AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1337330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1337330 MtrunA17_Chr4g0072571 97.633 169 4 0 1 169 1 169 5.00e-121 338
Msa1337330 MtrunA17_Chr8g0376021 41.803 122 49 3 18 120 18 136 5.92e-20 82.8
Msa1337330 MtrunA17_Chr1g0161901 41.176 119 58 3 28 136 80 196 1.82e-18 79.7
Msa1337330 MtrunA17_Chr2g0333741 40.146 137 42 4 8 105 17 152 2.07e-18 79.3
Msa1337330 MtrunA17_Chr5g0434121 66.667 57 16 1 45 98 87 143 1.17e-17 77.0
Msa1337330 MtrunA17_Chr3g0110091 64.286 56 19 1 44 99 85 139 3.00e-17 76.3
Msa1337330 MtrunA17_Chr1g0149811 53.623 69 30 1 23 89 70 138 9.49e-17 75.1
Msa1337330 MtrunA17_Chr4g0001081 72.727 44 12 0 42 85 64 107 3.37e-16 73.2
Msa1337330 MtrunA17_Chr3g0137111 47.674 86 33 2 7 80 22 107 3.51e-16 73.2
Msa1337330 MtrunA17_Chr7g0254221 74.286 35 9 0 45 79 33 67 4.96e-13 63.2
Msa1337330 MtrunA17_Chr1g0207691 57.447 47 20 0 32 78 51 97 8.97e-13 63.5
Msa1337330 MtrunA17_Chr7g0251581 75.758 33 8 0 45 77 39 71 5.46e-12 61.2
Msa1337330 MtrunA17_Chr7g0222361 29.936 157 78 5 44 169 47 202 3.72e-11 59.3
Msa1337330 MtrunA17_Chr7g0250871 36.458 96 54 3 3 96 5 95 4.23e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1337330 AT5G57520.1 48.851 174 57 8 3 169 2 150 6.09e-30 107
Msa1337330 AT5G25160.1 45.455 132 54 7 21 147 34 152 7.55e-22 88.6
Msa1337330 AT5G10970.1 44.094 127 58 4 23 147 78 193 8.44e-21 86.7
Msa1337330 AT1G24625.1 53.425 73 29 2 12 82 25 94 2.54e-18 79.0
Msa1337330 AT1G66140.1 75.556 45 11 0 41 85 79 123 1.07e-17 78.2
Msa1337330 AT1G80730.1 55.556 72 28 1 45 112 66 137 1.03e-16 74.7
Msa1337330 AT5G01860.1 40.000 80 40 2 14 93 38 109 2.15e-13 65.9
Msa1337330 AT5G14010.1 31.783 129 81 2 45 169 36 161 2.35e-12 62.0

