AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1307590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1307590 MtrunA17_Chr8g0341921 97.222 180 5 0 1 180 1 180 4.70e-126 352
Msa1307590 MtrunA17_Chr2g0330451 59.884 172 67 1 3 172 2 173 4.48e-60 185
Msa1307590 MtrunA17_Chr2g0330441 50.276 181 83 3 1 175 1 180 6.69e-58 179
Msa1307590 MtrunA17_Chr7g0260751 46.541 159 82 2 14 172 21 176 5.84e-48 154
Msa1307590 MtrunA17_Chr6g0488551 41.243 177 101 1 3 176 2 178 5.31e-47 152
Msa1307590 MtrunA17_Chr1g0184741 38.012 171 98 1 2 172 7 169 3.71e-34 119
Msa1307590 MtrunA17_Chr5g0437751 36.000 175 107 2 3 172 17 191 1.14e-33 119
Msa1307590 MtrunA17_Chr1g0190601 41.714 175 97 2 5 179 10 179 1.61e-32 115
Msa1307590 MtrunA17_Chr4g0005191 37.179 156 96 1 20 173 45 200 7.05e-32 114
Msa1307590 MtrunA17_Chr1g0187861 34.343 99 63 1 18 114 6 104 3.23e-17 75.1
Msa1307590 MtrunA17_Chr3g0106401 36.879 141 87 1 34 172 28 168 8.09e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1307590 AT1G55190.1 50.556 180 86 2 3 179 2 181 3.33e-63 193
Msa1307590 AT3G13720.1 52.907 172 78 1 3 171 2 173 5.07e-58 180
Msa1307590 AT3G13710.1 48.555 173 87 1 1 171 1 173 7.66e-56 174
Msa1307590 AT1G17700.1 47.191 178 91 2 3 177 2 179 1.16e-49 159
Msa1307590 AT1G08770.1 40.523 153 89 1 22 172 35 187 2.84e-37 128
Msa1307590 AT2G38360.1 36.420 162 101 1 13 172 33 194 1.08e-36 127
Msa1307590 AT5G01640.1 35.366 164 103 2 14 174 33 196 1.55e-32 116
Msa1307590 AT4G29658.2 34.483 174 111 2 3 173 2 175 9.85e-32 113
Msa1307590 AT3G56110.3 33.143 175 112 2 3 172 10 184 1.07e-30 111
Msa1307590 AT3G56110.1 33.143 175 112 2 3 172 10 184 1.07e-30 111
Msa1307590 AT3G56110.2 33.143 175 112 2 3 172 10 184 1.07e-30 111
Msa1307590 AT3G56110.4 33.143 175 112 2 3 172 10 184 1.07e-30 111
Msa1307590 AT2G40380.1 36.879 141 87 1 34 172 46 186 5.47e-29 107
Msa1307590 AT5G07110.1 39.437 142 84 1 35 174 45 186 1.52e-28 105
Msa1307590 AT5G56230.1 29.714 175 112 2 11 174 2 176 1.87e-28 104
Msa1307590 AT1G04260.1 28.846 156 111 0 18 173 4 159 1.01e-27 102
Msa1307590 AT5G05380.1 35.185 162 103 1 13 172 26 187 1.99e-27 103
Msa1307590 AT5G05380.4 35.185 162 103 1 13 172 69 230 5.67e-27 102
Msa1307590 AT5G05380.3 35.185 162 103 1 13 172 77 238 6.57e-27 102
Msa1307590 AT5G05380.2 35.185 162 103 1 13 172 93 254 7.93e-27 103
Msa1307590 AT1G55640.1 27.329 161 116 1 18 177 21 181 4.69e-22 88.6
Msa1307590 AT4G29658.1 36.364 110 68 1 66 173 3 112 3.42e-17 73.9
Msa1307590 AT4G00005.1 34.653 101 64 1 56 154 1 101 6.21e-12 60.1

