AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0347240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0347240 MtrunA17_Chr3g0079381 96.237 186 7 0 1 186 1 186 7.98e-135 374
Msa0347240 MtrunA17_Chr3g0079401 90.116 172 17 0 15 186 16 187 1.17e-117 331
Msa0347240 MtrunA17_Chr5g0398871 49.189 185 92 2 4 186 27 211 1.44e-64 197
Msa0347240 MtrunA17_Chr4g0056601 47.120 191 92 2 5 186 12 202 2.65e-58 181
Msa0347240 MtrunA17_Chr4g0018281 49.080 163 81 1 24 186 36 196 1.89e-50 161
Msa0347240 MtrunA17_Chr4g0018241 46.626 163 85 1 24 186 36 196 3.14e-45 148
Msa0347240 MtrunA17_Chr4g0018251 46.012 163 86 1 24 186 36 196 3.94e-44 145
Msa0347240 MtrunA17_Chr4g0011681 42.051 195 101 6 3 186 8 201 2.75e-43 143
Msa0347240 MtrunA17_Chr4g0011711 40.513 195 104 6 3 186 8 201 4.10e-40 135
Msa0347240 MtrunA17_Chr4g0011701 42.021 188 99 6 7 186 16 201 7.98e-40 134
Msa0347240 MtrunA17_Chr4g0011721 39.109 202 106 6 1 186 1 201 5.07e-39 132
Msa0347240 MtrunA17_Chr4g0067891 36.735 196 102 5 8 183 9 202 1.14e-35 124
Msa0347240 MtrunA17_Chr8g0391341 37.500 176 98 4 18 183 38 211 3.17e-34 120
Msa0347240 MtrunA17_Chr7g0230391 42.353 170 84 7 23 180 42 209 2.37e-33 118
Msa0347240 MtrunA17_Chr3g0079371 35.165 182 104 4 12 181 45 224 2.82e-31 113
Msa0347240 MtrunA17_Chr2g0301381 38.554 166 86 4 23 183 33 187 1.04e-29 108
Msa0347240 MtrunA17_Chr7g0269361 32.727 165 107 3 17 181 26 186 1.81e-29 107
Msa0347240 MtrunA17_Chr1g0195561 29.891 184 123 3 3 184 9 188 3.40e-29 107
Msa0347240 MtrunA17_Chr4g0070161 32.979 188 112 5 5 183 15 197 2.19e-25 97.4
Msa0347240 MtrunA17_Chr4g0018231 32.335 167 99 5 24 183 43 202 1.21e-19 82.4
Msa0347240 MtrunA17_Chr1g0147051 30.000 180 107 5 19 185 76 249 1.41e-15 73.9
Msa0347240 MtrunA17_Chr8g0345281 28.205 156 109 2 25 178 68 222 1.17e-14 71.2
Msa0347240 MtrunA17_Chr8g0345211 30.723 166 104 5 20 181 72 230 3.71e-14 69.7
Msa0347240 MtrunA17_Chr3g0126771 29.341 167 112 3 21 183 74 238 2.21e-13 67.4
Msa0347240 MtrunA17_Chr1g0192301 26.994 163 105 5 25 182 63 216 4.70e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0347240 AT5G62350.1 54.651 172 76 2 17 186 31 202 1.01e-66 203
Msa0347240 AT3G47380.1 48.969 194 87 4 5 186 9 202 9.02e-63 193
Msa0347240 AT4G25260.1 45.771 201 94 2 1 186 1 201 5.95e-59 183
Msa0347240 AT1G62770.1 48.404 188 88 4 5 183 9 196 1.91e-54 172
Msa0347240 AT4G12390.1 49.102 167 82 1 23 186 38 204 6.56e-50 160
Msa0347240 AT5G62360.1 43.293 164 90 2 23 186 42 202 1.53e-48 157
