AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584460

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584460 MtrunA17_Chr4g0014321 76.190 231 55 0 1 231 1 231 2.39e-129 364
Msa0584460 MtrunA17_Chr4g0013041 66.667 204 51 2 1 204 1 187 1.00e-90 265
Msa0584460 MtrunA17_Chr8g0351751 57.490 247 89 3 1 231 1 247 1.01e-86 257
Msa0584460 MtrunA17_Chr4g0014031 53.419 234 101 2 1 231 1 229 3.05e-76 229
Msa0584460 MtrunA17_Chr4g0014131 52.459 244 90 3 1 231 1 231 4.50e-70 214
Msa0584460 MtrunA17_Chr4g0014121 64.103 156 56 0 1 156 29 184 1.86e-58 183
Msa0584460 MtrunA17_Chr3g0110131 47.845 232 111 2 1 223 1 231 1.87e-57 182
Msa0584460 MtrunA17_Chr3g0107381 49.677 155 77 1 1 155 1 154 9.19e-52 167
Msa0584460 MtrunA17_Chr3g0107331 45.399 163 84 2 3 163 2 161 1.68e-45 149
Msa0584460 MtrunA17_Chr2g0296831 63.636 121 44 0 1 121 1 121 1.45e-44 145
Msa0584460 MtrunA17_Chr5g0420351 41.026 156 90 2 1 156 1 154 1.13e-40 136
Msa0584460 MtrunA17_Chr3g0107361 45.283 159 80 4 3 158 2 156 3.15e-39 133
Msa0584460 MtrunA17_Chr3g0107351 41.772 158 91 1 3 160 2 158 5.52e-39 132
Msa0584460 MtrunA17_Chr1g0197261 40.506 158 92 2 1 158 1 156 3.30e-38 130
Msa0584460 MtrunA17_Chr3g0107341 43.750 160 85 2 3 160 2 158 7.14e-38 129
Msa0584460 MtrunA17_Chr1g0197321 39.241 158 95 1 1 158 1 157 1.25e-36 126
Msa0584460 MtrunA17_Chr1g0188681 38.462 156 94 2 1 156 1 154 1.29e-36 126
Msa0584460 MtrunA17_Chr1g0193311 41.667 156 89 2 1 156 1 154 5.41e-35 122
Msa0584460 MtrunA17_Chr1g0197461 38.961 154 92 2 3 156 2 153 4.82e-34 119
Msa0584460 MtrunA17_Chr2g0283941 37.195 164 103 0 1 164 1 164 5.43e-34 122
Msa0584460 MtrunA17_Chr7g0218151 40.385 156 91 2 1 156 1 154 7.40e-34 119
Msa0584460 MtrunA17_Chr3g0107461 36.538 156 99 0 1 156 1 156 2.15e-33 118
Msa0584460 MtrunA17_Chr4g0012761 41.667 156 89 2 1 156 1 154 7.81e-33 116
Msa0584460 MtrunA17_Chr5g0432691 39.610 154 92 1 1 154 1 153 8.23e-33 116
Msa0584460 MtrunA17_Chr1g0188661 36.538 156 97 2 1 156 1 154 4.85e-29 107
Msa0584460 MtrunA17_Chr1g0188651 38.462 156 92 3 1 156 1 152 6.43e-26 99.0
Msa0584460 MtrunA17_Chr3g0105791 39.683 126 76 0 29 154 1 126 6.77e-26 98.2
Msa0584460 MtrunA17_Chr4g0031421 39.683 126 76 0 29 154 1 126 7.07e-26 98.2
Msa0584460 MtrunA17_Chr3g0106421 35.766 137 88 0 29 165 1 137 5.34e-24 95.5
Msa0584460 MtrunA17_Chr2g0296861 34.615 156 101 1 1 156 1 155 2.54e-23 92.0
