AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0595110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0595110 MtrunA17_Chr4g0014031 71.795 234 49 2 1 222 1 229 1.65e-112 321
Msa0595110 MtrunA17_Chr4g0014131 70.492 244 37 2 1 222 1 231 1.98e-110 316
Msa0595110 MtrunA17_Chr4g0014321 58.009 231 88 1 1 222 1 231 3.73e-96 280
Msa0595110 MtrunA17_Chr8g0351751 59.514 247 75 4 1 222 1 247 1.06e-92 271
Msa0595110 MtrunA17_Chr4g0013041 64.615 195 61 2 1 195 1 187 3.58e-89 261
Msa0595110 MtrunA17_Chr4g0014121 80.255 157 31 0 1 157 29 185 2.10e-81 241
Msa0595110 MtrunA17_Chr3g0110131 48.760 242 97 6 1 219 1 238 3.25e-63 196
Msa0595110 MtrunA17_Chr3g0107381 44.749 219 105 4 1 214 1 208 4.05e-61 191
Msa0595110 MtrunA17_Chr2g0296831 71.311 122 35 0 1 122 1 122 2.20e-51 162
Msa0595110 MtrunA17_Chr3g0107331 48.344 151 77 1 3 153 2 151 3.47e-45 148
Msa0595110 MtrunA17_Chr5g0432691 45.806 155 83 1 1 155 1 154 2.42e-44 145
Msa0595110 MtrunA17_Chr3g0107351 46.053 152 81 1 3 154 2 152 1.07e-43 144
Msa0595110 MtrunA17_Chr5g0420351 44.872 156 84 2 1 156 1 154 1.20e-41 139
Msa0595110 MtrunA17_Chr3g0107361 44.079 152 84 1 3 154 2 152 3.61e-41 137
Msa0595110 MtrunA17_Chr3g0107461 40.385 156 93 0 1 156 1 156 4.83e-41 137
Msa0595110 MtrunA17_Chr3g0107341 45.395 152 82 1 3 154 2 152 5.94e-41 137
Msa0595110 MtrunA17_Chr2g0283941 38.983 177 107 1 1 176 1 177 1.86e-39 135
Msa0595110 MtrunA17_Chr1g0188681 39.744 156 92 2 1 156 1 154 1.01e-36 126
Msa0595110 MtrunA17_Chr7g0218151 42.949 156 87 2 1 156 1 154 5.27e-36 124
Msa0595110 MtrunA17_Chr1g0197321 43.137 153 75 3 1 153 1 141 9.30e-36 124
Msa0595110 MtrunA17_Chr1g0188661 42.949 156 87 2 1 156 1 154 7.82e-35 121
Msa0595110 MtrunA17_Chr1g0197461 39.610 154 91 2 3 156 2 153 8.26e-35 121
Msa0595110 MtrunA17_Chr4g0012761 42.308 156 88 2 1 156 1 154 2.79e-34 120
Msa0595110 MtrunA17_Chr1g0197261 40.000 150 88 2 1 150 1 148 2.90e-33 117
Msa0595110 MtrunA17_Chr1g0188651 42.949 156 85 2 1 156 1 152 3.21e-33 117
Msa0595110 MtrunA17_Chr1g0193311 42.949 156 87 2 1 156 1 154 3.92e-33 117
Msa0595110 MtrunA17_Chr3g0105791 42.063 126 73 0 29 154 1 126 8.75e-33 115
Msa0595110 MtrunA17_Chr4g0031421 42.063 126 73 0 29 154 1 126 1.52e-31 112
Msa0595110 MtrunA17_Chr3g0106421 32.143 196 121 4 29 219 1 189 1.58e-28 107
Msa0595110 MtrunA17_Chr7g0267601 39.370 127 77 0 3 129 6 132 1.30e-25 103
Msa0595110 MtrunA17_Chr4g0008701 40.800 125 74 0 3 127 6 130 1.33e-25 103
Msa0595110 MtrunA17_Chr2g0296861 35.669 157 100 1 1 157 1 156 7.52e-25 95.9
Msa0595110 MtrunA17_Chr3g0128721 34.459 148 93 1 3 150 6 149 2.48e-21 91.7
Msa0595110 MtrunA17_Chr3g0106501 34.615 130 81 2 29 156 1 128 1.02e-20 84.7
Msa0595110 MtrunA17_Chr2g0296851 58.025 81 34 0 74 154 1 81 2.20e-20 82.4
Msa0595110 MtrunA17_Chr6g0457851 30.000 160 97 6 1 154 11 161 1.91e-14 71.2
Msa0595110 MtrunA17_Chr6g0449861 36.283 113 65 4 1 107 9 120 2.91e-14 70.9
