AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0489310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0489310 MtrunA17_Chr3g0079381 95.699 186 8 0 1 186 1 186 1.51e-126 353
Msa0489310 MtrunA17_Chr3g0079401 89.535 172 18 0 15 186 16 187 2.76e-117 330
Msa0489310 MtrunA17_Chr5g0398871 49.189 185 92 2 4 186 27 211 1.32e-64 197
Msa0489310 MtrunA17_Chr4g0056601 47.120 191 92 2 5 186 12 202 2.41e-58 181
Msa0489310 MtrunA17_Chr4g0018281 49.693 163 80 1 24 186 36 196 5.41e-51 162
Msa0489310 MtrunA17_Chr4g0018241 47.239 163 84 1 24 186 36 196 8.92e-46 149
Msa0489310 MtrunA17_Chr4g0018251 46.626 163 85 1 24 186 36 196 1.32e-44 146
Msa0489310 MtrunA17_Chr4g0011681 42.051 195 101 6 3 186 8 201 1.62e-43 144
Msa0489310 MtrunA17_Chr4g0011711 40.513 195 104 6 3 186 8 201 2.12e-40 136
Msa0489310 MtrunA17_Chr4g0011701 42.021 188 99 6 7 186 16 201 4.80e-40 135
Msa0489310 MtrunA17_Chr4g0011721 39.109 202 106 6 1 186 1 201 2.86e-39 133
Msa0489310 MtrunA17_Chr4g0067891 36.735 196 102 5 8 183 9 202 7.06e-36 124
Msa0489310 MtrunA17_Chr8g0391341 37.500 176 98 4 18 183 38 211 1.71e-34 121
Msa0489310 MtrunA17_Chr7g0230391 42.353 170 84 7 23 180 42 209 2.55e-33 118
Msa0489310 MtrunA17_Chr3g0079371 35.714 182 103 4 12 181 45 224 7.62e-32 114
Msa0489310 MtrunA17_Chr2g0301381 38.554 166 86 4 23 183 33 187 9.42e-30 108
Msa0489310 MtrunA17_Chr7g0269361 32.727 165 107 3 17 181 26 186 2.77e-29 107
Msa0489310 MtrunA17_Chr1g0195561 29.891 184 123 3 3 184 9 188 4.17e-29 106
Msa0489310 MtrunA17_Chr4g0070161 32.979 188 112 5 5 183 15 197 2.73e-25 97.1
Msa0489310 MtrunA17_Chr4g0018231 32.934 167 98 5 24 183 43 202 4.05e-20 83.6
Msa0489310 MtrunA17_Chr1g0147051 30.000 180 107 5 19 185 76 249 1.40e-15 73.9
Msa0489310 MtrunA17_Chr8g0345281 28.205 156 109 2 25 178 68 222 8.07e-15 71.6
Msa0489310 MtrunA17_Chr8g0345211 30.723 166 104 5 20 181 72 230 4.20e-14 69.7
Msa0489310 MtrunA17_Chr3g0126771 29.341 167 112 3 21 183 74 238 2.32e-13 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0489310 AT5G62350.1 55.233 172 75 2 17 186 31 202 3.12e-67 204
Msa0489310 AT3G47380.1 49.485 194 86 4 5 186 9 202 3.00e-63 194
Msa0489310 AT4G25260.1 45.274 201 95 2 1 186 1 201 1.35e-58 182
Msa0489310 AT1G62770.1 48.404 188 88 4 5 183 9 196 2.77e-54 171
Msa0489310 AT4G12390.1 49.102 167 82 1 23 186 38 204 7.39e-50 160
Msa0489310 AT5G62360.1 43.902 164 89 2 23 186 42 202 4.02e-49 158
Msa0489310 AT5G20740.1 40.415 193 102 3 1 181 1 192 2.63e-41 138
