGGGATAGTTATGAATAATGGTGACATCATGCAAAGACAATTCTTTATGAATTTGATGATGAATGATAATGGAGATGAGAAAGTCCCATTTGGTCATCCCCATGACGCTAGTCTTCAAAGTGGATTTTGGCCTAATCTACTACCTTGA
Protein sequence

>MS.gene019352.t1

MTRRKVKLAFIVNDAARKATYKKRKKGLLKKIDELSTLCGIEACAIIYGPYEPQPEIWPSPWGVQNVLSKFKTMPEMEQSKKMMNQETFMNQRVMKAKEQVKKQQKDNKEKEMTLLMFQCLNAGKIVQNNMSVVDVNHLTWLIDQNLKDIGRRLEAVDNNGQIQSQNQIMISPTQREVQFQMAPPSHVKNEEMSMMSRDHFGIVMNNGDIMQRQFFMNLMMNDNGDEKVPFGHPHDASLQSGFWPNLLP