AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0144530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0144530 MtrunA17_Chr1g0149811 96.958 263 7 1 1 263 1 262 0.0 532
Msa0144530 MtrunA17_Chr3g0137111 48.729 236 97 9 23 248 4 225 1.15e-57 183
Msa0144530 MtrunA17_Chr2g0333741 35.563 284 125 13 1 263 1 247 1.62e-31 117
Msa0144530 MtrunA17_Chr4g0001081 37.553 237 96 10 46 263 21 224 6.47e-31 114
Msa0144530 MtrunA17_Chr5g0434121 34.975 203 86 6 31 211 2 180 9.35e-26 101
Msa0144530 MtrunA17_Chr8g0376021 40.690 145 59 4 37 181 15 132 8.23e-25 98.6
Msa0144530 MtrunA17_Chr1g0161901 38.095 147 70 3 35 181 43 168 1.84e-24 98.2
Msa0144530 MtrunA17_Chr3g0110091 54.545 88 22 2 93 180 85 154 5.35e-24 96.7
Msa0144530 MtrunA17_Chr1g0207691 37.594 133 59 3 53 182 21 132 9.96e-19 81.6
Msa0144530 MtrunA17_Chr4g0072571 61.538 52 20 0 91 142 42 93 3.22e-16 74.3
Msa0144530 MtrunA17_Chr3g0081131 30.645 186 97 6 28 198 20 188 6.17e-16 75.9
Msa0144530 MtrunA17_Chr3g0081141 41.176 102 50 3 85 185 89 181 1.75e-14 72.0
Msa0144530 MtrunA17_Chr3g0081121 33.333 186 98 7 28 198 20 194 1.80e-14 71.6
Msa0144530 MtrunA17_Chr5g0396031 38.793 116 56 4 82 195 34 136 1.40e-13 69.7
Msa0144530 MtrunA17_Chr4g0053691 41.111 90 22 2 93 182 66 124 3.07e-13 66.2
Msa0144530 MtrunA17_Chr7g0251581 78.788 33 7 0 94 126 39 71 6.92e-13 65.5
Msa0144530 MtrunA17_Chr7g0254221 70.270 37 11 0 94 130 33 69 9.47e-13 64.3
Msa0144530 MtrunA17_Chr3g0079671 40.000 95 41 4 92 182 96 178 1.22e-11 63.5
Msa0144530 MtrunA17_Chr7g0224221 32.184 174 102 8 27 198 86 245 1.84e-11 63.5
Msa0144530 MtrunA17_Chr2g0310101 35.238 105 53 2 92 195 57 147 3.29e-11 61.2
Msa0144530 MtrunA17_Chr7g0222671 33.333 117 67 5 83 196 55 163 4.93e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0144530 AT5G10970.1 42.616 237 90 9 49 263 60 272 4.17e-44 150
Msa0144530 AT5G25160.1 49.419 172 66 7 51 222 18 168 2.91e-39 137
Msa0144530 AT1G80730.1 37.395 238 127 7 35 263 4 228 1.95e-32 119
Msa0144530 AT1G66140.1 49.515 103 35 3 91 183 80 175 5.80e-22 92.0
Msa0144530 AT1G24625.1 42.727 110 37 4 74 179 33 120 1.25e-16 76.6
Msa0144530 AT5G14010.1 42.697 89 39 3 94 178 36 116 3.86e-14 68.9
Msa0144530 AT5G57520.1 77.778 36 8 0 94 129 50 85 5.08e-14 68.2
Msa0144530 AT1G67030.1 38.938 113 55 3 70 180 13 113 3.39e-13 67.0