Msa0489310 AT5G20740.2 44.444 162 86 2 23 181 66 226 7.36e-41 138
Msa0489310 AT1G14890.1 36.508 189 106 3 6 185 34 217 9.13e-40 135
Msa0489310 AT4G00080.1 38.693 199 100 8 2 181 3 198 1.11e-39 134
Msa0489310 AT2G01610.1 36.979 192 103 4 10 185 30 219 2.74e-37 129
Msa0489310 AT1G62760.1 43.452 168 88 3 20 184 143 306 2.85e-36 128
Msa0489310 AT4G25250.1 35.802 162 103 1 22 182 35 196 3.24e-36 125
Msa0489310 AT1G70720.1 35.567 194 110 5 1 183 5 194 2.51e-31 112
Msa0489310 AT1G70720.2 35.567 194 110 5 1 183 17 206 2.60e-31 113
Msa0489310 AT1G23205.1 34.031 191 111 4 5 181 9 198 3.60e-30 110
Msa0489310 AT5G51520.1 35.976 164 96 2 24 179 37 199 4.10e-29 107
Msa0489310 AT3G62820.1 28.421 190 122 6 3 185 10 192 2.08e-20 84.3
Msa0489310 AT3G14310.1 32.911 158 100 4 25 179 59 213 4.75e-20 87.4
Msa0489310 AT5G62340.1 30.392 204 108 8 6 186 14 206 1.47e-19 82.4
Msa0489310 AT5G53370.2 30.061 163 107 4 18 179 104 260 4.04e-18 81.6
Msa0489310 AT5G53370.1 30.061 163 107 4 18 179 68 224 5.52e-18 81.3
Msa0489310 AT1G53830.1 28.834 163 114 2 18 179 55 216 7.15e-18 80.9
Msa0489310 AT3G49220.2 31.677 161 100 4 21 180 128 279 1.80e-17 79.7
Msa0489310 AT3G49220.3 31.875 160 99 4 21 179 128 278 2.25e-17 79.7
Msa0489310 AT3G49220.1 31.875 160 99 4 21 179 83 233 2.32e-17 79.3
Msa0489310 AT2G47670.1 28.125 160 112 2 24 183 48 204 2.73e-17 76.6
Msa0489310 AT3G47670.1 29.851 201 112 8 1 181 76 267 5.85e-14 68.6
Msa0489310 AT3G14300.1 28.177 181 116 6 12 182 258 434 9.62e-13 66.2
Msa0489310 AT3G14300.1 29.070 172 104 6 20 181 454 617 2.52e-12 65.1

Find 31 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGCACTCATTAATCAATA+TGG 0.347778 3_4:+9570844 Msa0489310:CDS
CCAATTGATGAGGGTCTTGT+TGG 0.397480 3_4:-9570465 None:intergenic
GGCTAATTGATAAAGCTGTT+TGG 0.400503 3_4:-9570489 None:intergenic
TAGGCTTAGCCGTTCACTTA+AGG 0.410233 3_4:+9570630 Msa0489310:CDS
AACAAAACTCAATCCACAAA+AGG 0.414225 3_4:+9570514 Msa0489310:CDS
TCAATGGTCAAGATTTCAAT+TGG 0.421550 3_4:+9570671 Msa0489310:CDS
AACCATTCTTGATCTAATAG+AGG 0.423736 3_4:-9570794 None:intergenic
AAATTACTGATAGTGTTGAT+AGG 0.448838 3_4:+9570611 Msa0489310:CDS
CTTAAACTTTGCAAGATCAA+TGG 0.453176 3_4:+9570655 Msa0489310:CDS
CCAACAAGACCCTCATCAAT+TGG 0.458410 3_4:+9570465 Msa0489310:CDS
GAGGATTTGATGAAATTTGT+TGG 0.467582 3_4:-9570379 None:intergenic
TGAATAGCAGCATATTCTCT+TGG 0.472801 3_4:-9570574 None:intergenic