Msa0347240 AT5G20740.1 40.933 193 101 3 1 181 1 192 1.06e-41 139
Msa0347240 AT5G20740.2 45.062 162 85 2 23 181 66 226 3.17e-41 139
Msa0347240 AT1G14890.1 36.508 189 106 3 6 185 34 217 1.32e-39 134
Msa0347240 AT4G00080.1 38.693 199 100 8 2 181 3 198 2.07e-39 134
Msa0347240 AT2G01610.1 36.979 192 103 4 10 185 30 219 4.31e-37 128
Msa0347240 AT1G62760.1 43.452 168 88 3 20 184 143 306 4.50e-36 128
Msa0347240 AT4G25250.1 35.185 162 104 1 22 182 35 196 8.76e-36 124
Msa0347240 AT1G70720.1 35.567 194 110 5 1 183 5 194 4.35e-31 112
Msa0347240 AT1G70720.2 35.567 194 110 5 1 183 17 206 4.96e-31 112
Msa0347240 AT1G23205.1 34.031 191 111 4 5 181 9 198 5.30e-30 109
Msa0347240 AT5G51520.1 35.366 164 97 2 24 179 37 199 1.30e-28 105
Msa0347240 AT3G62820.1 28.421 190 122 6 3 185 10 192 1.93e-20 84.7
Msa0347240 AT3G14310.1 32.911 158 100 4 25 179 59 213 4.03e-20 87.4
Msa0347240 AT5G62340.1 29.902 204 109 8 6 186 14 206 5.03e-19 81.3
Msa0347240 AT5G53370.2 30.061 163 107 4 18 179 104 260 6.66e-18 81.3
Msa0347240 AT5G53370.1 30.061 163 107 4 18 179 68 224 8.02e-18 80.9
Msa0347240 AT1G53830.1 28.834 163 114 2 18 179 55 216 1.15e-17 80.5
Msa0347240 AT3G49220.2 31.677 161 100 4 21 180 128 279 1.77e-17 79.7
Msa0347240 AT2G47670.1 28.125 160 112 2 24 183 48 204 2.00e-17 77.0
Msa0347240 AT3G49220.1 31.875 160 99 4 21 179 83 233 2.41e-17 79.3
Msa0347240 AT3G49220.3 31.875 160 99 4 21 179 128 278 2.47e-17 79.3
Msa0347240 AT3G47670.1 29.851 201 112 8 1 181 76 267 5.62e-14 68.6
Msa0347240 AT3G14300.1 28.177 181 116 6 12 182 258 434 9.17e-13 66.2
Msa0347240 AT3G14300.1 29.070 172 104 6 20 181 454 617 2.16e-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_1:-8210586 Msa0347240:CDS
CCAATTGATGAGGGTCTTGT+TGG 0.397480 3_1:+8210965 None:intergenic
GGCTAATTGATAAAGCTGTT+TGG 0.400503 3_1:+8210941 None:intergenic
TAGGCTTAGCCGTTCACTTA+AGG 0.410233 3_1:-8210800 Msa0347240:CDS
AACAAAACTCAATCCACAAA+AGG 0.414225 3_1:-8210916 Msa0347240:CDS
GAGGATTTGATGAAATTTGT+TGG 0.419280 3_1:+8211051 None:intergenic
TCAATGGTCAAGATTTCAAT+TGG 0.421550 3_1:-8210759 Msa0347240:CDS
AACCATTCTTGATCTAATAG+AGG 0.423736 3_1:+8210636 None:intergenic
AAATTACTGATAGTGTTGAT+AGG 0.448838 3_1:-8210819 Msa0347240:CDS
CTTAAACTTTGCAAGATCAA+TGG 0.453176 3_1:-8210775 Msa0347240:CDS
CCAACAAGACCCTCATCAAT+TGG 0.458410 3_1:-8210965 Msa0347240:CDS
GAGTTGAAGTTGCAATAGAT+AGG 0.465044 3_1:+8211073 None:intergenic
