AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0765040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0765040 MtrunA17_Chr5g0415741 78.571 126 4 1 1 103 1 126 3.48e-58 175
Msa0765040 MtrunA17_Chr5g0415761 63.542 96 34 1 9 103 33 128 2.24e-34 114
Msa0765040 MtrunA17_Chr5g0415771 68.675 83 26 0 20 102 44 126 4.65e-33 111
Msa0765040 MtrunA17_Chr7g0216481 55.422 83 37 0 20 102 51 133 6.28e-32 108
Msa0765040 MtrunA17_Chr5g0404831 45.556 90 48 1 13 101 25 114 1.22e-27 97.4
Msa0765040 MtrunA17_Chr3g0142051 48.780 82 42 0 20 101 31 112 1.03e-26 95.1
Msa0765040 MtrunA17_Chr1g0155721 46.429 84 45 0 20 103 31 114 1.11e-26 95.1
Msa0765040 MtrunA17_Chr2g0280411 38.298 94 58 0 6 99 20 113 6.50e-20 78.2
Msa0765040 MtrunA17_Chr8g0393201 42.045 88 51 0 14 101 246 333 6.22e-19 79.3
Msa0765040 MtrunA17_Chr2g0319291 34.066 91 59 1 10 99 24 114 1.11e-18 74.7
Msa0765040 MtrunA17_Chr7g0245141 39.241 79 48 0 20 98 49 127 1.61e-18 74.7
Msa0765040 MtrunA17_Chr8g0334481 35.443 79 51 0 20 98 51 129 2.25e-18 74.3
Msa0765040 MtrunA17_Chr4g0042051 36.250 80 51 0 20 99 35 114 1.43e-17 72.0
Msa0765040 MtrunA17_Chr8g0360031 35.294 85 53 2 18 100 90 174 1.52e-14 65.5
Msa0765040 MtrunA17_Chr3g0125821 32.941 85 55 2 18 100 87 171 3.32e-14 64.7
Msa0765040 MtrunA17_Chr4g0052481 28.866 97 67 1 6 100 70 166 3.70e-14 64.3
Msa0765040 MtrunA17_Chr2g0317731 34.118 85 54 2 18 100 87 171 1.26e-13 63.2
Msa0765040 MtrunA17_Chr1g0201781 30.000 80 53 2 22 100 83 160 7.91e-13 60.8
Msa0765040 MtrunA17_Chr1g0211871 35.135 74 44 2 20 92 89 159 1.57e-12 60.5
Msa0765040 MtrunA17_Chr7g0249461 34.118 85 55 1 20 103 101 185 1.86e-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
Msa0765040 AT1G69880.1 55.556 81 36 0 20 100 62 142 1.91e-29 103
Msa0765040 AT5G39950.1 43.373 83 47 0 20 102 50 132 3.50e-27 97.1
Msa0765040 AT1G45145.1 44.444 90 50 0 12 101 22 111 1.56e-26 95.1
Msa0765040 AT1G59730.1 45.783 83 45 0 20 102 46 128 1.87e-26 95.1
Msa0765040 AT3G51030.1 42.391 92 52 1 11 101 21 112 2.19e-25 92.0
Msa0765040 AT1G19730.1 47.368 95 48 2 9 101 19 113 2.48e-25 92.0
Msa0765040 AT5G42980.1 46.429 84 45 0 20 103 30 113 2.46e-24 89.4
Msa0765040 AT3G56420.1 40.260 77 46 0 20 96 65 141 1.92e-19 78.2
Msa0765040 AT3G56420.2 40.260 77 46 0 20 96 65 141 1.92e-19 78.2
Msa0765040 AT3G56420.3 40.260 77 46 0 20 96 65 141 1.92e-19 78.2
Msa0765040 AT3G08710.2 36.709 79 50 0 20 98 48 126 9.98e-18 73.2
Msa0765040 AT3G08710.3 36.709 79 50 0 20 98 48 126 9.98e-18 73.2
Msa0765040 AT3G08710.1 36.709 79 50 0 20 98 48 126 9.98e-18 73.2
Msa0765040 AT1G11530.1 32.653 98 66 0 2 99 9 106 3.29e-17 71.2
Msa0765040 AT3G17880.2 37.647 85 53 0 17 101 285 369 7.63e-17 74.3
Msa0765040 AT3G17880.1 37.647 85 53 0 17 101 292 376 9.00e-17 74.3
Msa0765040 AT4G03520.1 38.372 86 51 2 17 100 98 183 1.10e-15 68.9
Msa0765040 AT2G40790.2 35.714 84 54 0 20 103 65 148 1.28e-15 68.2
Msa0765040 AT2G40790.1 35.714 84 54 0 20 103 65 148 1.28e-15 68.2
Msa0765040 AT1G03680.1 39.506 81 47 2 22 100 97 177 2.51e-15 67.8
Msa0765040 AT3G15360.1 33.721 86 49 3 20 100 107 189 9.46e-15 66.6
Msa0765040 AT2G35010.2 36.145 83 49 2 21 100 110 191 2.05e-13 63.2
Msa0765040 AT2G35010.1 36.145 83 49 2 21 100 110 191 2.05e-13 63.2
Msa0765040 AT5G16400.1 35.294 85 54 1 20 103 100 184 2.26e-13 62.8
Msa0765040 AT1G52990.1 29.545 88 61 1 14 100 224 311 4.81e-13 63.5
Msa0765040 AT3G02730.1 35.294 85 54 1 20 103 90 174 8.58e-13 61.2
Msa0765040 AT1G31020.1 36.585 82 50 1 21 100 75 156 1.12e-12 60.5
Msa0765040 AT1G43560.1 30.986 71 48 1 20 89 79 149 1.97e-12 60.1