Msa0584460 MtrunA17_Chr7g0267601 34.356 163 100 3 1 157 1 162 1.85e-21 92.4
Msa0584460 MtrunA17_Chr4g0008701 33.742 163 101 3 1 157 1 162 2.57e-21 92.0
Msa0584460 MtrunA17_Chr3g0106501 30.597 134 93 0 29 162 1 134 2.64e-19 81.3
Msa0584460 MtrunA17_Chr3g0128721 35.484 124 78 2 3 125 6 128 1.01e-17 81.6
Msa0584460 MtrunA17_Chr6g0457851 30.625 160 96 6 1 154 11 161 1.44e-14 72.0
Msa0584460 MtrunA17_Chr1g0212151 35.043 117 61 4 1 103 1 116 3.27e-13 67.8
Msa0584460 MtrunA17_Chr6g0449861 37.288 118 59 5 1 104 9 125 1.69e-12 65.9
Msa0584460 MtrunA17_Chr6g0449851 36.667 120 67 5 1 114 1 117 2.97e-12 65.1
Msa0584460 MtrunA17_Chr2g0296851 46.429 84 45 0 77 160 4 87 8.30e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584460 AT5G48670.1 52.500 160 75 1 1 160 1 159 2.37e-48 162
Msa0584460 AT1G65300.1 38.690 168 102 1 3 170 2 168 5.05e-35 126
Msa0584460 AT5G26630.1 43.226 155 87 1 1 155 1 154 7.93e-35 124
Msa0584460 AT5G26650.1 40.523 153 90 1 4 156 2 153 6.92e-34 125
Msa0584460 AT5G27960.1 39.869 153 91 1 4 156 2 153 1.88e-33 123
Msa0584460 AT3G05860.2 40.000 150 89 1 1 150 1 149 2.67e-33 119
Msa0584460 AT3G05860.3 40.000 150 89 1 1 150 1 149 8.92e-33 119
Msa0584460 AT3G05860.1 40.000 150 89 1 1 150 1 149 1.08e-32 119
Msa0584460 AT5G27810.1 46.552 116 62 0 29 144 1 116 1.79e-32 114
Msa0584460 AT1G65330.1 39.869 153 91 1 3 155 2 153 4.30e-32 118
Msa0584460 AT1G31630.1 36.486 148 92 2 3 150 2 147 5.03e-30 114
Msa0584460 AT2G28700.1 36.184 152 92 2 1 150 1 149 2.89e-27 107
Msa0584460 AT1G31640.1 34.437 151 97 2 3 153 2 150 3.84e-27 108
Msa0584460 AT5G26580.1 35.484 155 85 2 1 155 1 140 2.26e-24 99.4
Msa0584460 AT1G22590.2 30.769 156 104 1 1 156 1 152 3.86e-23 92.0
Msa0584460 AT5G06500.1 36.364 154 96 1 1 154 1 152 6.68e-23 93.6
Msa0584460 AT2G40210.1 42.017 119 69 0 1 119 1 119 4.03e-20 88.2
Msa0584460 AT5G58890.1 29.114 237 135 9 1 226 1 215 1.62e-12 65.9
Msa0584460 AT5G55690.1 43.038 79 38 2 1 72 1 79 4.67e-12 64.3
Msa0584460 AT5G55690.2 43.038 79 38 2 1 72 1 79 4.67e-12 64.3

Find 60 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGCTTGTGCCATAGTTTA+TGG 0.132446 4_2:+3914905 Msa0584460:CDS
CTTCATTACTGAATGTAAAT+TGG 0.134340 4_2:-3915294 None:intergenic
CACAACAATGACTAGGAAAA+AGG 0.228363 4_2:+3914775 None:intergenic
TCATTGTCGATGATGATTCT+AGG 0.260008 4_2:+3914810 Msa0584460:CDS
