AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0106230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0106230 MtrunA17_Chr1g0161901 92.996 257 11 2 1 256 1 251 2.68e-179 492
Msa0106230 MtrunA17_Chr8g0376021 51.562 256 84 9 2 256 1 217 1.33e-74 226
Msa0106230 MtrunA17_Chr5g0434121 43.726 263 107 10 6 256 4 237 1.39e-55 178
Msa0106230 MtrunA17_Chr3g0110091 40.316 253 133 7 5 256 3 238 4.35e-55 177
Msa0106230 MtrunA17_Chr2g0333741 66.234 77 21 2 96 167 81 157 2.03e-27 105
Msa0106230 MtrunA17_Chr1g0149811 40.909 132 56 2 58 167 49 180 3.89e-24 97.4
Msa0106230 MtrunA17_Chr1g0207691 34.595 185 96 8 41 217 8 175 1.79e-20 86.3
Msa0106230 MtrunA17_Chr3g0137111 44.828 116 42 6 68 167 49 158 5.72e-20 85.5
Msa0106230 MtrunA17_Chr4g0001081 55.556 72 24 2 96 167 67 130 4.46e-18 80.5
Msa0106230 MtrunA17_Chr4g0072571 52.632 76 32 2 96 169 45 118 1.74e-16 74.7
Msa0106230 MtrunA17_Chr4g0053691 37.762 143 64 8 88 227 57 177 6.57e-15 70.9
Msa0106230 MtrunA17_Chr7g0254221 51.923 52 24 1 81 132 19 69 3.89e-12 62.8
Msa0106230 MtrunA17_Chr7g0251581 69.697 33 10 0 96 128 39 71 2.24e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0106230 AT1G66140.1 41.758 182 81 6 96 256 83 260 5.35e-37 131
Msa0106230 AT1G24625.1 40.000 210 86 9 54 256 33 209 4.32e-31 114
Msa0106230 AT1G80730.1 55.682 88 23 2 96 167 66 153 1.21e-23 95.9
Msa0106230 AT5G10970.1 54.321 81 33 2 90 167 96 175 1.00e-20 89.0
Msa0106230 AT5G25160.1 51.163 86 36 3 87 167 50 134 9.86e-20 85.5
Msa0106230 AT5G57520.1 51.515 66 32 0 96 161 50 115 1.44e-15 72.4
Msa0106230 AT5G14010.1 46.575 73 28 1 92 153 32 104 9.55e-15 70.5
Msa0106230 AT5G01860.1 57.500 40 17 0 96 135 65 104 2.32e-11 62.0

Find 47 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTTCCAAGTTCAAATT+TGG 0.203450 1_3:-15359072 None:intergenic
ATGAAGATGTCGGCGTATTT+TGG 0.224650 1_3:+15359667 Msa0106230:CDS
GACATCAGAATGCTCATAAA+AGG 0.253068 1_3:+15359403 Msa0106230:CDS
TTAGCTTCTTTACCTCTTCA+TGG 0.299313 1_3:+15359486 Msa0106230:CDS
AGAAGTTGTGGCACTGTCTT+TGG 0.313022 1_3:-15359163 None:intergenic
TTTATCTGCCTGAAACTTCC+AGG 0.347691 1_3:-15359690 None:intergenic
AAATTCGAGAAAGATTGTTT+TGG 0.369690 1_3:+15359621 Msa0106230:CDS
AGCTAAGCTTGTATACCTTT+CGG 0.370401 1_3:-15359469 None:intergenic
ACGATGATGGCATATGGTTT+TGG 0.377290 1_3:-15359557 None:intergenic
CCTATCCTGATCTTACTTTG+AGG 0.413927 1_3:+15359802 Msa0106230:CDS
