AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0441630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0441630 MtrunA17_Chr3g0079381 96.774 186 6 0 1 186 1 186 1.21e-135 376
Msa0441630 MtrunA17_Chr3g0079401 90.698 172 16 0 15 186 16 187 1.67e-118 333
Msa0441630 MtrunA17_Chr5g0398871 49.730 185 91 2 4 186 27 211 1.46e-65 200
Msa0441630 MtrunA17_Chr4g0056601 47.644 191 91 2 5 186 12 202 3.20e-59 184
Msa0441630 MtrunA17_Chr4g0018281 49.091 165 82 1 22 186 34 196 1.71e-50 161
Msa0441630 MtrunA17_Chr4g0018241 46.626 163 85 1 24 186 36 196 2.32e-45 148
Msa0441630 MtrunA17_Chr4g0018251 46.012 163 86 1 24 186 36 196 3.43e-44 145
Msa0441630 MtrunA17_Chr4g0011681 42.051 195 101 6 3 186 8 201 2.91e-43 143
Msa0441630 MtrunA17_Chr4g0011711 40.513 195 104 6 3 186 8 201 8.94e-40 134
Msa0441630 MtrunA17_Chr4g0011701 42.021 188 99 6 7 186 16 201 9.18e-40 134
Msa0441630 MtrunA17_Chr4g0011721 39.109 202 106 6 1 186 1 201 5.83e-39 132
Msa0441630 MtrunA17_Chr4g0067891 36.735 196 102 5 8 183 9 202 3.11e-36 125
Msa0441630 MtrunA17_Chr8g0391341 37.500 176 98 4 18 183 38 211 8.33e-35 122
Msa0441630 MtrunA17_Chr7g0230391 42.941 170 83 6 23 180 42 209 3.46e-34 120
Msa0441630 MtrunA17_Chr3g0079371 35.714 182 103 4 12 181 45 224 9.35e-32 114
Msa0441630 MtrunA17_Chr7g0269361 33.333 165 106 3 17 181 26 186 3.28e-30 109
Msa0441630 MtrunA17_Chr2g0301381 38.554 166 86 4 23 183 33 187 9.62e-30 108
Msa0441630 MtrunA17_Chr1g0195561 29.891 184 123 3 3 184 9 188 1.83e-29 107
Msa0441630 MtrunA17_Chr4g0070161 33.511 188 111 5 5 183 15 197 2.71e-26 99.8
Msa0441630 MtrunA17_Chr4g0018231 32.335 167 99 5 24 183 43 202 1.39e-19 82.0
Msa0441630 MtrunA17_Chr1g0147051 30.000 180 107 5 19 185 76 249 8.26e-16 74.7
Msa0441630 MtrunA17_Chr8g0345281 28.205 156 109 2 25 178 68 222 1.08e-14 71.2
Msa0441630 MtrunA17_Chr8g0345211 30.723 166 104 5 20 181 72 230 1.44e-14 70.9
Msa0441630 MtrunA17_Chr3g0126771 29.341 167 112 3 21 183 74 238 1.42e-13 68.2
Msa0441630 MtrunA17_Chr1g0192301 26.087 161 109 5 25 182 63 216 8.24e-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
Msa0441630 AT5G62350.1 54.651 172 76 2 17 186 31 202 3.44e-67 204
Msa0441630 AT3G47380.1 48.969 194 87 4 5 186 9 202 2.09e-63 194
Msa0441630 AT4G25260.1 45.771 201 94 2 1 186 1 201 2.57e-59 184
Msa0441630 AT1G62770.1 48.936 188 87 4 5 183 9 196 8.19e-55 173
Msa0441630 AT4G12390.1 49.701 167 81 1 23 186 38 204 6.47e-51 163
Msa0441630 AT5G62360.1 43.293 164 90 2 23 186 42 202 3.13e-49 159