Find 42 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGTGGTGTTGGTGAGGT+TGG 0.302565 8_4:+3393577 None:intergenic
CGTGTTATGTATTCAAGTTT+TGG 0.333581 8_4:+3393559 None:intergenic
TTGGTGGTGTTGGTGAGGTT+GGG 0.343332 8_4:+3393578 None:intergenic
TGGTGGCACATGGTGTGTTT+AGG 0.371034 8_4:-3393141 Msa1307590:CDS
GAGAGTAAGGATGCCATAAA+AGG 0.391453 8_4:+3393359 None:intergenic
GACACAGGATTTGTTCTTTG+AGG 0.425389 8_4:-3393116 Msa1307590:CDS
CTTCCGCATGAACTACACTA+TGG 0.443749 8_4:-3393407 Msa1307590:CDS
CAACGAATCAAAGCCGGCTT+AGG 0.455143 8_4:-3393529 Msa1307590:CDS
GGAAAACCATGTTCGATATC+CGG 0.464592 8_4:-3393492 Msa1307590:CDS
ACGAAAACAATGAGAGAGTA+AGG 0.467760 8_4:+3393346 None:intergenic
TACTGTTAATATTGTTGTTG+CGG 0.469310 8_4:-3393185 Msa1307590:CDS
TCGAATTGTGGTTGTTATCA+TGG 0.479422 8_4:-3393245 Msa1307590:CDS
GGTTGGGATTGTGCCGTAGT+TGG 0.481360 8_4:+3393594 None:intergenic
CGAACTCGGGATATTGCTTC+CGG 0.497967 8_4:+3393445 None:intergenic
CTACTTTCTTCGTGATCAGC+CGG 0.512744 8_4:-3393296 Msa1307590:CDS
TATTGCTTCCGGTACACCGG+TGG 0.522580 8_4:+3393456 None:intergenic
TGTGCCGTAGTTGGTTGTCA+TGG 0.530564 8_4:+3393603 None:intergenic
ATTGTTGTTGTGGTGGCACA+TGG 0.532243 8_4:-3393151 Msa1307590:CDS
ATGTTCGATATCCGGTCACT+AGG 0.539035 8_4:-3393484 Msa1307590:CDS
AGGTATCCCCACCGGTGTAC+CGG 0.543272 8_4:-3393464 Msa1307590:CDS
ACCACCATGACAACCAACTA+CGG 0.543309 8_4:-3393607 None:intergenic
ATTGCTTCCGGTACACCGGT+GGG 0.558731 8_4:+3393457 None:intergenic
TAGTGTTGCCATTGTTGTTG+TGG 0.561272 8_4:-3393161 Msa1307590:CDS
TGTTGCCATTGTTGTTGTGG+TGG 0.564562 8_4:-3393158 Msa1307590:CDS
ATGAGATGTTGACACGAACT+CGG 0.565181 8_4:+3393431 None:intergenic
TATCATGGCGTTTGTTACAG+TGG 0.580134 8_4:-3393230 Msa1307590:CDS
AGCCGACCCCATAAAATCAC+CGG 0.580520 8_4:+3393277 None:intergenic
GCTTGTTGATGATCGAATTG+TGG 0.583908 8_4:-3393257 Msa1307590:CDS
GCTTAGGAACTCGTCGACCA+TGG 0.590057 8_4:-3393513 Msa1307590:CDS
TGAGATGTTGACACGAACTC+GGG 0.591425 8_4:+3393432 None:intergenic
GGCAAACAACGAATCAAAGC+CGG 0.593585 8_4:-3393535 Msa1307590:CDS
TCGTTATCCTCATGGCGGCG+TGG 0.601265 8_4:-3393327 Msa1307590:CDS
GGATATTGCTTCCGGTACAC+CGG 0.614401 8_4:+3393453 None:intergenic
TGGTCGACGAGTTCCTAAGC+CGG 0.621177 8_4:+3393516 None:intergenic
ATGTGCCACCACAACAACAA+TGG 0.628584 8_4:+3393153 None:intergenic
TCACCATAGTGTAGTTCATG+CGG 0.655733 8_4:+3393404 None:intergenic
TGGTGTGTTTAGGAAGACAC+AGG 0.663016 8_4:-3393131 Msa1307590:CDS
AGAACAACCACGCCGCCATG+AGG 0.675722 8_4:+3393320 None:intergenic
TAGTGACCGGATATCGAACA+TGG 0.686812 8_4:+3393486 None:intergenic
CGGTCACTAGGTATCCCCAC+CGG 0.689635 8_4:-3393472 Msa1307590:CDS
TTGCTTCCGGTACACCGGTG+GGG 0.696070 8_4:+3393458 None:intergenic