TCCTTCAAATCTTCATCGCT+CGG 0.430932 1_3:-15359249 None:intergenic
GCCGAGCGATGAAGATTTGA+AGG 0.434759 1_3:+15359248 Msa0106230:CDS
CACAACTTCTTGTCTTACTA+AGG 0.439607 1_3:+15359176 Msa0106230:CDS
TTCTTTAGCTCACAAGCGTT+AGG 0.463186 1_3:+15359378 Msa0106230:CDS
TCGGCTCGAAGTTGAGAGTC+AGG 0.476212 1_3:-15359230 None:intergenic
GTAGTAGATGTTTGTTGAGG+AGG 0.483825 1_3:-15359780 None:intergenic
TCTTTCTCGAATTTCGCTGC+AGG 0.490019 1_3:-15359612 None:intergenic
GAAGACTCCAAATTTGAACT+TGG 0.507535 1_3:+15359065 Msa0106230:CDS
ACTAAGGCAGACATCAATCC+AGG 0.507613 1_3:+15359192 Msa0106230:CDS
ATCAGCATCGACGACGATGA+TGG 0.511996 1_3:-15359570 None:intergenic
CAAAGCGCGCTATGCAAGTA+GGG 0.513002 1_3:+15359439 Msa0106230:CDS
TAAAGCCTCAAAGTAAGATC+AGG 0.515851 1_3:-15359807 None:intergenic
TCTCTTGTAATTATTGTAGG+AGG 0.522769 1_3:+15359352 Msa0106230:CDS
TGATTCTTGTAAGTATATGT+TGG 0.525252 1_3:-15359127 None:intergenic
GCAAAGCGCGCTATGCAAGT+AGG 0.525984 1_3:+15359438 Msa0106230:CDS
ACATCAGAATGCTCATAAAA+GGG 0.526603 1_3:+15359404 Msa0106230:CDS
CCTCAAAGTAAGATCAGGAT+AGG 0.529476 1_3:-15359802 None:intergenic
GAGAAAACTCTATGAATCGT+TGG 0.530449 1_3:-15359333 None:intergenic
CATCGTCGTCGATGCTGATG+AGG 0.540974 1_3:+15359574 Msa0106230:CDS
AGGTCAAGGGAAATAGAACC+TGG 0.542650 1_3:-15359210 None:intergenic
AGTATATGTTGGAACCTACT+TGG 0.544787 1_3:-15359116 None:intergenic
TCGACGACGATGATGGCATA+TGG 0.558903 1_3:-15359563 None:intergenic
CGAAGTTGAGAGTCAGGTCA+AGG 0.567959 1_3:-15359224 None:intergenic
ATCGTCGTCGATGCTGATGA+GGG 0.568860 1_3:+15359575 Msa0106230:CDS
TTTAGCTCACAAGCGTTAGG+AGG 0.570693 1_3:+15359381 Msa0106230:CDS
TAGGTAGTAGATGTTTGTTG+AGG 0.576261 1_3:-15359783 None:intergenic
AACTCTATGAATCGTTGGTG+CGG 0.596598 1_3:-15359328 None:intergenic
TTAGAAGTAAGCAGCCAAGT+AGG 0.598009 1_3:+15359102 Msa0106230:CDS
AAAGAAGAAGAACCATGAAG+AGG 0.622542 1_3:-15359498 None:intergenic
CTTAGTAAGACAAGAAGTTG+TGG 0.624602 1_3:-15359175 None:intergenic
AAGTAGGGATGTTTACCGAA+AGG 0.636930 1_3:+15359454 Msa0106230:CDS
GAAGTTGAGAGTCAGGTCAA+GGG 0.642054 1_3:-15359223 None:intergenic
TTTATGCATAATGAAGATGT+CGG 0.651635 1_3:+15359657 Msa0106230:CDS
GACACTAATAGTGAAGTACT+AGG 0.655462 1_3:+15359279 Msa0106230:CDS
TCTTCATTATGCATAAACAT+CGG 0.674163 1_3:-15359651 None:intergenic
TCATAAAAGGGAGAGAACGA+TGG 0.677286 1_3:+15359416 Msa0106230:CDS