Msa0441630 AT5G20740.1 40.933 193 101 3 1 181 1 192 4.33e-41 138
Msa0441630 AT5G20740.2 45.062 162 85 2 23 181 66 226 1.09e-40 138
Msa0441630 AT1G14890.1 37.037 189 105 3 6 185 34 217 1.47e-40 137
Msa0441630 AT4G00080.1 39.086 197 102 8 2 181 3 198 1.98e-39 134
Msa0441630 AT2G01610.1 37.500 192 102 4 10 185 30 219 4.06e-38 130
Msa0441630 AT1G62760.1 43.452 168 88 3 20 184 143 306 1.86e-36 129
Msa0441630 AT4G25250.1 35.185 162 104 1 22 182 35 196 2.78e-35 123
Msa0441630 AT1G70720.1 35.567 194 110 5 1 183 5 194 1.72e-31 113
Msa0441630 AT1G70720.2 35.567 194 110 5 1 183 17 206 2.10e-31 113
Msa0441630 AT1G23205.1 34.031 191 111 4 5 181 9 198 2.13e-30 110
Msa0441630 AT5G51520.1 35.976 164 96 2 24 179 37 199 1.61e-29 108
Msa0441630 AT3G62820.1 28.877 187 125 5 3 185 10 192 4.39e-21 86.3
Msa0441630 AT3G14310.1 29.487 156 108 2 25 179 59 213 4.19e-20 87.4
Msa0441630 AT5G62340.1 29.902 204 109 8 6 186 14 206 4.48e-19 81.3
Msa0441630 AT2G47670.1 28.750 160 111 2 24 183 48 204 2.32e-18 79.3
Msa0441630 AT5G53370.2 30.061 163 107 4 18 179 104 260 3.97e-18 81.6
Msa0441630 AT5G53370.1 30.061 163 107 4 18 179 68 224 4.96e-18 81.3
Msa0441630 AT1G53830.1 29.448 163 113 2 18 179 55 216 5.06e-18 81.3
Msa0441630 AT3G49220.2 31.677 161 100 4 21 180 128 279 1.61e-17 79.7
Msa0441630 AT3G49220.3 31.875 160 99 4 21 179 128 278 2.04e-17 79.7
Msa0441630 AT3G49220.1 31.875 160 99 4 21 179 83 233 2.25e-17 79.7
Msa0441630 AT3G14300.1 27.933 179 119 5 12 182 258 434 1.54e-13 68.6
Msa0441630 AT3G14300.1 28.994 169 108 5 20 181 454 617 4.36e-13 67.4
Msa0441630 AT3G47670.1 29.851 201 112 8 1 181 76 267 2.99e-13 66.6

Find 30 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGCACTCATTAATCAATA+TGG 0.347778 3_3:-10056492 Msa0441630:CDS
CCAATTGATGAGGGTCTTGT+TGG 0.397480 3_3:+10056871 None:intergenic
GGCTAATTGATAAAGCTGTT+TGG 0.400503 3_3:+10056847 None:intergenic
TAGGCTTAGCCGTTCACTTA+AGG 0.410233 3_3:-10056706 Msa0441630:CDS
GAGGATTTGATGAAATTTGT+TGG 0.419280 3_3:+10056957 None:intergenic
TCAATGGTCAAGATTTCAAT+TGG 0.421550 3_3:-10056665 Msa0441630:CDS
AACCATTCTTGATCTAATAG+AGG 0.423736 3_3:+10056542 None:intergenic
AAATTACTGATAGTGTTGAT+AGG 0.448838 3_3:-10056725 Msa0441630:CDS
CTTAAACTTTGCAAGATCAA+TGG 0.453176 3_3:-10056681 Msa0441630:CDS
CCAACAAGACCCTCATCAAT+TGG 0.458410 3_3:-10056871 Msa0441630:CDS
GAGTTGAAGTTGCAATAGAT+AGG 0.465044 3_3:+10056979 None:intergenic