Msa0595110 MtrunA17_Chr1g0212151 32.558 129 75 4 1 123 1 123 3.78e-14 70.5
Msa0595110 MtrunA17_Chr6g0449851 37.168 113 64 4 1 107 1 112 4.18e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0595110 AT5G48670.1 54.194 155 68 2 1 154 1 153 7.81e-46 155
Msa0595110 AT5G26630.1 44.390 205 103 2 1 195 1 204 1.01e-43 146
Msa0595110 AT1G65330.1 43.452 168 85 2 3 161 2 168 1.70e-41 142
Msa0595110 AT1G65300.1 44.737 152 83 1 3 154 2 152 2.66e-41 142
Msa0595110 AT5G26650.1 41.071 168 88 2 5 162 3 169 1.32e-37 134
Msa0595110 AT5G27960.1 41.071 168 88 3 5 162 3 169 2.92e-37 132
Msa0595110 AT1G31630.1 36.310 168 96 3 3 161 2 167 1.15e-35 129
Msa0595110 AT2G28700.1 37.288 177 106 2 1 175 1 174 1.05e-33 123
Msa0595110 AT3G05860.2 36.709 158 99 1 1 158 1 157 1.67e-32 117
Msa0595110 AT1G31640.1 38.411 151 91 2 3 153 2 150 2.15e-32 122
Msa0595110 AT3G05860.1 36.709 158 99 1 1 158 1 157 6.81e-32 117
Msa0595110 AT3G05860.3 36.709 158 99 1 1 158 1 157 6.83e-32 117
Msa0595110 AT5G27810.1 53.763 93 43 0 29 121 1 93 3.37e-31 111
Msa0595110 AT1G22590.2 31.481 162 107 1 1 162 1 158 2.28e-26 100
Msa0595110 AT5G26580.1 35.065 154 85 2 1 154 1 139 9.22e-26 102
Msa0595110 AT5G06500.1 35.032 157 100 2 1 157 1 155 4.28e-23 93.6
Msa0595110 AT2G40210.1 40.945 127 74 1 1 127 1 126 1.76e-20 89.0
Msa0595110 AT5G58890.1 37.795 127 68 5 6 123 6 130 1.47e-15 74.3
Msa0595110 AT5G55690.1 41.026 78 39 2 1 71 1 78 7.39e-13 66.6
Msa0595110 AT5G55690.2 41.026 78 39 2 1 71 1 78 7.39e-13 66.6
Msa0595110 AT2G15660.1 30.702 114 74 2 37 150 30 138 2.99e-12 64.3

Find 59 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4_2:-23808066 Msa0595110:CDS
CCCTTTGGTGAGATCAATTC+TGG 0.238779 4_2:-23807749 Msa0595110:CDS
GAGCGAAGAAATGGCAATTA+TGG 0.251384 4_2:-23807870 Msa0595110:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4_2:+23807939 None:intergenic
ATCCTTCAAGGTAGTAAATC+AGG 0.301540 4_2:+23807719 None:intergenic
AAGAAAGGGTCTATTGAAAA+AGG 0.312767 4_2:-23808299 Msa0595110:CDS
ATCTCTGGCTGAGGCTCATA+AGG 0.350996 4_2:+23808223 None:intergenic
ATGAGCCTCAGCCAGAGATT+TGG 0.374512 4_2:-23808219 Msa0595110:CDS
ATAATGTCATCATTACTAAT+AGG 0.386658 4_2:+23807827 None:intergenic
GCCCTGATTTACTACCTTGA+AGG 0.388674 4_2:-23807721 None:intergenic
TCTTCGCTCCTAGATGTTGC+TGG 0.395294 4_2:+23807884 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.408286 4_2:-23807807 Msa0595110:CDS
GAAGGACATTGGTAGACGTT+TGG 0.410243 4_2:-23807930 Msa0595110:CDS
TCTGGTGAAGGCCAAATCTC+TGG 0.413104 4_2:+23808208 None:intergenic
AACATCTAGGAGCGAAGAAA+TGG 0.419677 4_2:-23807879 Msa0595110:CDS
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4_2:-23808065 Msa0595110:CDS
AGCGAAGAAATGGCAATTAT+GGG 0.425600 4_2:-23807869 Msa0595110:CDS
GTTGATTGACCATAATTTGA+AGG 0.445081 4_2:-23807948 Msa0595110:CDS
CTAGATGTTGCTGGAGGTGG+TGG 0.448647 4_2:+23807893 None:intergenic