Find 15 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGCAAAATCTTTCATAAC+TGG 0.263663 5_2:+25512405 None:intergenic
GCTTGATGTTGATGAGTTAA+TGG 0.271195 5_2:-25512355 Msa0765040:intron
TTATTGATTTCACAGCTAAA+TGG 0.322109 5_2:-25512452 Msa0765040:CDS
TTCTTAATGAGTAAAATAGT+TGG 0.439170 5_2:+25512192 None:intergenic
TAAAGTGGTTGGAGTGAGAA+AGG 0.465747 5_2:-25512154 Msa0765040:CDS
GGGAGTTTCTCAAACATTCC+AGG 0.482800 5_2:-25512226 Msa0765040:CDS
GTGTGGACCTTGCAAAGTTA+TGG 0.487071 5_2:-25512430 Msa0765040:CDS
AGGAAATGTTGTTGATAAAG+TGG 0.502411 5_2:-25512169 Msa0765040:CDS
AATGTTGTTGATAAAGTGGT+TGG 0.520853 5_2:-25512165 Msa0765040:CDS
ATACACAAAATTATACAAGT+TGG 0.527315 5_2:+25512779 None:intergenic
GATTTCACAGCTAAATGGTG+TGG 0.590907 5_2:-25512447 Msa0765040:CDS
TAGTTGGCAATGAATGCACC+TGG 0.594643 5_2:+25512208 None:intergenic
ACTGGATCCATAACTTTGCA+AGG 0.602265 5_2:+25512423 None:intergenic
AGTGGTTGGAGTGAGAAAGG+AGG 0.605043 5_2:-25512151 Msa0765040:CDS
TGAGAAAGGAGGAACTACAA+AGG 0.675876 5_2:-25512140 Msa0765040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACACAAAATTATACAAGT+TGG + chr5_2:25512126-25512145 None:intergenic 20.0%
!!! TGTTTTTTCTTTTGTATAGA+TGG - chr5_2:25512427-25512446 Msa0765040:CDS 20.0%
!!! TGTTTTTTCCACAATATAAA+TGG - chr5_2:25512648-25512667 Msa0765040:intron 20.0%
!! TTCTTAATGAGTAAAATAGT+TGG + chr5_2:25512713-25512732 None:intergenic 20.0%
!!! ACTATTTTACTCATTAAGAA+AGG - chr5_2:25512713-25512732 Msa0765040:intron 20.0%
!!! TTATTGATTTCACAGCTAAA+TGG - chr5_2:25512450-25512469 Msa0765040:CDS 25.0%
! TAACAAACTAGTTAAAGTGA+AGG + chr5_2:25512588-25512607 None:intergenic 25.0%
! AGGAAATGTTGTTGATAAAG+TGG - chr5_2:25512733-25512752 Msa0765040:intron 30.0%
! AATGTTGTTGATAAAGTGGT+TGG - chr5_2:25512737-25512756 Msa0765040:intron 30.0%
GCAGCAAAATCTTTCATAAC+TGG + chr5_2:25512500-25512519 None:intergenic 35.0%
! GCTTGATGTTGATGAGTTAA+TGG - chr5_2:25512547-25512566 Msa0765040:intron 35.0%
TCCACAATATAAATGGCAAC+AGG - chr5_2:25512655-25512674 Msa0765040:intron 35.0%
CCACAATATAAATGGCAACA+GGG - chr5_2:25512656-25512675 Msa0765040:intron 35.0%
GGAATGGAATGTAAGGACAT+GGG + chr5_2:25512171-25512190 None:intergenic 40.0%
TGGAATGGAATGTAAGGACA+TGG + chr5_2:25512172-25512191 None:intergenic 40.0%
TAGCAGTGGAATGGAATGTA+AGG + chr5_2:25512178-25512197 None:intergenic 40.0%