AACAAAACTCAATCCACAAA+AGG 0.469923 3_3:-10056822 Msa0441630:CDS
TGAATAGCAGCATATTCTCT+TGG 0.472801 3_3:+10056762 None:intergenic
GAGATTCAACACAAAGTGTT+GGG 0.484787 3_3:+10056916 None:intergenic
AGTACTTGTAGTGATGGATT+TGG 0.488408 3_3:-10056594 Msa0441630:CDS
AACCTCTATTAGATCAAGAA+TGG 0.496455 3_3:-10056544 Msa0441630:CDS
AAGAATGGTTAATCTTGCTC+AGG 0.503787 3_3:-10056529 Msa0441630:CDS
AAGAAGAACATTTGTTGCCA+TGG 0.516513 3_3:+10057019 None:intergenic
AGAGATTCAACACAAAGTGT+TGG 0.533099 3_3:+10056915 None:intergenic
TAGATAGGAGAGTTAAGAGA+AGG 0.542534 3_3:+10056994 None:intergenic
GTTTAAGCTCCTTAAGTGAA+CGG 0.545857 3_3:+10056697 None:intergenic
ACTTGTAGTGATGGATTTGG+TGG 0.550252 3_3:-10056591 Msa0441630:CDS
TCAATATGGTACTAATCACT+AGG 0.550549 3_3:-10056478 None:intergenic
CAATATGGTACTAATCACTA+GGG 0.573803 3_3:-10056477 None:intergenic
ATATAAGTAATGTTCAAACA+TGG 0.577147 3_3:-10056641 Msa0441630:CDS
CTGTTTGGACCAATTGATGA+GGG 0.590554 3_3:+10056862 None:intergenic
GATGCAAGTACTTGTAGTGA+TGG 0.592136 3_3:-10056600 Msa0441630:CDS
TATAAGTAATGTTCAAACAT+GGG 0.606584 3_3:-10056640 Msa0441630:CDS
GCTGTTTGGACCAATTGATG+AGG 0.633670 3_3:+10056861 None:intergenic
GTATGATGTTGTGCTACATG+AGG 0.681149 3_3:+10056938 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAGTAATGTTCAAACA+TGG - chr3_3:10056855-10056874 Msa0441630:CDS 20.0%
!! TATAAGTAATGTTCAAACAT+GGG - chr3_3:10056856-10056875 Msa0441630:CDS 20.0%
! ACAAAGTGCAAAAAGTTTAA+AGG - chr3_3:10056704-10056723 Msa0441630:CDS 25.0%
!!! AAATTACTGATAGTGTTGAT+AGG - chr3_3:10056771-10056790 Msa0441630:CDS 25.0%
GAGGATTTGATGAAATTTGT+TGG + chr3_3:10056542-10056561 None:intergenic 30.0%
!!! TTGTGGATTGAGTTTTGTTT+AGG + chr3_3:10056673-10056692 None:intergenic 30.0%
AACAAAACTCAATCCACAAA+AGG - chr3_3:10056674-10056693 Msa0441630:CDS 30.0%
CTTAAACTTTGCAAGATCAA+TGG - chr3_3:10056815-10056834 Msa0441630:CDS 30.0%
TCAATGGTCAAGATTTCAAT+TGG - chr3_3:10056831-10056850 Msa0441630:CDS 30.0%
AACCTCTATTAGATCAAGAA+TGG - chr3_3:10056952-10056971 Msa0441630:CDS 30.0%
AACCATTCTTGATCTAATAG+AGG + chr3_3:10056957-10056976 None:intergenic 30.0%
CTTGCACTCATTAATCAATA+TGG - chr3_3:10057004-10057023 Msa0441630:CDS 30.0%
TAGATAGGAGAGTTAAGAGA+AGG + chr3_3:10056505-10056524 None:intergenic 35.0%
GAGTTGAAGTTGCAATAGAT+AGG + chr3_3:10056520-10056539 None:intergenic 35.0%
! GAGATTCAACACAAAGTGTT+GGG + chr3_3:10056583-10056602 None:intergenic 35.0%
AGAGATTCAACACAAAGTGT+TGG + chr3_3:10056584-10056603 None:intergenic 35.0%