Msa0144530 AT3G58070.1 31.638 177 92 7 23 190 23 179 6.47e-12 64.3
Msa0144530 AT5G01860.1 56.250 48 18 1 80 127 54 98 7.43e-11 60.8

Find 32 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCAAACTCAAGAATCTTTA+TGG 0.122503 1_4:+4120611 Msa0144530:CDS
ATGGCTTCTTTGCCTCTTTA+TGG 0.168485 1_4:+4120471 Msa0144530:CDS
CTTTGTTTATTATGCATAAT+AGG 0.201649 1_4:-4120438 None:intergenic
CCTTCTCATGTTTCATCTAA+TGG 0.202335 1_4:+4120549 Msa0144530:CDS
CATGTTTCATCTAATGGATT+TGG 0.228057 1_4:+4120555 Msa0144530:CDS
AATGGATTTGGAAACTCTTA+TGG 0.229174 1_4:+4120567 Msa0144530:CDS
ATAGCTTCAGCTTCTGCTTT+TGG 0.233602 1_4:+4120411 Msa0144530:CDS
TTGCCTCTTTATGGTGCTTT+TGG 0.261823 1_4:+4120480 Msa0144530:CDS
ATGAAACATGAGAAGGCTTA+TGG 0.351379 1_4:-4120542 None:intergenic
CTCATAACTTCTTTAGATGT+TGG 0.385754 1_4:+4120219 Msa0144530:CDS
TGCAAAGGTGTGCTTGGACT+TGG 0.428789 1_4:-4120057 None:intergenic
TTCTATAGCTCACAAGCATT+AGG 0.451109 1_4:+4120318 Msa0144530:CDS
TTTGGTGGTAATAAACCTCT+TGG 0.453972 1_4:+4120498 Msa0144530:CDS
AAAGGTGTGCTTGGACTTGG+AGG 0.516654 1_4:-4120054 None:intergenic
TGGAATAGCAAAACTAGGTA+TGG 0.517898 1_4:+4120644 Msa0144530:CDS
ATCTTTATGGATCAACAACC+TGG 0.518646 1_4:+4120624 Msa0144530:CDS
CAACCTGGAATAGCAAAACT+AGG 0.529841 1_4:+4120639 Msa0144530:CDS
CCACCAAAAGCACCATAAAG+AGG 0.536698 1_4:-4120483 None:intergenic
CATCAAGAGGAAGTGTTGGT+AGG 0.548091 1_4:+4120691 Msa0144530:CDS
GAAGAAACAACAATCTATTG+AGG 0.558110 1_4:+4120095 Msa0144530:CDS
AAACAATAATACTCTTGATG+TGG 0.560949 1_4:+4120257 Msa0144530:CDS
ATTAATGGAAAGACTAAGCA+AGG 0.563627 1_4:+4120002 None:intergenic
TATGGACATCATCATCATCA+TGG 0.564611 1_4:+4120585 Msa0144530:CDS
TCTTGAGAAGAGAAGATGCA+TGG 0.579539 1_4:-4120027 None:intergenic
GGTAGAAGAAGATATCACTA+AGG 0.583712 1_4:+4120116 Msa0144530:CDS
ACATCATCAAGAGGAAGTGT+TGG 0.585725 1_4:+4120687 Msa0144530:CDS
TATAGCTCACAAGCATTAGG+TGG 0.606344 1_4:+4120321 Msa0144530:CDS
AGAACAACAACATCATCAAG+AGG 0.611847 1_4:+4120678 Msa0144530:CDS
ATATTCATAATCATAGCTTG+AGG 0.612882 1_4:-4120785 None:intergenic
TAAACAAAGTTATGCAAACA+TGG 0.616969 1_4:+4120452 Msa0144530:CDS
CCATTAGATGAAACATGAGA+AGG 0.626125 1_4:-4120549 None:intergenic
GAGTGTGCTTGAATTCCAAG+AGG 0.647089 1_4:-4120513 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGTTTATTATGCATAAT+AGG - chr1_4:4120441-4120460 None:intergenic 20.0%
!!! CTTTGTTTATTATGCATAAT+AGG - chr1_4:4120441-4120460 None:intergenic 20.0%