AGTACTTGTAGTGATGGATT+TGG 0.488408 3_4:+9570742 Msa0489310:CDS
GTGTTGAAGTTGCAATAGAT+AGG 0.495548 3_4:-9570357 None:intergenic
AACCTCTATTAGATCAAGAA+TGG 0.496455 3_4:+9570792 Msa0489310:CDS
GAGATTCAACACAAAGTGTT+GGG 0.500666 3_4:-9570420 None:intergenic
AAGAATGGTTAATCTTGCTC+AGG 0.503787 3_4:+9570807 Msa0489310:CDS
AAGAAGAACATTTGTTGCCA+TGG 0.516513 3_4:-9570317 None:intergenic
ACAAAACTCAATCCACAAAA+GGG 0.537573 3_4:+9570515 Msa0489310:CDS
TAGATAGGAGAGTTAAGAGA+AGG 0.542534 3_4:-9570342 None:intergenic
GTTTAAGCTCCTTAAGTGAA+CGG 0.545857 3_4:-9570639 None:intergenic
AGAGATTCAACACAAAGTGT+TGG 0.548978 3_4:-9570421 None:intergenic
ACTTGTAGTGATGGATTTGG+TGG 0.550252 3_4:+9570745 Msa0489310:CDS
TCAATATGGTACTAATCACT+AGG 0.550549 3_4:+9570858 Msa0489310:CDS
CAATATGGTACTAATCACTA+GGG 0.573803 3_4:+9570859 Msa0489310:CDS
ATATAAGTAATGTTCAAACA+TGG 0.577147 3_4:+9570695 Msa0489310:CDS
CTGTTTGGACCAATTGATGA+GGG 0.590554 3_4:-9570474 None:intergenic
GATGCAAGTACTTGTAGTGA+TGG 0.592136 3_4:+9570736 Msa0489310:CDS
TATAAGTAATGTTCAAACAT+GGG 0.606584 3_4:+9570696 Msa0489310:CDS
GTATGTTGTTGTGCTACATG+AGG 0.618809 3_4:-9570398 None:intergenic
GCTGTTTGGACCAATTGATG+AGG 0.633670 3_4:-9570475 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAGTAATGTTCAAACA+TGG + chr3_4:9570695-9570714 Msa0489310:CDS 20.0%
!! TATAAGTAATGTTCAAACAT+GGG + chr3_4:9570696-9570715 Msa0489310:CDS 20.0%
! ACAATGTGCAAAAAGTTTAA+AGG + chr3_4:9570544-9570563 Msa0489310:CDS 25.0%
!!! AAATTACTGATAGTGTTGAT+AGG + chr3_4:9570611-9570630 Msa0489310:CDS 25.0%
GAGGATTTGATGAAATTTGT+TGG - chr3_4:9570382-9570401 None:intergenic 30.0%
!!! TTGTGGATTGAGTTTTGTTT+AGG - chr3_4:9570513-9570532 None:intergenic 30.0%
AACAAAACTCAATCCACAAA+AGG + chr3_4:9570514-9570533 Msa0489310:CDS 30.0%
ACAAAACTCAATCCACAAAA+GGG + chr3_4:9570515-9570534 Msa0489310:CDS 30.0%
CTTAAACTTTGCAAGATCAA+TGG + chr3_4:9570655-9570674 Msa0489310:CDS 30.0%
TCAATGGTCAAGATTTCAAT+TGG + chr3_4:9570671-9570690 Msa0489310:CDS 30.0%
AACCTCTATTAGATCAAGAA+TGG + chr3_4:9570792-9570811 Msa0489310:CDS 30.0%
AACCATTCTTGATCTAATAG+AGG - chr3_4:9570797-9570816 None:intergenic 30.0%
CTTGCACTCATTAATCAATA+TGG + chr3_4:9570844-9570863 Msa0489310:CDS 30.0%
TAGATAGGAGAGTTAAGAGA+AGG - chr3_4:9570345-9570364 None:intergenic 35.0%
GTGTTGAAGTTGCAATAGAT+AGG - chr3_4:9570360-9570379 None:intergenic 35.0%
! GAGATTCAACACAAAGTGTT+GGG - chr3_4:9570423-9570442 None:intergenic 35.0%
AGAGATTCAACACAAAGTGT+TGG - chr3_4:9570424-9570443 None:intergenic 35.0%