GGCTAATTGATAAAGCTGTT+TGG + chr3_3:10056652-10056671 None:intergenic 35.0%
! CTTTGTAACAAAGCCTTTTG+TGG + chr3_3:10056690-10056709 None:intergenic 35.0%
TGAATAGCAGCATATTCTCT+TGG + chr3_3:10056737-10056756 None:intergenic 35.0%
GTTTAAGCTCCTTAAGTGAA+CGG + chr3_3:10056802-10056821 None:intergenic 35.0%
!! AGTACTTGTAGTGATGGATT+TGG - chr3_3:10056902-10056921 Msa0441630:CDS 35.0%
TTTGGTGGAAAAACACTTGA+TGG - chr3_3:10056920-10056939 Msa0441630:CDS 35.0%
TTGGTGGAAAAACACTTGAT+GGG - chr3_3:10056921-10056940 Msa0441630:CDS 35.0%
AAGAATGGTTAATCTTGCTC+AGG - chr3_3:10056967-10056986 Msa0441630:CDS 35.0%
GTATGATGTTGTGCTACATG+AGG + chr3_3:10056561-10056580 None:intergenic 40.0%
CTGTTTGGACCAATTGATGA+GGG + chr3_3:10056637-10056656 None:intergenic 40.0%
GATGCAAGTACTTGTAGTGA+TGG - chr3_3:10056896-10056915 Msa0441630:CDS 40.0%
!! ACTTGTAGTGATGGATTTGG+TGG - chr3_3:10056905-10056924 Msa0441630:CDS 40.0%
! CCAATTGATGAGGGTCTTGT+TGG + chr3_3:10056628-10056647 None:intergenic 45.0%
CCAACAAGACCCTCATCAAT+TGG - chr3_3:10056625-10056644 Msa0441630:CDS 45.0%
GCTGTTTGGACCAATTGATG+AGG + chr3_3:10056638-10056657 None:intergenic 45.0%
TAGGCTTAGCCGTTCACTTA+AGG - chr3_3:10056790-10056809 Msa0441630:CDS 45.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 10056479 10057039 10056479 ID=Msa0441630;Name=Msa0441630
chr3_3 mRNA 10056479 10057039 10056479 ID=Msa0441630-mRNA-1;Parent=Msa0441630;Name=Msa0441630-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|186
chr3_3 exon 10056479 10057039 10056479 ID=Msa0441630-mRNA-1:exon:2144;Parent=Msa0441630-mRNA-1
chr3_3 CDS 10056479 10057039 10056479 ID=Msa0441630-mRNA-1:cds;Parent=Msa0441630-mRNA-1
Gene Sequence

>Msa0441630

ATGGCAACAAATGTTCTTCTTTTCCTTCTCTTAACTCTCCTATCTATTGCAACTTCAACTCCAACAAATTTCATCAAATCCTCATGTAGCACAACATCATACCCAACACTTTGTGTTGAATCTCTTTCTGTCTACGCAACAACAATCCAACAAGACCCTCATCAATTGGTCCAAACAGCTTTATCAATTAGCCTAAACAAAACTCAATCCACAAAAGGCTTTGTTACAAAGTGCAAAAAGTTTAAAGGTCTTAAACCAAGAGAATATGCTGCTATTCATGATTGTGTTGAAGAAATTACTGATAGTGTTGATAGGCTTAGCCGTTCACTTAAGGAGCTTAAACTTTGCAAGATCAATGGTCAAGATTTCAATTGGCATATAAGTAATGTTCAAACATGGGTTAGCGCAGCTATGACTGATGCAAGTACTTGTAGTGATGGATTTGGTGGAAAAACACTTGATGGGAGAATGAAAACCTCTATTAGATCAAGAATGGTTAATCTTGCTCAGGTTACTAGTAATGCTCTTGCACTCATTAATCAATATGGTACTAATCACTAG
Protein sequence

>Msa0441630

MATNVLLFLLLTLLSIATSTPTNFIKSSCSTTSYPTLCVESLSVYATTIQQDPHQLVQTALSISLNKTQSTKGFVTKCKKFKGLKPREYAAIHDCVEEITDSVDRLSRSLKELKLCKINGQDFNWHISNVQTWVSAAMTDASTCSDGFGGKTLDGRMKTSIRSRMVNLAQVTSNALALINQYGTNH*