TTCATTTAAGGTAGTAGATT+TGG 0.271423 4_2:-3915460 None:intergenic
TTCATTACTGAATGTAAATT+GGG 0.292002 4_2:-3915293 None:intergenic
ATGTAAATTGGGGTGGTATT+TGG 0.295627 4_2:-3915282 None:intergenic
CATTGAAAGTCAATCTTTCA+TGG 0.320633 4_2:+3915372 Msa0584460:CDS
TACATTCAGTAATGAAGAAA+TGG 0.368381 4_2:+3915300 Msa0584460:CDS
TACCAACCTCCTTCAATTTG+TGG 0.372241 4_2:-3915213 None:intergenic
ATGTTGTCGCCATTATTCAT+AGG 0.374511 4_2:-3915352 None:intergenic
ACGAGCCTCAACCAGAGATT+TGG 0.379412 4_2:+3914933 Msa0584460:CDS
GGAAAGCAACATACAATAGA+AGG 0.409123 4_2:+3914831 Msa0584460:CDS
TAATGAAGAAATGGCAATGA+TGG 0.426450 4_2:+3915309 Msa0584460:CDS
GGAGATGAGTCGGTGCCATT+TGG 0.429830 4_2:+3915415 Msa0584460:CDS
TGTGGTGACGGCCAAATCTC+TGG 0.438262 4_2:-3914944 None:intergenic
AATTGAAGGAGGTTGGTAGA+AGG 0.442772 4_2:+3915218 Msa0584460:CDS
GAAGGAGGTTGGTAGAAGGT+TGG 0.444882 4_2:+3915222 Msa0584460:CDS
TATGCTGAATAATATGTCAT+TGG 0.454426 4_2:+3915159 Msa0584460:CDS
TGGTAGAAGGTTGGAAGCAG+AGG 0.457415 4_2:+3915231 Msa0584460:CDS
GTTGATTGACCACAAATTGA+AGG 0.458305 4_2:+3915204 Msa0584460:CDS
AGAGATTTGGCCGTCACCAC+AGG 0.458628 4_2:+3914946 Msa0584460:CDS
AAGAGACTTACATGAAAGAA+AGG 0.463147 4_2:+3915038 Msa0584460:CDS
ATCTCTGGTTGAGGCTCGTA+GGG 0.464949 4_2:-3914929 None:intergenic
TTGATTCAAAACATCTTTGT+TGG 0.470119 4_2:+3915182 Msa0584460:CDS
GCTGGAATGCCTATGAATAA+TGG 0.487571 4_2:+3915343 Msa0584460:CDS
ATTGAAAGTCAATCTTTCAT+GGG 0.502132 4_2:+3915373 Msa0584460:CDS
CTCGTAGGGTCCATAAACTA+TGG 0.509841 4_2:-3914915 None:intergenic
AGTAGATTTGGTAAAACTCT+AGG 0.510937 4_2:-3915448 None:intergenic
CTAGGATCGACTTCGCCAAA+TGG 0.512642 4_2:-3915430 None:intergenic
GACCACAAATTGAAGGAGGT+TGG 0.522187 4_2:+3915211 Msa0584460:CDS
CATGAAAGAAAGGGTTCTGA+AGG 0.524930 4_2:+3915048 Msa0584460:CDS
AATCTCTGGTTGAGGCTCGT+AGG 0.528825 4_2:-3914930 None:intergenic
ATAGGCATTCCAGCATGGCC+AGG 0.531063 4_2:-3915334 None:intergenic
GACGGCCAAATCTCTGGTTG+AGG 0.536979 4_2:-3914938 None:intergenic
GCGGAAGGGTCTACTGAAGA+AGG 0.542122 4_2:+3914853 Msa0584460:CDS
AGAATCATCATCGACAATGA+AGG 0.542377 4_2:-3914807 None:intergenic
ATGATGGGTCCTGGCCATGC+TGG 0.546828 4_2:+3915325 Msa0584460:CDS
GTTTGGACTCCCTGTGGTGA+CGG 0.547732 4_2:-3914956 None:intergenic
AAATTCAGAACAATGACTGT+GGG 0.557360 4_2:+3914989 Msa0584460:CDS
AAGGCATGATAACAAGGAGA+TGG 0.564923 4_2:+3915093 Msa0584460:CDS
AACATACAATAGAAGGCGGA+AGG 0.566279 4_2:+3914838 Msa0584460:CDS