CACAACCATGGCTAGAAGTA+AGG 0.461347 4_2:-23808377 None:intergenic
CTCCTAGATGTTGCTGGAGG+TGG 0.462235 4_2:+23807890 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4_2:+23808237 None:intergenic
ATCATACAAGAAAAGAAGAA+AGG 0.473094 4_2:-23808314 Msa0595110:CDS
CTTGACACAAAGGGTTCTGA+AGG 0.478789 4_2:-23808104 Msa0595110:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4_2:-23807798 Msa0595110:CDS
TTGATTTGAGTTATCTTACT+TGG 0.482489 4_2:-23807970 Msa0595110:CDS
TGCAGCATCATTGACAATGA+AGG 0.502295 4_2:+23808345 None:intergenic
GATGTTGCTGGAGGTGGTGG+TGG 0.506713 4_2:+23807896 None:intergenic
AGAGACTTTCTTGACACAAA+GGG 0.517022 4_2:-23808113 Msa0595110:CDS
GACCATAATTTGAAGGACAT+TGG 0.517963 4_2:-23807941 Msa0595110:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4_2:-23807927 Msa0595110:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4_2:+23808116 None:intergenic
TCATACAAGAAAAGAAGAAA+GGG 0.526600 4_2:-23808313 Msa0595110:CDS
CACCACCTCCAGCAACATCT+AGG 0.527539 4_2:-23807892 Msa0595110:CDS
TTTAACCTTACTTCTAGCCA+TGG 0.533701 4_2:+23808372 None:intergenic
ATGTATCATTGTCTCAATGA+AGG 0.546520 4_2:-23808022 Msa0595110:CDS
GAAATGGCAATTATGGGTCA+TGG 0.549964 4_2:-23807863 Msa0595110:CDS
CCAGAATTGATCTCACCAAA+GGG 0.554343 4_2:+23807749 None:intergenic
GTGCAAGAGACAGTGCCCTT+TGG 0.557727 4_2:-23807764 Msa0595110:CDS
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4_2:-23808247 Msa0595110:CDS
GAAGGCCAAATCTCTGGCTG+AGG 0.560020 4_2:+23808214 None:intergenic
TCTCTGGCTGAGGCTCATAA+GGG 0.571102 4_2:+23808224 None:intergenic
GAGATTTGGCCTTCACCAGA+GGG 0.580805 4_2:-23808205 Msa0595110:CDS
TGTGCACAACAATATTTCAA+CGG 0.585275 4_2:-23807993 Msa0595110:CDS
TCCTTCAAGGTAGTAAATCA+GGG 0.588454 4_2:+23807720 None:intergenic
TCCAGAATTGATCTCACCAA+AGG 0.590517 4_2:+23807748 None:intergenic
ATTATGGGTCATGGCCATGT+TGG 0.596869 4_2:-23807854 Msa0595110:CDS
GATTTGGCCTTCACCAGAGG+GGG 0.601928 4_2:-23808203 Msa0595110:CDS
TTGATGGACTCAATGGTGGC+TGG 0.607204 4_2:-23807791 Msa0595110:CDS
AAGAGACTTTCTTGACACAA+AGG 0.607804 4_2:-23808114 Msa0595110:CDS
AGAGATTTGGCCTTCACCAG+AGG 0.617598 4_2:-23808206 Msa0595110:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4_2:+23808243 None:intergenic
TACTAATAGGTATTCCAACA+TGG 0.652496 4_2:+23807840 None:intergenic
TCATTGTCAATGATGCTGCA+AGG 0.652548 4_2:-23808342 Msa0595110:CDS
TCGCTCCTAGATGTTGCTGG+AGG 0.665029 4_2:+23807887 None:intergenic
ATTATTGATGGACTCAATGG+TGG 0.666274 4_2:-23807795 Msa0595110:CDS
CACAGGCTTCAATGCCACAG+AGG 0.694030 4_2:+23808260 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.703414 4_2:-23808204 Msa0595110:CDS
GCTGAACTTAGCATCCTCTG+TGG 0.716967 4_2:-23808274 Msa0595110:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG - chr4_2:23808028-23808047 Msa0595110:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG - chr4_2:23808029-23808048 Msa0595110:CDS 20.0%
!! ATAATGTCATCATTACTAAT+AGG + chr4_2:23808270-23808289 None:intergenic 20.0%