!!! TTTTCATGTTGATTTTGCAA+AGG - chr1_4:4120075-4120094 None:intergenic 25.0%
! AAACAATAATACTCTTGATG+TGG + chr1_4:4120257-4120276 Msa0144530:CDS 25.0%
! TAAACAAAGTTATGCAAACA+TGG + chr1_4:4120452-4120471 Msa0144530:CDS 25.0%
!!! TTTTCATGTTGATTTTGCAA+AGG - chr1_4:4120075-4120094 None:intergenic 25.0%
! AAACAATAATACTCTTGATG+TGG + chr1_4:4120257-4120276 Msa0144530:CDS 25.0%
! TAAACAAAGTTATGCAAACA+TGG + chr1_4:4120452-4120471 Msa0144530:CDS 25.0%
GAAGAAACAACAATCTATTG+AGG + chr1_4:4120095-4120114 Msa0144530:CDS 30.0%
CTCATAACTTCTTTAGATGT+TGG + chr1_4:4120219-4120238 Msa0144530:CDS 30.0%
!! CATGTTTCATCTAATGGATT+TGG + chr1_4:4120555-4120574 Msa0144530:CDS 30.0%
! AATGGATTTGGAAACTCTTA+TGG + chr1_4:4120567-4120586 Msa0144530:CDS 30.0%
GTCAAACTCAAGAATCTTTA+TGG + chr1_4:4120611-4120630 Msa0144530:CDS 30.0%
GAAGAAACAACAATCTATTG+AGG + chr1_4:4120095-4120114 Msa0144530:CDS 30.0%
CTCATAACTTCTTTAGATGT+TGG + chr1_4:4120219-4120238 Msa0144530:CDS 30.0%
!! CATGTTTCATCTAATGGATT+TGG + chr1_4:4120555-4120574 Msa0144530:CDS 30.0%
! AATGGATTTGGAAACTCTTA+TGG + chr1_4:4120567-4120586 Msa0144530:CDS 30.0%
GTCAAACTCAAGAATCTTTA+TGG + chr1_4:4120611-4120630 Msa0144530:CDS 30.0%
GGTAGAAGAAGATATCACTA+AGG + chr1_4:4120116-4120135 Msa0144530:CDS 35.0%
TTCTATAGCTCACAAGCATT+AGG + chr1_4:4120318-4120337 Msa0144530:CDS 35.0%
! TCTCTCTTTTGTGAGCATTT+TGG - chr1_4:4120350-4120369 None:intergenic 35.0%
GAGAGATCAATAGCAAAAAG+AGG + chr1_4:4120366-4120385 Msa0144530:CDS 35.0%
GCAAAAAGAGGACAAAGATT+TGG + chr1_4:4120378-4120397 Msa0144530:CDS 35.0%
! TTTGGTGGTAATAAACCTCT+TGG + chr1_4:4120498-4120517 Msa0144530:CDS 35.0%
ATGAAACATGAGAAGGCTTA+TGG - chr1_4:4120545-4120564 None:intergenic 35.0%
CCATTAGATGAAACATGAGA+AGG - chr1_4:4120552-4120571 None:intergenic 35.0%
CCTTCTCATGTTTCATCTAA+TGG + chr1_4:4120549-4120568 Msa0144530:CDS 35.0%
TATGGACATCATCATCATCA+TGG + chr1_4:4120585-4120604 Msa0144530:CDS 35.0%
ATCTTTATGGATCAACAACC+TGG + chr1_4:4120624-4120643 Msa0144530:CDS 35.0%
!!! ATACCTAGTTTTGCTATTCC+AGG - chr1_4:4120645-4120664 None:intergenic 35.0%
TGGAATAGCAAAACTAGGTA+TGG + chr1_4:4120644-4120663 Msa0144530:CDS 35.0%
AGAACAACAACATCATCAAG+AGG + chr1_4:4120678-4120697 Msa0144530:CDS 35.0%
GGTAGAAGAAGATATCACTA+AGG + chr1_4:4120116-4120135 Msa0144530:CDS 35.0%
TTCTATAGCTCACAAGCATT+AGG + chr1_4:4120318-4120337 Msa0144530:CDS 35.0%