GCATGAGCTTGAATCCCAAG+AGG 0.685243 1_3:-15359525 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTCTCTTGTAATTATTGT+AGG + chr1_3:15359349-15359368 Msa0106230:CDS 20.0%
!!! TTTTCTCTTGTAATTATTGT+AGG + chr1_3:15359349-15359368 Msa0106230:CDS 20.0%
! TGATTCTTGTAAGTATATGT+TGG - chr1_3:15359130-15359149 None:intergenic 25.0%
!! AAATTCGAGAAAGATTGTTT+TGG + chr1_3:15359621-15359640 Msa0106230:CDS 25.0%
! TCTTCATTATGCATAAACAT+CGG - chr1_3:15359654-15359673 None:intergenic 25.0%
! TTTATGCATAATGAAGATGT+CGG + chr1_3:15359657-15359676 Msa0106230:CDS 25.0%
! TGATTCTTGTAAGTATATGT+TGG - chr1_3:15359130-15359149 None:intergenic 25.0%
!! AAATTCGAGAAAGATTGTTT+TGG + chr1_3:15359621-15359640 Msa0106230:CDS 25.0%
! TCTTCATTATGCATAAACAT+CGG - chr1_3:15359654-15359673 None:intergenic 25.0%
! TTTATGCATAATGAAGATGT+CGG + chr1_3:15359657-15359676 Msa0106230:CDS 25.0%
TCTCTTGTAATTATTGTAGG+AGG + chr1_3:15359352-15359371 Msa0106230:CDS 30.0%
ACATCAGAATGCTCATAAAA+GGG + chr1_3:15359404-15359423 Msa0106230:CDS 30.0%
TCTCTTGTAATTATTGTAGG+AGG + chr1_3:15359352-15359371 Msa0106230:CDS 30.0%
ACATCAGAATGCTCATAAAA+GGG + chr1_3:15359404-15359423 Msa0106230:CDS 30.0%
GAAGACTCCAAATTTGAACT+TGG + chr1_3:15359065-15359084 Msa0106230:CDS 35.0%
TCAGCTTCCAAGTTCAAATT+TGG - chr1_3:15359075-15359094 None:intergenic 35.0%
AGTATATGTTGGAACCTACT+TGG - chr1_3:15359119-15359138 None:intergenic 35.0%
CTTAGTAAGACAAGAAGTTG+TGG - chr1_3:15359178-15359197 None:intergenic 35.0%
CACAACTTCTTGTCTTACTA+AGG + chr1_3:15359176-15359195 Msa0106230:CDS 35.0%
! GACACTAATAGTGAAGTACT+AGG + chr1_3:15359279-15359298 Msa0106230:CDS 35.0%
GAGAAAACTCTATGAATCGT+TGG - chr1_3:15359336-15359355 None:intergenic 35.0%
GACATCAGAATGCTCATAAA+AGG + chr1_3:15359403-15359422 Msa0106230:CDS 35.0%
AGCTAAGCTTGTATACCTTT+CGG - chr1_3:15359472-15359491 None:intergenic 35.0%
TTAGCTTCTTTACCTCTTCA+TGG + chr1_3:15359486-15359505 Msa0106230:CDS 35.0%
AAAGAAGAAGAACCATGAAG+AGG - chr1_3:15359501-15359520 None:intergenic 35.0%
! TCTTCTTCTTTTCATCCTCT+TGG + chr1_3:15359510-15359529 Msa0106230:CDS 35.0%
! CTTCTTCTTTTCATCCTCTT+GGG + chr1_3:15359511-15359530 Msa0106230:CDS 35.0%
! TAGGTAGTAGATGTTTGTTG+AGG - chr1_3:15359786-15359805 None:intergenic 35.0%
TAAAGCCTCAAAGTAAGATC+AGG - chr1_3:15359810-15359829 None:intergenic 35.0%
GAAGACTCCAAATTTGAACT+TGG + chr1_3:15359065-15359084 Msa0106230:CDS 35.0%