TGAATAGCAGCATATTCTCT+TGG 0.472801 3_1:+8210856 None:intergenic
GAGATTCAACACAAAGTGTT+GGG 0.484787 3_1:+8211010 None:intergenic
AGTACTTGTAGTGATGGATT+TGG 0.488408 3_1:-8210688 Msa0347240:CDS
AACCTCTATTAGATCAAGAA+TGG 0.496455 3_1:-8210638 Msa0347240:CDS
AAGAATGGTTAATCTTGCTC+AGG 0.503787 3_1:-8210623 Msa0347240:CDS
AAGAAGAACATTTGTTGCCA+TGG 0.516513 3_1:+8211113 None:intergenic
AGAGATTCAACACAAAGTGT+TGG 0.533099 3_1:+8211009 None:intergenic
ACAAAACTCAATCCACAAAA+GGG 0.537573 3_1:-8210915 Msa0347240:CDS
TAGATAGGAGAGTTAAGAGA+AGG 0.542534 3_1:+8211088 None:intergenic
GTTTAAGCTCCTTAAGTGAA+CGG 0.545857 3_1:+8210791 None:intergenic
ACTTGTAGTGATGGATTTGG+TGG 0.550252 3_1:-8210685 Msa0347240:CDS
TCAATATGGTACTAATCACT+AGG 0.554200 3_1:-8210572 None:intergenic
ATATAAGTAATGTTCAAACA+TGG 0.577147 3_1:-8210735 Msa0347240:CDS
CTGTTTGGACCAATTGATGA+GGG 0.590554 3_1:+8210956 None:intergenic
GATGCAAGTACTTGTAGTGA+TGG 0.592136 3_1:-8210694 Msa0347240:CDS
CAATATGGTACTAATCACTA+GGG 0.596788 3_1:-8210571 None:intergenic
TATAAGTAATGTTCAAACAT+GGG 0.606584 3_1:-8210734 Msa0347240:CDS
GCTGTTTGGACCAATTGATG+AGG 0.633670 3_1:+8210955 None:intergenic
GTATGATGTTGTGCTACATG+AGG 0.681149 3_1:+8211032 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAGTAATGTTCAAACA+TGG - chr3_1:8210949-8210968 Msa0347240:CDS 20.0%
!! TATAAGTAATGTTCAAACAT+GGG - chr3_1:8210950-8210969 Msa0347240:CDS 20.0%
! ACAATGTGCAAAAAGTTTAA+AGG - chr3_1:8210798-8210817 Msa0347240:CDS 25.0%
!!! AAATTACTGATAGTGTTGAT+AGG - chr3_1:8210865-8210884 Msa0347240:CDS 25.0%
GAGGATTTGATGAAATTTGT+TGG + chr3_1:8210636-8210655 None:intergenic 30.0%
!!! TTGTGGATTGAGTTTTGTTT+AGG + chr3_1:8210767-8210786 None:intergenic 30.0%
AACAAAACTCAATCCACAAA+AGG - chr3_1:8210768-8210787 Msa0347240:CDS 30.0%
ACAAAACTCAATCCACAAAA+GGG - chr3_1:8210769-8210788 Msa0347240:CDS 30.0%
CTTAAACTTTGCAAGATCAA+TGG - chr3_1:8210909-8210928 Msa0347240:CDS 30.0%
TCAATGGTCAAGATTTCAAT+TGG - chr3_1:8210925-8210944 Msa0347240:CDS 30.0%
AACCTCTATTAGATCAAGAA+TGG - chr3_1:8211046-8211065 Msa0347240:CDS 30.0%
AACCATTCTTGATCTAATAG+AGG + chr3_1:8211051-8211070 None:intergenic 30.0%
CTTGCACTCATTAATCAATA+TGG - chr3_1:8211098-8211117 Msa0347240:CDS 30.0%
TAGATAGGAGAGTTAAGAGA+AGG + chr3_1:8210599-8210618 None:intergenic 35.0%
GAGTTGAAGTTGCAATAGAT+AGG + chr3_1:8210614-8210633 None:intergenic 35.0%
! GAGATTCAACACAAAGTGTT+GGG + chr3_1:8210677-8210696 None:intergenic 35.0%
AGAGATTCAACACAAAGTGT+TGG + chr3_1:8210678-8210697 None:intergenic 35.0%