GGCTAATTGATAAAGCTGTT+TGG - chr3_4:9570492-9570511 None:intergenic 35.0%
! CATTGTAACAAACCCTTTTG+TGG - chr3_4:9570530-9570549 None:intergenic 35.0%
TGAATAGCAGCATATTCTCT+TGG - chr3_4:9570577-9570596 None:intergenic 35.0%
GTTTAAGCTCCTTAAGTGAA+CGG - chr3_4:9570642-9570661 None:intergenic 35.0%
!! AGTACTTGTAGTGATGGATT+TGG + chr3_4:9570742-9570761 Msa0489310:CDS 35.0%
TTTGGTGGAAAAACACTTGA+TGG + chr3_4:9570760-9570779 Msa0489310:CDS 35.0%
TTGGTGGAAAAACACTTGAT+GGG + chr3_4:9570761-9570780 Msa0489310:CDS 35.0%
AAGAATGGTTAATCTTGCTC+AGG + chr3_4:9570807-9570826 Msa0489310:CDS 35.0%
GTATGTTGTTGTGCTACATG+AGG - chr3_4:9570401-9570420 None:intergenic 40.0%
CTGTTTGGACCAATTGATGA+GGG - chr3_4:9570477-9570496 None:intergenic 40.0%
GATGCAAGTACTTGTAGTGA+TGG + chr3_4:9570736-9570755 Msa0489310:CDS 40.0%
!! ACTTGTAGTGATGGATTTGG+TGG + chr3_4:9570745-9570764 Msa0489310:CDS 40.0%
! CCAATTGATGAGGGTCTTGT+TGG - chr3_4:9570468-9570487 None:intergenic 45.0%
CCAACAAGACCCTCATCAAT+TGG + chr3_4:9570465-9570484 Msa0489310:CDS 45.0%
GCTGTTTGGACCAATTGATG+AGG - chr3_4:9570478-9570497 None:intergenic 45.0%
TAGGCTTAGCCGTTCACTTA+AGG + chr3_4:9570630-9570649 Msa0489310:CDS 45.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 9570319 9570879 9570319 ID=Msa0489310;Name=Msa0489310
chr3_4 mRNA 9570319 9570879 9570319 ID=Msa0489310-mRNA-1;Parent=Msa0489310;Name=Msa0489310-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|186
chr3_4 exon 9570319 9570879 9570319 ID=Msa0489310-mRNA-1:exon:3116;Parent=Msa0489310-mRNA-1
chr3_4 CDS 9570319 9570879 9570319 ID=Msa0489310-mRNA-1:cds;Parent=Msa0489310-mRNA-1
Gene Sequence

>Msa0489310

ATGGCAACAAATGTTCTTCTTTTCCTTCTCTTAACTCTCCTATCTATTGCAACTTCAACACCAACAAATTTCATCAAATCCTCATGTAGCACAACAACATACCCAACACTTTGTGTTGAATCTCTCTCTGTCTATGCAACAACAATCCAACAAGACCCTCATCAATTGGTCCAAACAGCTTTATCAATTAGCCTAAACAAAACTCAATCCACAAAAGGGTTTGTTACAATGTGCAAAAAGTTTAAAGGTCTTAAACCAAGAGAATATGCTGCTATTCATGATTGTGTTGAAGAAATTACTGATAGTGTTGATAGGCTTAGCCGTTCACTTAAGGAGCTTAAACTTTGCAAGATCAATGGTCAAGATTTCAATTGGCATATAAGTAATGTTCAAACATGGGTTAGCGCAGCTATGACTGATGCAAGTACTTGTAGTGATGGATTTGGTGGAAAAACACTTGATGGGAGAATGAAAACCTCTATTAGATCAAGAATGGTTAATCTTGCTCAGGTTACTAGTAATGCTCTTGCACTCATTAATCAATATGGTACTAATCACTAG
Protein sequence

>Msa0489310

MATNVLLFLLLTLLSIATSTPTNFIKSSCSTTTYPTLCVESLSVYATTIQQDPHQLVQTALSISLNKTQSTKGFVTMCKKFKGLKPREYAAIHDCVEEITDSVDRLSRSLKELKLCKINGQDFNWHISNVQTWVSAAMTDASTCSDGFGGKTLDGRMKTSIRSRMVNLAQVTSNALALINQYGTNH*