AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0492560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0492560 MtrunA17_Chr3g0085311 97.354 189 5 0 1 189 1 189 9.07e-136 377
Msa0492560 MtrunA17_Chr3g0085291 92.063 189 13 1 1 189 1 187 4.19e-128 357
Msa0492560 MtrunA17_Chr3g0085301 64.550 189 67 0 1 189 6 194 2.71e-88 257
Msa0492560 MtrunA17_Chr3g0085321 64.021 189 68 0 1 189 1 189 1.08e-87 255
Msa0492560 MtrunA17_Chr3g0090231 59.459 185 70 1 4 188 5 184 1.79e-78 232
Msa0492560 MtrunA17_Chr4g0040551 59.669 181 68 1 8 188 9 184 2.99e-78 231
Msa0492560 MtrunA17_Chr1g0177051 48.370 184 88 5 10 188 4 185 1.22e-53 169
Msa0492560 MtrunA17_Chr4g0005081 50.955 157 73 2 34 188 42 196 2.57e-48 155
Msa0492560 MtrunA17_Chr4g0005071 49.045 157 76 2 34 188 41 195 2.22e-46 150
Msa0492560 MtrunA17_Chr4g0005041 48.408 157 77 2 34 188 43 197 2.28e-45 148
Msa0492560 MtrunA17_Chr1g0175911 49.324 148 71 3 43 188 46 191 4.91e-45 147
Msa0492560 MtrunA17_Chr4g0005031 46.497 157 80 2 34 188 66 220 2.76e-43 144
Msa0492560 MtrunA17_Chr7g0243501 43.548 186 99 3 7 188 8 191 1.30e-41 139
Msa0492560 MtrunA17_Chr7g0259091 48.993 149 73 2 43 188 45 193 2.46e-41 138
Msa0492560 MtrunA17_Chr7g0259071 48.000 150 73 4 43 188 42 190 3.81e-41 137
Msa0492560 MtrunA17_Chr4g0037481 41.830 153 84 2 39 188 41 191 2.55e-40 135
Msa0492560 MtrunA17_Chr7g0259101 48.993 149 73 2 43 188 45 193 2.36e-38 135
Msa0492560 MtrunA17_Chr7g0259101 46.309 149 77 2 43 188 244 392 1.15e-36 131
Msa0492560 MtrunA17_Chr4g0005011 45.890 146 75 3 43 186 51 194 1.08e-37 129
Msa0492560 MtrunA17_Chr4g0005111 38.776 147 89 1 43 188 43 189 3.46e-36 124
Msa0492560 MtrunA17_Chr4g0005131 40.884 181 98 3 11 188 16 190 5.54e-36 124
Msa0492560 MtrunA17_Chr5g0446751 38.220 191 99 5 7 188 8 188 6.80e-34 119
Msa0492560 MtrunA17_Chr7g0259121 44.444 153 78 2 43 188 40 192 6.83e-33 117
Msa0492560 MtrunA17_Chr3g0136631 40.397 151 85 2 43 188 38 188 2.08e-31 112
Msa0492560 MtrunA17_Chr3g0136641 40.000 150 86 3 43 188 38 187 3.14e-30 109
Msa0492560 MtrunA17_Chr4g0024961 31.169 154 104 1 38 189 25 178 1.89e-20 84.0
Msa0492560 MtrunA17_Chr4g0024951 32.919 161 101 2 31 189 23 178 3.46e-20 83.2
Msa0492560 MtrunA17_Chr4g0068381 33.793 145 94 1 46 188 35 179 5.24e-20 82.8
Msa0492560 MtrunA17_Chr4g0005091 32.903 155 88 2 36 188 34 174 1.40e-19 81.6
Msa0492560 MtrunA17_Chr4g0068391 31.765 170 94 4 3 168 8 159 1.48e-19 81.6
Msa0492560 MtrunA17_Chr1g0169281 38.298 94 57 1 76 169 141 233 6.19e-13 65.1
Msa0492560 MtrunA17_Chr1g0169511 39.362 94 56 1 76 169 135 227 1.11e-12 64.3
Msa0492560 MtrunA17_Chr1g0169291 39.362 94 56 1 76 169 135 227 1.48e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0492560 AT1G65870.1 49.689 161 79 2 30 188 29 189 1.73e-48 156
Msa0492560 AT5G42500.1 45.399 163 85 3 28 188 25 185 2.42e-44 145
Msa0492560 AT1G22900.1 46.452 155 79 3 36 188 41 193 2.25e-42 141
Msa0492560 AT2G21100.1 43.243 148 82 1 43 188 40 187 2.61e-42 140