GGCTAATTGATAAAGCTGTT+TGG + chr3_1:8210746-8210765 None:intergenic 35.0%
! CATTGTAACAAACCCTTTTG+TGG + chr3_1:8210784-8210803 None:intergenic 35.0%
TGAATAGCAGCATATTCTCT+TGG + chr3_1:8210831-8210850 None:intergenic 35.0%
GTTTAAGCTCCTTAAGTGAA+CGG + chr3_1:8210896-8210915 None:intergenic 35.0%
!! AGTACTTGTAGTGATGGATT+TGG - chr3_1:8210996-8211015 Msa0347240:CDS 35.0%
TTTGGTGGAAAAACACTTGA+TGG - chr3_1:8211014-8211033 Msa0347240:CDS 35.0%
TTGGTGGAAAAACACTTGAT+GGG - chr3_1:8211015-8211034 Msa0347240:CDS 35.0%
AAGAATGGTTAATCTTGCTC+AGG - chr3_1:8211061-8211080 Msa0347240:CDS 35.0%
GTATGATGTTGTGCTACATG+AGG + chr3_1:8210655-8210674 None:intergenic 40.0%
CTGTTTGGACCAATTGATGA+GGG + chr3_1:8210731-8210750 None:intergenic 40.0%
GATGCAAGTACTTGTAGTGA+TGG - chr3_1:8210990-8211009 Msa0347240:CDS 40.0%
!! ACTTGTAGTGATGGATTTGG+TGG - chr3_1:8210999-8211018 Msa0347240:CDS 40.0%
! CCAATTGATGAGGGTCTTGT+TGG + chr3_1:8210722-8210741 None:intergenic 45.0%
CCAACAAGACCCTCATCAAT+TGG - chr3_1:8210719-8210738 Msa0347240:CDS 45.0%
GCTGTTTGGACCAATTGATG+AGG + chr3_1:8210732-8210751 None:intergenic 45.0%
TAGGCTTAGCCGTTCACTTA+AGG - chr3_1:8210884-8210903 Msa0347240:CDS 45.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 8210573 8211133 8210573 ID=Msa0347240;Name=Msa0347240
chr3_1 mRNA 8210573 8211133 8210573 ID=Msa0347240-mRNA-1;Parent=Msa0347240;Name=Msa0347240-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|186
chr3_1 exon 8210573 8211133 8210573 ID=Msa0347240-mRNA-1:exon:2361;Parent=Msa0347240-mRNA-1
chr3_1 CDS 8210573 8211133 8210573 ID=Msa0347240-mRNA-1:cds;Parent=Msa0347240-mRNA-1
Gene Sequence

>Msa0347240

ATGGCAACAAATGTTCTTCTTTTCCTTCTCTTAACTCTCCTATCTATTGCAACTTCAACTCCAACAAATTTCATCAAATCCTCATGTAGCACAACATCATACCCAACACTTTGTGTTGAATCTCTTTCTGTCTATGCAACAACAATCCAACAAGACCCTCATCAATTGGTCCAAACAGCTTTATCAATTAGCCTAAACAAAACTCAATCCACAAAAGGGTTTGTTACAATGTGCAAAAAGTTTAAAGGTCTTAAACCAAGAGAATATGCTGCTATTCATGATTGTGTTGAAGAAATTACTGATAGTGTTGATAGGCTTAGCCGTTCACTTAAGGAGCTTAAACTTTGCAAGATCAATGGTCAAGATTTCAATTGGCATATAAGTAATGTTCAAACATGGGTTAGCGCAGCTATGACTGATGCAAGTACTTGTAGTGATGGATTTGGTGGAAAAACACTTGATGGGAGAATGAAAACCTCTATTAGATCAAGAATGGTTAATCTTGCTCAGGTTACTAGTAATGCTCTTGCACTCATTAATCAATATGGTACTAATCACTAG
Protein sequence

>Msa0347240

MATNVLLFLLLTLLSIATSTPTNFIKSSCSTTSYPTLCVESLSVYATTIQQDPHQLVQTALSISLNKTQSTKGFVTMCKKFKGLKPREYAAIHDCVEEITDSVDRLSRSLKELKLCKINGQDFNWHISNVQTWVSAAMTDASTCSDGFGGKTLDGRMKTSIRSRMVNLAQVTSNALALINQYGTNH*