! ATCATACAAGAAAAGAAGAA+AGG - chr4_2:23807780-23807799 Msa0595110:CDS 25.0%
! TCATACAAGAAAAGAAGAAA+GGG - chr4_2:23807781-23807800 Msa0595110:CDS 25.0%
!! TTGATTTGAGTTATCTTACT+TGG - chr4_2:23808124-23808143 Msa0595110:CDS 25.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4_2:23808287-23808306 Msa0595110:CDS 25.0%
AAGAAAGGGTCTATTGAAAA+AGG - chr4_2:23807795-23807814 Msa0595110:CDS 30.0%
ATGTATCATTGTCTCAATGA+AGG - chr4_2:23808072-23808091 Msa0595110:CDS 30.0%
TGTGCACAACAATATTTCAA+CGG - chr4_2:23808101-23808120 Msa0595110:CDS 30.0%
GTTGATTGACCATAATTTGA+AGG - chr4_2:23808146-23808165 Msa0595110:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG + chr4_2:23808158-23808177 None:intergenic 30.0%
TACTAATAGGTATTCCAACA+TGG + chr4_2:23808257-23808276 None:intergenic 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4_2:23808296-23808315 Msa0595110:CDS 30.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4_2:23807981-23808000 None:intergenic 35.0%
AAGAGACTTTCTTGACACAA+AGG - chr4_2:23807980-23807999 Msa0595110:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG - chr4_2:23807981-23808000 Msa0595110:CDS 35.0%
GACCATAATTTGAAGGACAT+TGG - chr4_2:23808153-23808172 Msa0595110:CDS 35.0%
AGCGAAGAAATGGCAATTAT+GGG - chr4_2:23808225-23808244 Msa0595110:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4_2:23808299-23808318 Msa0595110:CDS 35.0%
TGCAGCATCATTGACAATGA+AGG + chr4_2:23807752-23807771 None:intergenic 40.0%
TCATTGTCAATGATGCTGCA+AGG - chr4_2:23807752-23807771 Msa0595110:CDS 40.0%
!! TGAATTTTGAGAGCACGGAT+TGG + chr4_2:23807918-23807937 None:intergenic 40.0%
!! CGTCATGAATTTTGAGAGCA+CGG + chr4_2:23807923-23807942 None:intergenic 40.0%
AACATCTAGGAGCGAAGAAA+TGG - chr4_2:23808215-23808234 Msa0595110:CDS 40.0%
GAGCGAAGAAATGGCAATTA+TGG - chr4_2:23808224-23808243 Msa0595110:CDS 40.0%
GAAATGGCAATTATGGGTCA+TGG - chr4_2:23808231-23808250 Msa0595110:CDS 40.0%
CCAGAATTGATCTCACCAAA+GGG + chr4_2:23808348-23808367 None:intergenic 40.0%
TCCAGAATTGATCTCACCAA+AGG + chr4_2:23808349-23808368 None:intergenic 40.0%
CTCATAAGGGCCATACACTA+TGG + chr4_2:23807860-23807879 None:intergenic 45.0%
! CTTGACACAAAGGGTTCTGA+AGG - chr4_2:23807990-23808009 Msa0595110:CDS 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4_2:23808164-23808183 Msa0595110:CDS 45.0%
ATTATGGGTCATGGCCATGT+TGG - chr4_2:23808240-23808259 Msa0595110:CDS 45.0%
CCCTTTGGTGAGATCAATTC+TGG - chr4_2:23808345-23808364 Msa0595110:CDS 45.0%
GCTGAACTTAGCATCCTCTG+TGG - chr4_2:23807820-23807839 Msa0595110:CDS 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4_2:23807847-23807866 Msa0595110:CDS 50.0%
TCTCTGGCTGAGGCTCATAA+GGG + chr4_2:23807873-23807892 None:intergenic 50.0%
ATCTCTGGCTGAGGCTCATA+AGG + chr4_2:23807874-23807893 None:intergenic 50.0%
ATGAGCCTCAGCCAGAGATT+TGG - chr4_2:23807875-23807894 Msa0595110:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+TGG + chr4_2:23807889-23807908 None:intergenic 50.0%