CATTCCATTCCACTGCTAAA+TGG - chr5_2:25512180-25512199 Msa0765040:CDS 40.0%
CATTCCATTTAGCAGTGGAA+TGG + chr5_2:25512187-25512206 None:intergenic 40.0%
ATGAGCATTCCATTTAGCAG+TGG + chr5_2:25512192-25512211 None:intergenic 40.0%
GATTTCACAGCTAAATGGTG+TGG - chr5_2:25512455-25512474 Msa0765040:CDS 40.0%
ACTGGATCCATAACTTTGCA+AGG + chr5_2:25512482-25512501 None:intergenic 40.0%
ACAAATCAGTTCTCAAGTGC+TGG + chr5_2:25512631-25512650 None:intergenic 40.0%
! CCCTGTTGCCATTTATATTG+TGG + chr5_2:25512659-25512678 None:intergenic 40.0%
TAAAGTGGTTGGAGTGAGAA+AGG - chr5_2:25512748-25512767 Msa0765040:intron 40.0%
TGAGAAAGGAGGAACTACAA+AGG - chr5_2:25512762-25512781 Msa0765040:CDS 40.0%
GTGTGGACCTTGCAAAGTTA+TGG - chr5_2:25512472-25512491 Msa0765040:intron 45.0%
GGGAGTTTCTCAAACATTCC+AGG - chr5_2:25512676-25512695 Msa0765040:intron 45.0%
TAGTTGGCAATGAATGCACC+TGG + chr5_2:25512697-25512716 None:intergenic 45.0%
AGTGGTTGGAGTGAGAAAGG+AGG - chr5_2:25512751-25512770 Msa0765040:intron 50.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 25512116 25512808 25512116 ID=Msa0765040;Name=Msa0765040
chr5_2 mRNA 25512116 25512808 25512116 ID=Msa0765040-mRNA-1;Parent=Msa0765040;Name=Msa0765040-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0.5|0.66|3|0|103
chr5_2 exon 25512752 25512808 25512752 ID=Msa0765040-mRNA-1:exon:10299;Parent=Msa0765040-mRNA-1
chr5_2 exon 25512356 25512478 25512356 ID=Msa0765040-mRNA-1:exon:10298;Parent=Msa0765040-mRNA-1
chr5_2 exon 25512116 25512247 25512116 ID=Msa0765040-mRNA-1:exon:10297;Parent=Msa0765040-mRNA-1
chr5_2 CDS 25512752 25512808 25512752 ID=Msa0765040-mRNA-1:cds;Parent=Msa0765040-mRNA-1
chr5_2 CDS 25512356 25512478 25512356 ID=Msa0765040-mRNA-1:cds;Parent=Msa0765040-mRNA-1
chr5_2 CDS 25512116 25512247 25512116 ID=Msa0765040-mRNA-1:cds;Parent=Msa0765040-mRNA-1
Gene Sequence

>Msa0765040

ATGAGTTCCAACTTGTATAATTTTGTGTATGTTGATAGATCAACAGAATCATCCCATATGGTTATTGATTTCACAGCTAAATGGTGTGGACCTTGCAAAGTTATGGATCCAGTTATGAAAGATTTTGCTGCAAAATACACTGATGTTGAGTTCATTAAGCTTGATGTTGATGAGTTAATGGGAGTTTCTCAAACATTCCAGGTGCATTCATTGCCAACTATTTTACTCATTAAGAAAGGAAATGTTGTTGATAAAGTGGTTGGAGTGAGAAAGGAGGAACTACAAAGGATGATTGAAAAACAAAGAAACTAA
Protein sequence

>Msa0765040

MSSNLYNFVYVDRSTESSHMVIDFTAKWCGPCKVMDPVMKDFAAKYTDVEFIKLDVDELMGVSQTFQVHSLPTILLIKKGNVVDKVVGVRKEELQRMIEKQRN*