TCAGCTTCCAAGTTCAAATT+TGG - chr1_3:15359075-15359094 None:intergenic 35.0%
AGTATATGTTGGAACCTACT+TGG - chr1_3:15359119-15359138 None:intergenic 35.0%
CTTAGTAAGACAAGAAGTTG+TGG - chr1_3:15359178-15359197 None:intergenic 35.0%
CACAACTTCTTGTCTTACTA+AGG + chr1_3:15359176-15359195 Msa0106230:CDS 35.0%
! GACACTAATAGTGAAGTACT+AGG + chr1_3:15359279-15359298 Msa0106230:CDS 35.0%
GAGAAAACTCTATGAATCGT+TGG - chr1_3:15359336-15359355 None:intergenic 35.0%
GACATCAGAATGCTCATAAA+AGG + chr1_3:15359403-15359422 Msa0106230:CDS 35.0%
AGCTAAGCTTGTATACCTTT+CGG - chr1_3:15359472-15359491 None:intergenic 35.0%
TTAGCTTCTTTACCTCTTCA+TGG + chr1_3:15359486-15359505 Msa0106230:CDS 35.0%
AAAGAAGAAGAACCATGAAG+AGG - chr1_3:15359501-15359520 None:intergenic 35.0%
! TCTTCTTCTTTTCATCCTCT+TGG + chr1_3:15359510-15359529 Msa0106230:CDS 35.0%
! CTTCTTCTTTTCATCCTCTT+GGG + chr1_3:15359511-15359530 Msa0106230:CDS 35.0%
! TAGGTAGTAGATGTTTGTTG+AGG - chr1_3:15359786-15359805 None:intergenic 35.0%
TAAAGCCTCAAAGTAAGATC+AGG - chr1_3:15359810-15359829 None:intergenic 35.0%
TTAGAAGTAAGCAGCCAAGT+AGG + chr1_3:15359102-15359121 Msa0106230:CDS 40.0%
TCCTTCAAATCTTCATCGCT+CGG - chr1_3:15359252-15359271 None:intergenic 40.0%
AACTCTATGAATCGTTGGTG+CGG - chr1_3:15359331-15359350 None:intergenic 40.0%
! TTCTTTAGCTCACAAGCGTT+AGG + chr1_3:15359378-15359397 Msa0106230:CDS 40.0%
TCATAAAAGGGAGAGAACGA+TGG + chr1_3:15359416-15359435 Msa0106230:CDS 40.0%
AAGTAGGGATGTTTACCGAA+AGG + chr1_3:15359454-15359473 Msa0106230:CDS 40.0%
!! ACGATGATGGCATATGGTTT+TGG - chr1_3:15359560-15359579 None:intergenic 40.0%
! ATGAAGATGTCGGCGTATTT+TGG + chr1_3:15359667-15359686 Msa0106230:CDS 40.0%
!!! TATTTTGGCCTGGAAGTTTC+AGG + chr1_3:15359682-15359701 Msa0106230:CDS 40.0%
TTTATCTGCCTGAAACTTCC+AGG - chr1_3:15359693-15359712 None:intergenic 40.0%
! GTAGTAGATGTTTGTTGAGG+AGG - chr1_3:15359783-15359802 None:intergenic 40.0%
CCTCAAAGTAAGATCAGGAT+AGG - chr1_3:15359805-15359824 None:intergenic 40.0%
CCTATCCTGATCTTACTTTG+AGG + chr1_3:15359802-15359821 Msa0106230:CDS 40.0%
TTAGAAGTAAGCAGCCAAGT+AGG + chr1_3:15359102-15359121 Msa0106230:CDS 40.0%
TCCTTCAAATCTTCATCGCT+CGG - chr1_3:15359252-15359271 None:intergenic 40.0%
AACTCTATGAATCGTTGGTG+CGG - chr1_3:15359331-15359350 None:intergenic 40.0%
! TTCTTTAGCTCACAAGCGTT+AGG + chr1_3:15359378-15359397 Msa0106230:CDS 40.0%
TCATAAAAGGGAGAGAACGA+TGG + chr1_3:15359416-15359435 Msa0106230:CDS 40.0%