! TCTCTCTTTTGTGAGCATTT+TGG - chr1_4:4120350-4120369 None:intergenic 35.0%
GAGAGATCAATAGCAAAAAG+AGG + chr1_4:4120366-4120385 Msa0144530:CDS 35.0%
GCAAAAAGAGGACAAAGATT+TGG + chr1_4:4120378-4120397 Msa0144530:CDS 35.0%
! TTTGGTGGTAATAAACCTCT+TGG + chr1_4:4120498-4120517 Msa0144530:CDS 35.0%
ATGAAACATGAGAAGGCTTA+TGG - chr1_4:4120545-4120564 None:intergenic 35.0%
CCATTAGATGAAACATGAGA+AGG - chr1_4:4120552-4120571 None:intergenic 35.0%
CCTTCTCATGTTTCATCTAA+TGG + chr1_4:4120549-4120568 Msa0144530:CDS 35.0%
TATGGACATCATCATCATCA+TGG + chr1_4:4120585-4120604 Msa0144530:CDS 35.0%
ATCTTTATGGATCAACAACC+TGG + chr1_4:4120624-4120643 Msa0144530:CDS 35.0%
!!! ATACCTAGTTTTGCTATTCC+AGG - chr1_4:4120645-4120664 None:intergenic 35.0%
TGGAATAGCAAAACTAGGTA+TGG + chr1_4:4120644-4120663 Msa0144530:CDS 35.0%
AGAACAACAACATCATCAAG+AGG + chr1_4:4120678-4120697 Msa0144530:CDS 35.0%
TCTTGAGAAGAGAAGATGCA+TGG - chr1_4:4120030-4120049 None:intergenic 40.0%
!! TGATTTTGCAAAGGTGTGCT+TGG - chr1_4:4120066-4120085 None:intergenic 40.0%
TATAGCTCACAAGCATTAGG+TGG + chr1_4:4120321-4120340 Msa0144530:CDS 40.0%
! ATAGCTTCAGCTTCTGCTTT+TGG + chr1_4:4120411-4120430 Msa0144530:CDS 40.0%
ATGGCTTCTTTGCCTCTTTA+TGG + chr1_4:4120471-4120490 Msa0144530:CDS 40.0%
! TTGCCTCTTTATGGTGCTTT+TGG + chr1_4:4120480-4120499 Msa0144530:CDS 40.0%
GACATCATCATCATCATGGT+TGG + chr1_4:4120589-4120608 Msa0144530:CDS 40.0%
CAACCTGGAATAGCAAAACT+AGG + chr1_4:4120639-4120658 Msa0144530:CDS 40.0%
! ACATCATCAAGAGGAAGTGT+TGG + chr1_4:4120687-4120706 Msa0144530:CDS 40.0%
TCTTGAGAAGAGAAGATGCA+TGG - chr1_4:4120030-4120049 None:intergenic 40.0%
!! TGATTTTGCAAAGGTGTGCT+TGG - chr1_4:4120066-4120085 None:intergenic 40.0%
TATAGCTCACAAGCATTAGG+TGG + chr1_4:4120321-4120340 Msa0144530:CDS 40.0%
! ATAGCTTCAGCTTCTGCTTT+TGG + chr1_4:4120411-4120430 Msa0144530:CDS 40.0%
ATGGCTTCTTTGCCTCTTTA+TGG + chr1_4:4120471-4120490 Msa0144530:CDS 40.0%
! TTGCCTCTTTATGGTGCTTT+TGG + chr1_4:4120480-4120499 Msa0144530:CDS 40.0%
GACATCATCATCATCATGGT+TGG + chr1_4:4120589-4120608 Msa0144530:CDS 40.0%
CAACCTGGAATAGCAAAACT+AGG + chr1_4:4120639-4120658 Msa0144530:CDS 40.0%
! ACATCATCAAGAGGAAGTGT+TGG + chr1_4:4120687-4120706 Msa0144530:CDS 40.0%
!! CCACCAAAAGCACCATAAAG+AGG - chr1_4:4120486-4120505 None:intergenic 45.0%