GAAATGGCAATGATGGGTCC+TGG 0.575149 4_2:+3915316 Msa0584460:CDS
AATGAAGAAATGGCAATGAT+GGG 0.575476 4_2:+3915310 Msa0584460:CDS
AGAGACTTACATGAAAGAAA+GGG 0.577279 4_2:+3915039 Msa0584460:CDS
TATGAACTAAGCACTTTGTG+TGG 0.579542 4_2:+3914878 Msa0584460:CDS
GATACAAAGGCATGATAACA+AGG 0.593660 4_2:+3915087 Msa0584460:CDS
TCATTACTGAATGTAAATTG+GGG 0.597362 4_2:-3915292 None:intergenic
TATTCATAGGCATTCCAGCA+TGG 0.618391 4_2:-3915339 None:intergenic
AAAATTCAGAACAATGACTG+TGG 0.623795 4_2:+3914988 Msa0584460:CDS
GGCTTGATGATGAAAAGTAA+TGG 0.629083 4_2:+3915394 Msa0584460:CDS
TTACTGAATGTAAATTGGGG+TGG 0.630120 4_2:-3915289 None:intergenic
GATTGACCACAAATTGAAGG+AGG 0.630849 4_2:+3915207 Msa0584460:CDS
GAGATTTGGCCGTCACCACA+GGG 0.642312 4_2:+3914947 Msa0584460:CDS
GAAAAGTAATGGAGATGAGT+CGG 0.663391 4_2:+3915405 Msa0584460:CDS
ATTCAGAACAATGACTGTGG+GGG 0.672862 4_2:+3914991 Msa0584460:CDS
ACATACAATAGAAGGCGGAA+GGG 0.677825 4_2:+3914839 Msa0584460:CDS
AATTCAGAACAATGACTGTG+GGG 0.687730 4_2:+3914990 Msa0584460:CDS
AAGCAACATACAATAGAAGG+CGG 0.694844 4_2:+3914834 Msa0584460:CDS
AGCGCTGTTTGGACTCCCTG+TGG 0.708767 4_2:-3914962 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAAAATTGAAGATACAA+AGG + chr4_2:3915074-3915093 Msa0584460:CDS 20.0%
!! TTCATTACTGAATGTAAATT+GGG - chr4_2:3915296-3915315 None:intergenic 20.0%
! TATGCTGAATAATATGTCAT+TGG + chr4_2:3915159-3915178 Msa0584460:CDS 25.0%
! TTGATTCAAAACATCTTTGT+TGG + chr4_2:3915182-3915201 Msa0584460:CDS 25.0%
! TCATTACTGAATGTAAATTG+GGG - chr4_2:3915295-3915314 None:intergenic 25.0%
! CTTCATTACTGAATGTAAAT+TGG - chr4_2:3915297-3915316 None:intergenic 25.0%
! TACATTCAGTAATGAAGAAA+TGG + chr4_2:3915300-3915319 Msa0584460:CDS 25.0%
! ATTGAAAGTCAATCTTTCAT+GGG + chr4_2:3915373-3915392 Msa0584460:CDS 25.0%
AAAATTCAGAACAATGACTG+TGG + chr4_2:3914988-3915007 Msa0584460:CDS 30.0%
AAATTCAGAACAATGACTGT+GGG + chr4_2:3914989-3915008 Msa0584460:CDS 30.0%
AAGAGACTTACATGAAAGAA+AGG + chr4_2:3915038-3915057 Msa0584460:CDS 30.0%
AGAGACTTACATGAAAGAAA+GGG + chr4_2:3915039-3915058 Msa0584460:CDS 30.0%
TAATGAAGAAATGGCAATGA+TGG + chr4_2:3915309-3915328 Msa0584460:CDS 30.0%
AATGAAGAAATGGCAATGAT+GGG + chr4_2:3915310-3915329 Msa0584460:CDS 30.0%
CATTGAAAGTCAATCTTTCA+TGG + chr4_2:3915372-3915391 Msa0584460:CDS 30.0%
! AGTAGATTTGGTAAAACTCT+AGG - chr4_2:3915451-3915470 None:intergenic 30.0%