Find 36 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAGGAAGGTGTGACTTCT+TGG 0.254359 tig0001526:+42256 Msa1337330:CDS
TTTCAAGCTTGTGAGCATTT+TGG 0.263848 tig0001526:-42038 None:intergenic
TTTAAGTGAAGAAAAGTATT+AGG 0.266610 tig0001526:-41859 None:intergenic
ATCATCATCATCTTCATCTA+TGG 0.308958 tig0001526:+41948 Msa1337330:CDS
TGATGAATATTCTCATTATC+TGG 0.318086 tig0001526:-41886 None:intergenic
GAGAAGTTTGAAGGGTGTTC+TGG 0.318303 tig0001526:-42123 None:intergenic
GTTTAGTTATGGAAATTCTA+AGG 0.345981 tig0001526:+42239 Msa1337330:CDS
TTCTCTACTAATTACCATCT+TGG 0.347245 tig0001526:+42141 Msa1337330:CDS
AGAAAAGATCAGTTTAGTTA+TGG 0.369153 tig0001526:+42228 Msa1337330:CDS
TCATCACATGACCTTGTCTA+TGG 0.389808 tig0001526:-42194 None:intergenic
GCCAACTTGATTTGTCCTTA+AGG 0.395324 tig0001526:+42325 Msa1337330:CDS
CATTTATAATCAGAGCCTTA+AGG 0.403759 tig0001526:-42340 None:intergenic
TAGTACTTCTGAAAATGTTC+AGG 0.411786 tig0001526:+42293 Msa1337330:CDS
TAATTAGTAGAGAAGTTTGA+AGG 0.473837 tig0001526:-42132 None:intergenic
GAATATTCTCATTATCTGGT+TGG 0.475223 tig0001526:-41882 None:intergenic
AGTTATGGAAATTCTAAGGA+AGG 0.495820 tig0001526:+42243 Msa1337330:CDS
GGACACTTGCAAAGAAGAGT+AGG 0.507806 tig0001526:+42061 Msa1337330:CDS
AAAATGCTCACAAGCTTGAA+AGG 0.509103 tig0001526:+42040 Msa1337330:CDS
AGGTGTGACTTCTTGGTCAA+GGG 0.515201 tig0001526:+42263 Msa1337330:CDS
AATTACCATCTTGGAAGTCA+TGG 0.516260 tig0001526:+42150 Msa1337330:CDS
CATTTCCATGACTTCCAAGA+TGG 0.523980 tig0001526:-42155 None:intergenic
AATTAGTAGAGAAGTTTGAA+GGG 0.551396 tig0001526:-42131 None:intergenic
AAGGTGTGACTTCTTGGTCA+AGG 0.556847 tig0001526:+42262 Msa1337330:CDS
GCCTTAAGGACAAATCAAGT+TGG 0.573380 tig0001526:-42326 None:intergenic
GACACTTGCAAAGAAGAGTA+GGG 0.576451 tig0001526:+42062 Msa1337330:CDS
CATCTTCATCTATGGAGCAA+AGG 0.583885 tig0001526:+41956 Msa1337330:CDS
TATAGCTCTCAAGCTTTGGG+AGG 0.587863 tig0001526:+42012 Msa1337330:CDS
GATGATGATGAAGAAGAAGA+TGG 0.596144 tig0001526:-41934 None:intergenic
TACTTCTGAAAATGTTCAGG+AGG 0.608835 tig0001526:+42296 Msa1337330:CDS
GGTGTGACTTCTTGGTCAAG+GGG 0.612067 tig0001526:+42264 Msa1337330:CDS
TTCAGCATAAGAAGATTGCA+TGG 0.617834 tig0001526:-42097 None:intergenic
ATAGACAAGGTCATGTGATG+AGG 0.622400 tig0001526:+42196 Msa1337330:CDS
CTTGACAACAACCATAGACA+AGG 0.646735 tig0001526:+42183 Msa1337330:CDS
CAAGGTCATGTGATGAGGCA+TGG 0.652675 tig0001526:+42201 Msa1337330:CDS
GGTCATGTGATGAGGCATGG+TGG 0.708373 tig0001526:+42204 Msa1337330:CDS
AGCATAAGAAGATTGCATGG+CGG 0.769594 tig0001526:-42094 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAGTGAAGAAAAGTATT+AGG - tig0001526:41862-41881 None:intergenic 20.0%
! TGATGAATATTCTCATTATC+TGG - tig0001526:41889-41908 None:intergenic 25.0%
! AATTAGTAGAGAAGTTTGAA+GGG - tig0001526:42134-42153 None:intergenic 25.0%
! TAATTAGTAGAGAAGTTTGA+AGG - tig0001526:42135-42154 None:intergenic 25.0%
! AGAAAAGATCAGTTTAGTTA+TGG + tig0001526:42228-42247 Msa1337330:CDS 25.0%
! GTTTAGTTATGGAAATTCTA+AGG + tig0001526:42239-42258 Msa1337330:CDS 25.0%
GAATATTCTCATTATCTGGT+TGG - tig0001526:41885-41904 None:intergenic 30.0%
ATCATCATCATCTTCATCTA+TGG + tig0001526:41948-41967 Msa1337330:CDS 30.0%
! TTTTATAGCTCTCAAGCTTT+GGG + tig0001526:42009-42028 Msa1337330:CDS 30.0%
TTCTCTACTAATTACCATCT+TGG + tig0001526:42141-42160 Msa1337330:CDS 30.0%
! AGTTATGGAAATTCTAAGGA+AGG + tig0001526:42243-42262 Msa1337330:CDS 30.0%
! TAGTACTTCTGAAAATGTTC+AGG + tig0001526:42293-42312 Msa1337330:CDS 30.0%
! GATGATGATGAAGAAGAAGA+TGG - tig0001526:41937-41956 None:intergenic 35.0%
! GTTTTATAGCTCTCAAGCTT+TGG + tig0001526:42008-42027 Msa1337330:CDS 35.0%
! TTTCAAGCTTGTGAGCATTT+TGG - tig0001526:42041-42060 None:intergenic 35.0%
AAAATGCTCACAAGCTTGAA+AGG + tig0001526:42040-42059 Msa1337330:CDS 35.0%
TTCAGCATAAGAAGATTGCA+TGG - tig0001526:42100-42119 None:intergenic 35.0%
AATTACCATCTTGGAAGTCA+TGG + tig0001526:42150-42169 Msa1337330:CDS 35.0%
! TACTTCTGAAAATGTTCAGG+AGG + tig0001526:42296-42315 Msa1337330:CDS 35.0%
CATCTTCATCTATGGAGCAA+AGG + tig0001526:41956-41975 Msa1337330:CDS 40.0%
GACACTTGCAAAGAAGAGTA+GGG + tig0001526:42062-42081 Msa1337330:CDS 40.0%
AGCATAAGAAGATTGCATGG+CGG - tig0001526:42097-42116 None:intergenic 40.0%
CATTTCCATGACTTCCAAGA+TGG - tig0001526:42158-42177 None:intergenic 40.0%
CTTGACAACAACCATAGACA+AGG + tig0001526:42183-42202 Msa1337330:CDS 40.0%
TCATCACATGACCTTGTCTA+TGG - tig0001526:42197-42216 None:intergenic 40.0%
ATAGACAAGGTCATGTGATG+AGG + tig0001526:42196-42215 Msa1337330:CDS 40.0%
!! GCCAACTTGATTTGTCCTTA+AGG + tig0001526:42325-42344 Msa1337330:CDS 40.0%
GCCTTAAGGACAAATCAAGT+TGG - tig0001526:42329-42348 None:intergenic 40.0%
!! TATAGCTCTCAAGCTTTGGG+AGG + tig0001526:42012-42031 Msa1337330:CDS 45.0%
GGACACTTGCAAAGAAGAGT+AGG + tig0001526:42061-42080 Msa1337330:CDS 45.0%
!! GAGAAGTTTGAAGGGTGTTC+TGG - tig0001526:42126-42145 None:intergenic 45.0%
! CTAAGGAAGGTGTGACTTCT+TGG + tig0001526:42256-42275 Msa1337330:CDS 45.0%
AAGGTGTGACTTCTTGGTCA+AGG + tig0001526:42262-42281 Msa1337330:CDS 45.0%
AGGTGTGACTTCTTGGTCAA+GGG + tig0001526:42263-42282 Msa1337330:CDS 45.0%
CAAGGTCATGTGATGAGGCA+TGG + tig0001526:42201-42220 Msa1337330:CDS 50.0%
GGTGTGACTTCTTGGTCAAG+GGG + tig0001526:42264-42283 Msa1337330:CDS 50.0%
GGTCATGTGATGAGGCATGG+TGG + tig0001526:42204-42223 Msa1337330:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0001526 gene 41844 42353 41844 ID=Msa1337330;Name=Msa1337330
tig0001526 mRNA 41844 42353 41844 ID=Msa1337330-mRNA-1;Parent=Msa1337330;Name=Msa1337330-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|169
tig0001526 exon 41844 42353 41844 ID=Msa1337330-mRNA-1:exon:1082;Parent=Msa1337330-mRNA-1
tig0001526 CDS 41844 42353 41844 ID=Msa1337330-mRNA-1:cds;Parent=Msa1337330-mRNA-1
Gene Sequence