! CCTCTTTATGGTGCTTTTGG+TGG + chr1_4:4120483-4120502 Msa0144530:CDS 45.0%
GAGTGTGCTTGAATTCCAAG+AGG - chr1_4:4120516-4120535 None:intergenic 45.0%
!! CATCAAGAGGAAGTGTTGGT+AGG + chr1_4:4120691-4120710 Msa0144530:CDS 45.0%
!! CCACCAAAAGCACCATAAAG+AGG - chr1_4:4120486-4120505 None:intergenic 45.0%
! CCTCTTTATGGTGCTTTTGG+TGG + chr1_4:4120483-4120502 Msa0144530:CDS 45.0%
GAGTGTGCTTGAATTCCAAG+AGG - chr1_4:4120516-4120535 None:intergenic 45.0%
!! CATCAAGAGGAAGTGTTGGT+AGG + chr1_4:4120691-4120710 Msa0144530:CDS 45.0%
! AAAGGTGTGCTTGGACTTGG+AGG - chr1_4:4120057-4120076 None:intergenic 50.0%
! TGCAAAGGTGTGCTTGGACT+TGG - chr1_4:4120060-4120079 None:intergenic 50.0%
! AAAGGTGTGCTTGGACTTGG+AGG - chr1_4:4120057-4120076 None:intergenic 50.0%
! TGCAAAGGTGTGCTTGGACT+TGG - chr1_4:4120060-4120079 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 4120006 4120797 4120006 ID=Msa0144530;Name=Msa0144530
chr1_4 mRNA 4120006 4120797 4120006 ID=Msa0144530-mRNA-1;Parent=Msa0144530;Name=Msa0144530-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|263
chr1_4 exon 4120006 4120797 4120006 ID=Msa0144530-mRNA-1:exon:1682;Parent=Msa0144530-mRNA-1
chr1_4 CDS 4120006 4120797 4120006 ID=Msa0144530-mRNA-1:cds;Parent=Msa0144530-mRNA-1
Gene Sequence

>Msa0144530

ATGGAAAGACTAAGCAAGGAACCATGCATCTTCTCTTCTCAAGAAACTCCTCCAAGTCCAAGCACACCTTTGCAAAATCAACATGAAAAGAAGAAACAACAATCTATTGAGGTAGAAGAAGATATCACTAAGGTAGAAACTTTATTTGATCTAAATGTATCTAGCAATGATTCTAATCTTGATTGTAATAGTCAGCAAGAAACAGAACTCAATCTCATAACTTCTTTAGATGTTGGTAATTCATCATCACAAAACAATAATACTCTTGATGTGGAACAAAGAATTTTTTCTTGTAACTATTGTCATAGAAAATTCTATAGCTCACAAGCATTAGGTGGACACCAAAATGCTCACAAAAGAGAGAGATCAATAGCAAAAAGAGGACAAAGATTTGGAACACAAATAATAGCTTCAGCTTCTGCTTTTGGATTTCCTATTATGCATAATAAACAAAGTTATGCAAACATGGCTTCTTTGCCTCTTTATGGTGCTTTTGGTGGTAATAAACCTCTTGGAATTCAAGCACACTCTATGATCCATAAGCCTTCTCATGTTTCATCTAATGGATTTGGAAACTCTTATGGACATCATCATCATCATGGTTGGTCAAACTCAAGAATCTTTATGGATCAACAACCTGGAATAGCAAAACTAGGTATGGCTGATTTTCATAGAACAACAACATCATCAAGAGGAAGTGTTGGTAGGTTTGAAGTCGTAGATACTATGATTAATTCTGCAGCTAATAAAGAAATGAAGCAGAAGCAGCTTGATTTAAACCTCAAGCTATGA

Protein sequence

>Msa0144530

MERLSKEPCIFSSQETPPSPSTPLQNQHEKKKQQSIEVEEDITKVETLFDLNVSSNDSNLDCNSQQETELNLITSLDVGNSSSQNNNTLDVEQRIFSCNYCHRKFYSSQALGGHQNAHKRERSIAKRGQRFGTQIIASASAFGFPIMHNKQSYANMASLPLYGAFGGNKPLGIQAHSMIHKPSHVSSNGFGNSYGHHHHHGWSNSRIFMDQQPGIAKLGMADFHRTTTSSRGSVGRFEVVDTMINSAANKEMKQKQLDLNLKL*