AGAATCATCATCGACAATGA+AGG - chr4_2:3914810-3914829 None:intergenic 35.0%
TCATTGTCGATGATGATTCT+AGG + chr4_2:3914810-3914829 Msa0584460:CDS 35.0%
GGAAAGCAACATACAATAGA+AGG + chr4_2:3914831-3914850 Msa0584460:CDS 35.0%
AAGCAACATACAATAGAAGG+CGG + chr4_2:3914834-3914853 Msa0584460:CDS 35.0%
TATGAACTAAGCACTTTGTG+TGG + chr4_2:3914878-3914897 Msa0584460:CDS 35.0%
! ATAGCTTGTGCCATAGTTTA+TGG + chr4_2:3914905-3914924 Msa0584460:CDS 35.0%
AATTCAGAACAATGACTGTG+GGG + chr4_2:3914990-3915009 Msa0584460:CDS 35.0%
! GATACAAAGGCATGATAACA+AGG + chr4_2:3915087-3915106 Msa0584460:CDS 35.0%
GTTGATTGACCACAAATTGA+AGG + chr4_2:3915204-3915223 Msa0584460:CDS 35.0%
ATGTAAATTGGGGTGGTATT+TGG - chr4_2:3915285-3915304 None:intergenic 35.0%
TTACTGAATGTAAATTGGGG+TGG - chr4_2:3915292-3915311 None:intergenic 35.0%
ATGTTGTCGCCATTATTCAT+AGG - chr4_2:3915355-3915374 None:intergenic 35.0%
!! GGCTTGATGATGAAAAGTAA+TGG + chr4_2:3915394-3915413 Msa0584460:CDS 35.0%
! GAAAAGTAATGGAGATGAGT+CGG + chr4_2:3915405-3915424 Msa0584460:CDS 35.0%
AACATACAATAGAAGGCGGA+AGG + chr4_2:3914838-3914857 Msa0584460:CDS 40.0%
ACATACAATAGAAGGCGGAA+GGG + chr4_2:3914839-3914858 Msa0584460:CDS 40.0%
!!! TGAATTTTGAGAGCGCTGTT+TGG - chr4_2:3914976-3914995 None:intergenic 40.0%
ATTCAGAACAATGACTGTGG+GGG + chr4_2:3914991-3915010 Msa0584460:CDS 40.0%
! CATGAAAGAAAGGGTTCTGA+AGG + chr4_2:3915048-3915067 Msa0584460:CDS 40.0%
AAGGCATGATAACAAGGAGA+TGG + chr4_2:3915093-3915112 Msa0584460:CDS 40.0%
GATTGACCACAAATTGAAGG+AGG + chr4_2:3915207-3915226 Msa0584460:CDS 40.0%
TACCAACCTCCTTCAATTTG+TGG - chr4_2:3915216-3915235 None:intergenic 40.0%
!! AATTGAAGGAGGTTGGTAGA+AGG + chr4_2:3915218-3915237 Msa0584460:CDS 40.0%
TATTCATAGGCATTCCAGCA+TGG - chr4_2:3915342-3915361 None:intergenic 40.0%
GCTGGAATGCCTATGAATAA+TGG + chr4_2:3915343-3915362 Msa0584460:CDS 40.0%
CTCGTAGGGTCCATAAACTA+TGG - chr4_2:3914918-3914937 None:intergenic 45.0%
GACCACAAATTGAAGGAGGT+TGG + chr4_2:3915211-3915230 Msa0584460:CDS 45.0%
ATCTCTGGTTGAGGCTCGTA+GGG - chr4_2:3914932-3914951 None:intergenic 50.0%
AATCTCTGGTTGAGGCTCGT+AGG - chr4_2:3914933-3914952 None:intergenic 50.0%
ACGAGCCTCAACCAGAGATT+TGG + chr4_2:3914933-3914952 Msa0584460:CDS 50.0%
GGGGGAGAAGAGCAACAAAA+CGG + chr4_2:3915009-3915028 Msa0584460:CDS 50.0%
!! GAAGGAGGTTGGTAGAAGGT+TGG + chr4_2:3915222-3915241 Msa0584460:CDS 50.0%