>Msa1337330

ATGAATAATTTTCATCCTAATACTTTTCTTCACTTAAACCAACCAGATAATGAGAATATTCATCATCTGAATCTAGATCTTGTTCTTGAACCATCTTCTTCTTCATCATCATCATCTTCATCTATGGAGCAAAGGATATTCTCATGCAATTATTGTCAGAGAAAGTTTTATAGCTCTCAAGCTTTGGGAGGACACCAAAATGCTCACAAGCTTGAAAGGACACTTGCAAAGAAGAGTAGGGAGATGAGTTCCGCCATGCAATCTTCTTATGCTGAATTACCAGAACACCCTTCAAACTTCTCTACTAATTACCATCTTGGAAGTCATGGAAATGCTCATCTTGACAACAACCATAGACAAGGTCATGTGATGAGGCATGGTGGAAGAAAAGATCAGTTTAGTTATGGAAATTCTAAGGAAGGTGTGACTTCTTGGTCAAGGGGTTATAATAGTACTTCTGAAAATGTTCAGGAGGATATTAGCCAACTTGATTTGTCCTTAAGGCTCTGA
Protein sequence

>Msa1337330

MNNFHPNTFLHLNQPDNENIHHLNLDLVLEPSSSSSSSSSSMEQRIFSCNYCQRKFYSSQALGGHQNAHKLERTLAKKSREMSSAMQSSYAELPEHPSNFSTNYHLGSHGNAHLDNNHRQGHVMRHGGRKDQFSYGNSKEGVTSWSRGYNSTSENVQEDISQLDLSLRL*