AAGTAGGGATGTTTACCGAA+AGG + chr1_3:15359454-15359473 Msa0106230:CDS 40.0%
!! ACGATGATGGCATATGGTTT+TGG - chr1_3:15359560-15359579 None:intergenic 40.0%
! ATGAAGATGTCGGCGTATTT+TGG + chr1_3:15359667-15359686 Msa0106230:CDS 40.0%
!!! TATTTTGGCCTGGAAGTTTC+AGG + chr1_3:15359682-15359701 Msa0106230:CDS 40.0%
TTTATCTGCCTGAAACTTCC+AGG - chr1_3:15359693-15359712 None:intergenic 40.0%
! GTAGTAGATGTTTGTTGAGG+AGG - chr1_3:15359783-15359802 None:intergenic 40.0%
CCTCAAAGTAAGATCAGGAT+AGG - chr1_3:15359805-15359824 None:intergenic 40.0%
CCTATCCTGATCTTACTTTG+AGG + chr1_3:15359802-15359821 Msa0106230:CDS 40.0%
AGAAGTTGTGGCACTGTCTT+TGG - chr1_3:15359166-15359185 None:intergenic 45.0%
ACTAAGGCAGACATCAATCC+AGG + chr1_3:15359192-15359211 Msa0106230:CDS 45.0%
AGGTCAAGGGAAATAGAACC+TGG - chr1_3:15359213-15359232 None:intergenic 45.0%
GAAGTTGAGAGTCAGGTCAA+GGG - chr1_3:15359226-15359245 None:intergenic 45.0%
! TTTAGCTCACAAGCGTTAGG+AGG + chr1_3:15359381-15359400 Msa0106230:CDS 45.0%
TCTTTCTCGAATTTCGCTGC+AGG - chr1_3:15359615-15359634 None:intergenic 45.0%
AGAAGTTGTGGCACTGTCTT+TGG - chr1_3:15359166-15359185 None:intergenic 45.0%
ACTAAGGCAGACATCAATCC+AGG + chr1_3:15359192-15359211 Msa0106230:CDS 45.0%
AGGTCAAGGGAAATAGAACC+TGG - chr1_3:15359213-15359232 None:intergenic 45.0%
GAAGTTGAGAGTCAGGTCAA+GGG - chr1_3:15359226-15359245 None:intergenic 45.0%
! TTTAGCTCACAAGCGTTAGG+AGG + chr1_3:15359381-15359400 Msa0106230:CDS 45.0%
TCTTTCTCGAATTTCGCTGC+AGG - chr1_3:15359615-15359634 None:intergenic 45.0%
CGAAGTTGAGAGTCAGGTCA+AGG - chr1_3:15359227-15359246 None:intergenic 50.0%
GCCGAGCGATGAAGATTTGA+AGG + chr1_3:15359248-15359267 Msa0106230:CDS 50.0%
CAAAGCGCGCTATGCAAGTA+GGG + chr1_3:15359439-15359458 Msa0106230:CDS 50.0%
GCATGAGCTTGAATCCCAAG+AGG - chr1_3:15359528-15359547 None:intergenic 50.0%
! TCGACGACGATGATGGCATA+TGG - chr1_3:15359566-15359585 None:intergenic 50.0%
!! ATCAGCATCGACGACGATGA+TGG - chr1_3:15359573-15359592 None:intergenic 50.0%
ATCGTCGTCGATGCTGATGA+GGG + chr1_3:15359575-15359594 Msa0106230:CDS 50.0%
CGAAGTTGAGAGTCAGGTCA+AGG - chr1_3:15359227-15359246 None:intergenic 50.0%
GCCGAGCGATGAAGATTTGA+AGG + chr1_3:15359248-15359267 Msa0106230:CDS 50.0%
CAAAGCGCGCTATGCAAGTA+GGG + chr1_3:15359439-15359458 Msa0106230:CDS 50.0%
GCATGAGCTTGAATCCCAAG+AGG - chr1_3:15359528-15359547 None:intergenic 50.0%