AAACTTGAATACATAACACG+TGG 0.716753 8_4:-3393556 Msa1307590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGTTTCTAAGCCTTTTA+TGG - chr8_4:3393310-3393329 Msa1307590:CDS 25.0%
!! TACTGTTAATATTGTTGTTG+CGG - chr8_4:3393497-3393516 Msa1307590:CDS 25.0%
!! GTTATGTATTCAAGTTTTGG+TGG + chr8_4:3393123-3393142 None:intergenic 30.0%
!! CGTGTTATGTATTCAAGTTT+TGG + chr8_4:3393126-3393145 None:intergenic 30.0%
AAACTTGAATACATAACACG+TGG - chr8_4:3393126-3393145 Msa1307590:CDS 30.0%
!!! TATTCAAGTTTTGGTGGTGT+TGG + chr8_4:3393117-3393136 None:intergenic 35.0%
! ATATCGAACATGGTTTTCCA+TGG + chr8_4:3393189-3393208 None:intergenic 35.0%
ACGAAAACAATGAGAGAGTA+AGG + chr8_4:3393339-3393358 None:intergenic 35.0%
! CATTGTTTTCGTTATCCTCA+TGG - chr8_4:3393347-3393366 Msa1307590:CDS 35.0%
TCGAATTGTGGTTGTTATCA+TGG - chr8_4:3393437-3393456 Msa1307590:CDS 35.0%
GGAAAACCATGTTCGATATC+CGG - chr8_4:3393190-3393209 Msa1307590:CDS 40.0%
ATGAGATGTTGACACGAACT+CGG + chr8_4:3393254-3393273 None:intergenic 40.0%
TCACCATAGTGTAGTTCATG+CGG + chr8_4:3393281-3393300 None:intergenic 40.0%
GAGAGTAAGGATGCCATAAA+AGG + chr8_4:3393326-3393345 None:intergenic 40.0%
! TGTTTTCGTTATCCTCATGG+CGG - chr8_4:3393350-3393369 Msa1307590:CDS 40.0%
! TGATCAGCCGGTGATTTTAT+GGG - chr8_4:3393398-3393417 Msa1307590:CDS 40.0%
!! GCTTGTTGATGATCGAATTG+TGG - chr8_4:3393425-3393444 Msa1307590:CDS 40.0%
! TATCATGGCGTTTGTTACAG+TGG - chr8_4:3393452-3393471 Msa1307590:CDS 40.0%
! TAGTGTTGCCATTGTTGTTG+TGG - chr8_4:3393521-3393540 Msa1307590:CDS 40.0%
! GACACAGGATTTGTTCTTTG+AGG - chr8_4:3393566-3393585 Msa1307590:CDS 40.0%
!!! AAGTTTTGGTGGTGTTGGTG+AGG + chr8_4:3393112-3393131 None:intergenic 45.0%
GGCAAACAACGAATCAAAGC+CGG - chr8_4:3393147-3393166 Msa1307590:CDS 45.0%
TAGTGACCGGATATCGAACA+TGG + chr8_4:3393199-3393218 None:intergenic 45.0%
ATGTTCGATATCCGGTCACT+AGG - chr8_4:3393198-3393217 Msa1307590:CDS 45.0%
TGAGATGTTGACACGAACTC+GGG + chr8_4:3393253-3393272 None:intergenic 45.0%
CTTCCGCATGAACTACACTA+TGG - chr8_4:3393275-3393294 Msa1307590:CDS 45.0%
CTACTTTCTTCGTGATCAGC+CGG - chr8_4:3393386-3393405 Msa1307590:CDS 45.0%
! GTGATCAGCCGGTGATTTTA+TGG - chr8_4:3393397-3393416 Msa1307590:CDS 45.0%
! GATCAGCCGGTGATTTTATG+GGG - chr8_4:3393399-3393418 Msa1307590:CDS 45.0%
! TGTTGCCATTGTTGTTGTGG+TGG - chr8_4:3393524-3393543 Msa1307590:CDS 45.0%
ATGTGCCACCACAACAACAA+TGG + chr8_4:3393532-3393551 None:intergenic 45.0%
! ATTGTTGTTGTGGTGGCACA+TGG - chr8_4:3393531-3393550 Msa1307590:CDS 45.0%
TGGTGTGTTTAGGAAGACAC+AGG - chr8_4:3393551-3393570 Msa1307590:CDS 45.0%