! AGAGATTTGGCCTTCACCAG+AGG - chr4_2:23807888-23807907 Msa0595110:CDS 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4_2:23807889-23807908 Msa0595110:CDS 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4_2:23807890-23807909 Msa0595110:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4_2:23808167-23808186 Msa0595110:CDS 50.0%
TCTTCGCTCCTAGATGTTGC+TGG + chr4_2:23808213-23808232 None:intergenic 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4_2:23808303-23808322 Msa0595110:CDS 50.0%
CACAGGCTTCAATGCCACAG+AGG + chr4_2:23807837-23807856 None:intergenic 55.0%
AGGGCCATACACTATGGCAC+AGG + chr4_2:23807854-23807873 None:intergenic 55.0%
GAAGGCCAAATCTCTGGCTG+AGG + chr4_2:23807883-23807902 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4_2:23807891-23807910 Msa0595110:CDS 55.0%
CTAGATGTTGCTGGAGGTGG+TGG + chr4_2:23808204-23808223 None:intergenic 55.0%
CACCACCTCCAGCAACATCT+AGG - chr4_2:23808202-23808221 Msa0595110:CDS 55.0%
CTCCTAGATGTTGCTGGAGG+TGG + chr4_2:23808207-23808226 None:intergenic 55.0%
TCGCTCCTAGATGTTGCTGG+AGG + chr4_2:23808210-23808229 None:intergenic 55.0%
GTGCAAGAGACAGTGCCCTT+TGG - chr4_2:23808330-23808349 Msa0595110:CDS 55.0%
GATTGGACCCCCTCTGGTGA+AGG + chr4_2:23807901-23807920 None:intergenic 60.0%
! GATGTTGCTGGAGGTGGTGG+TGG + chr4_2:23808201-23808220 None:intergenic 60.0%
!! AGCACGGATTGGACCCCCTC+TGG + chr4_2:23807907-23807926 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 23807724 23808392 23807724 ID=Msa0595110;Name=Msa0595110
chr4_2 mRNA 23807724 23808392 23807724 ID=Msa0595110-mRNA-1;Parent=Msa0595110;Name=Msa0595110-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|222
chr4_2 exon 23807724 23808392 23807724 ID=Msa0595110-mRNA-1:exon:6434;Parent=Msa0595110-mRNA-1
chr4_2 CDS 23807724 23808392 23807724 ID=Msa0595110-mRNA-1:cds;Parent=Msa0595110-mRNA-1
Gene Sequence

>Msa0595110

ATGGCTAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGCTGCAAGGAAAGAATCATACAAGAAAAGAAGAAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCATCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCAGCCAGAGATTTGGCCTTCACCAGAGGGGGTCCAATCCGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTTCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGTCATTACTCATGTATCATTGTCTCAATGAAGGTAGAGTTGTGCACAACAATATTTCAACGGTTGATTTGAGTTATCTTACTTGGTTGATTGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACCACCACCTCCAGCAACATCTAGGAGCGAAGAAATGGCAATTATGGGTCATGGCCATGTTGGAATACCTATTAGTAATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCCTTTGGTGAGATCAATTCTGGAGTTTGCCCTGATTTACTACCTTGA
Protein sequence

>Msa0595110

MARSKVKLAFIVNDAARKESYKKRRKGLLKKVAELSILCGIEACAIVYGPYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLKKQRKENREQEMSLLMYHCLNEGRVVHNNISTVDLSYLTWLIDHNLKDIGRRLAATVPPPPPATSRSEEMAIMGHGHVGIPISNDDIMQSQLLMDSMVAGNVQETVPFGEINSGVCPDLLP*