TGGTAGAAGGTTGGAAGCAG+AGG + chr4_2:3915231-3915250 Msa0584460:CDS 50.0%
!! GAAATGGCAATGATGGGTCC+TGG + chr4_2:3915316-3915335 Msa0584460:CDS 50.0%
! CTAGGATCGACTTCGCCAAA+TGG - chr4_2:3915433-3915452 None:intergenic 50.0%
GCGGAAGGGTCTACTGAAGA+AGG + chr4_2:3914853-3914872 Msa0584460:CDS 55.0%
GACGGCCAAATCTCTGGTTG+AGG - chr4_2:3914941-3914960 None:intergenic 55.0%
!! TGTGGTGACGGCCAAATCTC+TGG - chr4_2:3914947-3914966 None:intergenic 55.0%
AGAGATTTGGCCGTCACCAC+AGG + chr4_2:3914946-3914965 Msa0584460:CDS 55.0%
GAGATTTGGCCGTCACCACA+GGG + chr4_2:3914947-3914966 Msa0584460:CDS 55.0%
GTTTGGACTCCCTGTGGTGA+CGG - chr4_2:3914959-3914978 None:intergenic 55.0%
ATAGGCATTCCAGCATGGCC+AGG - chr4_2:3915337-3915356 None:intergenic 55.0%
!! GGAGATGAGTCGGTGCCATT+TGG + chr4_2:3915415-3915434 Msa0584460:CDS 55.0%
AGCGCTGTTTGGACTCCCTG+TGG - chr4_2:3914965-3914984 None:intergenic 60.0%
!! ATGATGGGTCCTGGCCATGC+TGG + chr4_2:3915325-3915344 Msa0584460:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 3914782 3915477 3914782 ID=Msa0584460;Name=Msa0584460
chr4_2 mRNA 3914782 3915477 3914782 ID=Msa0584460-mRNA-1;Parent=Msa0584460;Name=Msa0584460-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|231
chr4_2 exon 3914782 3915477 3914782 ID=Msa0584460-mRNA-1:exon:1060;Parent=Msa0584460-mRNA-1
chr4_2 CDS 3914782 3915477 3914782 ID=Msa0584460-mRNA-1:cds;Parent=Msa0584460-mRNA-1
Gene Sequence

>Msa0584460

ATGACTAGGAAAAAGGTGAAACTTGCCTTCATTGTCGATGATGATTCTAGGAAAGCAACATACAATAGAAGGCGGAAGGGTCTACTGAAGAAGGTTTATGAACTAAGCACTTTGTGTGGAGTTATAGCTTGTGCCATAGTTTATGGACCCTACGAGCCTCAACCAGAGATTTGGCCGTCACCACAGGGAGTCCAAACAGCGCTCTCAAAATTCAGAACAATGACTGTGGGGGAGAAGAGCAACAAAACGGTTGATCAAGAGACTTACATGAAAGAAAGGGTTCTGAAGGCTAAAGAAAAATTGAAGATACAAAGGCATGATAACAAGGAGATGGAGATGAAATTGCTCATGATTCAATGTCTTTTTGAAAATAAATTTATGCTGAATAATATGTCATTGGTTGATTCAAAACATCTTTGTTGGTTGATTGACCACAAATTGAAGGAGGTTGGTAGAAGGTTGGAAGCAGAGGATAATAGTAGTCAACATCAAATTCAACTCCAAATACCACCCCAATTTACATTCAGTAATGAAGAAATGGCAATGATGGGTCCTGGCCATGCTGGAATGCCTATGAATAATGGCGACAACATTGAAAGTCAATCTTTCATGGGCTTGATGATGAAAAGTAATGGAGATGAGTCGGTGCCATTTGGCGAAGTCGATCCTAGAGTTTTACCAAATCTACTACCTTAA
Protein sequence

>Msa0584460

MTRKKVKLAFIVDDDSRKATYNRRRKGLLKKVYELSTLCGVIACAIVYGPYEPQPEIWPSPQGVQTALSKFRTMTVGEKSNKTVDQETYMKERVLKAKEKLKIQRHDNKEMEMKLLMIQCLFENKFMLNNMSLVDSKHLCWLIDHKLKEVGRRLEAEDNSSQHQIQLQIPPQFTFSNEEMAMMGPGHAGMPMNNGDNIESQSFMGLMMKSNGDESVPFGEVDPRVLPNLLP*