!! TTGGTGGTGTTGGTGAGGTT+GGG + chr8_4:3393107-3393126 None:intergenic 50.0%
!! TTTGGTGGTGTTGGTGAGGT+TGG + chr8_4:3393108-3393127 None:intergenic 50.0%
! CAACGAATCAAAGCCGGCTT+AGG - chr8_4:3393153-3393172 Msa1307590:CDS 50.0%
GGATATTGCTTCCGGTACAC+CGG + chr8_4:3393232-3393251 None:intergenic 50.0%
CGAACTCGGGATATTGCTTC+CGG + chr8_4:3393240-3393259 None:intergenic 50.0%
! AGCCGGTGATTTTATGGGGT+CGG - chr8_4:3393403-3393422 Msa1307590:CDS 50.0%
AGCCGACCCCATAAAATCAC+CGG + chr8_4:3393408-3393427 None:intergenic 50.0%
TGGTGGCACATGGTGTGTTT+AGG - chr8_4:3393541-3393560 Msa1307590:CDS 50.0%
GGTTGGGATTGTGCCGTAGT+TGG + chr8_4:3393091-3393110 None:intergenic 55.0%
TGGTCGACGAGTTCCTAAGC+CGG + chr8_4:3393169-3393188 None:intergenic 55.0%
GCTTAGGAACTCGTCGACCA+TGG - chr8_4:3393169-3393188 Msa1307590:CDS 55.0%
ATTGCTTCCGGTACACCGGT+GGG + chr8_4:3393228-3393247 None:intergenic 55.0%
TATTGCTTCCGGTACACCGG+TGG + chr8_4:3393229-3393248 None:intergenic 55.0%
CGGTGGGGATACCTAGTGAC+CGG + chr8_4:3393212-3393231 None:intergenic 60.0%
CGGTCACTAGGTATCCCCAC+CGG - chr8_4:3393210-3393229 Msa1307590:CDS 60.0%
AGGTATCCCCACCGGTGTAC+CGG - chr8_4:3393218-3393237 Msa1307590:CDS 60.0%
TTGCTTCCGGTACACCGGTG+GGG + chr8_4:3393227-3393246 None:intergenic 60.0%
TCGTTATCCTCATGGCGGCG+TGG - chr8_4:3393355-3393374 Msa1307590:CDS 60.0%
AGAACAACCACGCCGCCATG+AGG + chr8_4:3393365-3393384 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 3393081 3393623 3393081 ID=Msa1307590;Name=Msa1307590
chr8_4 mRNA 3393081 3393623 3393081 ID=Msa1307590-mRNA-1;Parent=Msa1307590;Name=Msa1307590-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|180
chr8_4 exon 3393081 3393623 3393081 ID=Msa1307590-mRNA-1:exon:999;Parent=Msa1307590-mRNA-1
chr8_4 CDS 3393081 3393623 3393081 ID=Msa1307590-mRNA-1:cds;Parent=Msa1307590-mRNA-1
Gene Sequence

>Msa1307590

ATGACAACCAACTACGGCACAATCCCAACCTCACCAACACCACCAAAACTTGAATACATAACACGTGGCAAACAACGAATCAAAGCCGGCTTAGGAACTCGTCGACCATGGAAAACCATGTTCGATATCCGGTCACTAGGTATCCCCACCGGTGTACCGGAAGCAATATCCCGAGTTCGTGTCAACATCTCATACTTCCGCATGAACTACACTATGGTGATGCTTTTGATTTTGTTTCTAAGCCTTTTATGGCATCCTTACTCTCTCATTGTTTTCGTTATCCTCATGGCGGCGTGGTTGTTCTTCTACTTTCTTCGTGATCAGCCGGTGATTTTATGGGGTCGGCTTGTTGATGATCGAATTGTGGTTGTTATCATGGCGTTTGTTACAGTGGCTTTGTTGCTTCTTACGCAAGCTACTGTTAATATTGTTGTTGCGGTTAGTGTTGCCATTGTTGTTGTGGTGGCACATGGTGTGTTTAGGAAGACACAGGATTTGTTCTTTGAGGAAGAAGAAGAAGTTATTGTTTCTGTTGCTTCTTGA
Protein sequence

>Msa1307590

MTTNYGTIPTSPTPPKLEYITRGKQRIKAGLGTRRPWKTMFDIRSLGIPTGVPEAISRVRVNISYFRMNYTMVMLLILFLSLLWHPYSLIVFVILMAAWLFFYFLRDQPVILWGRLVDDRIVVVIMAFVTVALLLLTQATVNIVVAVSVAIVVVVAHGVFRKTQDLFFEEEEEVIVSVAS*