! TCGACGACGATGATGGCATA+TGG - chr1_3:15359566-15359585 None:intergenic 50.0%
!! ATCAGCATCGACGACGATGA+TGG - chr1_3:15359573-15359592 None:intergenic 50.0%
ATCGTCGTCGATGCTGATGA+GGG + chr1_3:15359575-15359594 Msa0106230:CDS 50.0%
! TCGGCTCGAAGTTGAGAGTC+AGG - chr1_3:15359233-15359252 None:intergenic 55.0%
GCAAAGCGCGCTATGCAAGT+AGG + chr1_3:15359438-15359457 Msa0106230:CDS 55.0%
CATCGTCGTCGATGCTGATG+AGG + chr1_3:15359574-15359593 Msa0106230:CDS 55.0%
!!! GATGTCGGCGTATTTTGGCC+TGG + chr1_3:15359672-15359691 Msa0106230:CDS 55.0%
! TCGGCTCGAAGTTGAGAGTC+AGG - chr1_3:15359233-15359252 None:intergenic 55.0%
GCAAAGCGCGCTATGCAAGT+AGG + chr1_3:15359438-15359457 Msa0106230:CDS 55.0%
CATCGTCGTCGATGCTGATG+AGG + chr1_3:15359574-15359593 Msa0106230:CDS 55.0%
!!! GATGTCGGCGTATTTTGGCC+TGG + chr1_3:15359672-15359691 Msa0106230:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 15359060 15359830 15359060 ID=Msa0106230;Name=Msa0106230
chr1_3 mRNA 15359060 15359830 15359060 ID=Msa0106230-mRNA-1;Parent=Msa0106230;Name=Msa0106230-mRNA-1;_AED=0.18;_eAED=0.19;_QI=0|-1|0|1|-1|1|1|0|256
chr1_3 exon 15359060 15359830 15359060 ID=Msa0106230-mRNA-1:exon:5884;Parent=Msa0106230-mRNA-1
chr1_3 CDS 15359060 15359830 15359060 ID=Msa0106230-mRNA-1:cds;Parent=Msa0106230-mRNA-1
Gene Sequence

>Msa0106230

ATGATGAAGACTCCAAATTTGAACTTGGAAGCTGAAAATAGTTTAGAAGTAAGCAGCCAAGTAGGTTCCAACATATACTTACAAGAATCATCTCATGATCTTACCAAAGACAGTGCCACAACTTCTTGTCTTACTAAGGCAGACATCAATCCAGGTTCTATTTCCCTTGACCTGACTCTCAACTTCGAGCCGAGCGATGAAGATTTGAAGGAAACAAGCGACACTAATAGTGAAGTACTAGGAGCTAATCAAGCTCATAATACTGTTTCCGCACCAACGATTCATAGAGTTTTCTCTTGTAATTATTGTAGGAGGAAATTCTTTAGCTCACAAGCGTTAGGAGGACATCAGAATGCTCATAAAAGGGAGAGAACGATGGCAAAGCGCGCTATGCAAGTAGGGATGTTTACCGAAAGGTATACAAGCTTAGCTTCTTTACCTCTTCATGGTTCTTCTTCTTTTCATCCTCTTGGGATTCAAGCTCATGCTGCAATGCACCAAAACCATATGCCATCATCGTCGTCGATGCTGATGAGGGCTCAAAATATGAGACCTGCAGCGAAATTCGAGAAAGATTGTTTTGGAGCAGCACCGATGTTTATGCATAATGAAGATGTCGGCGTATTTTGGCCTGGAAGTTTCAGGCAGATAAATCAAAGTGTTCATAATTCAAATTTGAATCATAACTCAAATTTAAATACTAGTTTTGTAGCAACTGAACCTCCTCAACAAACATCTACTACCTATCCTGATCTTACTTTGAGGCTTTAA
Protein sequence

>Msa0106230

MMKTPNLNLEAENSLEVSSQVGSNIYLQESSHDLTKDSATTSCLTKADINPGSISLDLTLNFEPSDEDLKETSDTNSEVLGANQAHNTVSAPTIHRVFSCNYCRRKFFSSQALGGHQNAHKRERTMAKRAMQVGMFTERYTSLASLPLHGSSSFHPLGIQAHAAMHQNHMPSSSSMLMRAQNMRPAAKFEKDCFGAAPMFMHNEDVGVFWPGSFRQINQSVHNSNLNHNSNLNTSFVATEPPQQTSTTYPDLTLRL*