Msa0492560 AT2G21100.2 43.243 148 82 1 43 188 40 187 2.61e-42 140
Msa0492560 AT5G42510.1 44.516 155 82 2 36 188 30 182 5.67e-41 137
Msa0492560 AT3G13650.1 43.151 146 82 1 43 188 41 185 2.24e-40 135
Msa0492560 AT1G55210.1 44.966 149 81 1 40 188 39 186 2.04e-39 133
Msa0492560 AT1G55210.2 44.966 149 81 1 40 188 39 186 2.04e-39 133
Msa0492560 AT5G49040.1 44.295 149 79 3 43 188 43 190 1.97e-38 130
Msa0492560 AT1G58170.1 38.421 190 109 3 1 188 1 184 3.47e-38 130
Msa0492560 AT5G49030.3 47.656 128 65 1 43 168 43 170 2.57e-34 128
Msa0492560 AT3G13662.1 46.825 126 66 1 43 168 40 164 2.63e-34 119
Msa0492560 AT4G38700.1 41.772 158 84 3 39 188 32 189 2.94e-32 115
Msa0492560 AT3G58090.1 51.402 107 52 0 82 188 165 271 2.17e-31 115
Msa0492560 AT2G21110.1 34.536 194 112 4 1 188 1 185 4.24e-29 107
Msa0492560 AT3G13660.1 41.525 118 69 0 71 188 7 124 1.03e-27 101
Msa0492560 AT4G11210.1 29.032 186 125 4 1 186 1 179 2.52e-18 79.0
Msa0492560 AT4G23690.1 31.293 147 93 4 45 186 40 183 6.49e-13 64.7
Msa0492560 AT4G11190.1 29.286 140 97 2 47 186 42 179 3.27e-11 59.7

Find 41 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTACTGCTAAGAGTCTT+TGG 0.272946 3_4:+16362095 Msa0492560:CDS
ACTAATTCACCAAGTGGATT+TGG 0.298818 3_4:+16361818 Msa0492560:CDS
TCAGTGCTTTGTTTATTTGT+TGG 0.319384 3_4:-16361713 None:intergenic
TTCAAATGGCTACCTCTCTT+AGG 0.324065 3_4:+16361603 None:intergenic
TCGGCGGCACCGGCGTGTTT+AGG 0.331194 3_4:+16362059 Msa0492560:CDS
GGCCCAAGGGATGTTTGGTT+TGG 0.342447 3_4:+16361907 Msa0492560:CDS
CTGCCTATTGTCGGCGGCAC+CGG 0.359439 3_4:+16362049 Msa0492560:CDS
GGTAGGGCCCAAGGGATGTT+TGG 0.361631 3_4:+16361902 Msa0492560:CDS
CCACTTGGTGAATTAGTTGA+TGG 0.386177 3_4:-16361812 None:intergenic
TAACATTATGTTGGATTGTT+CGG 0.388038 3_4:-16361690 None:intergenic
ACGCCGGTGCCGCCGACAAT+AGG 0.397084 3_4:-16362052 None:intergenic
ATCCCTTGGGCCCTACCAAC+AGG 0.403996 3_4:-16361896 None:intergenic
TCTCTAACCGTGTCTTGAAC+AGG 0.414606 3_4:-16362025 None:intergenic
TGCTACTGCTAAGAGTCTTT+GGG 0.419480 3_4:+16362096 Msa0492560:CDS
GTTCTTGTTCTTCAGTTAAG+AGG 0.422148 3_4:-16361862 None:intergenic
ATTTGTTGGTAACATTATGT+TGG 0.456073 3_4:-16361699 None:intergenic
ATTAATCTTGCTTTCACTGA+AGG 0.457487 3_4:+16361962 Msa0492560:CDS
GGTAGTACTCTTAGTATGCT+TGG 0.469670 3_4:+16361995 Msa0492560:CDS
TCTATAATTTGTACAACCGT+TGG 0.476718 3_4:-16361788 None:intergenic
ATGCCAAACCAAACATCCCT+TGG 0.482816 3_4:-16361910 None:intergenic
ATTTGGAACAACATTCATGA+TGG 0.515290 3_4:+16361835 Msa0492560:CDS
AAACCTGTTGGTAGGGCCCA+AGG 0.521091 3_4:+16361893 Msa0492560:CDS
TAACATCAAAACCTGTTGGT+AGG 0.522247 3_4:+16361885 Msa0492560:CDS
CTTTACCTTCTAAGATGTCA+TGG 0.530269 3_4:-16361763 None:intergenic
TGCCAAACCAAACATCCCTT+GGG 0.530603 3_4:-16361909 None:intergenic
AACATCAAAACCTGTTGGTA+GGG 0.532522 3_4:+16361886 Msa0492560:CDS
GTACTCTTAGTATGCTTGGA+AGG 0.545035 3_4:+16361999 Msa0492560:CDS
GTTAGAGAACTGCCTATTGT+CGG 0.546616 3_4:+16362040 Msa0492560:CDS
GAACTAACATCAAAACCTGT+TGG 0.553309 3_4:+16361881 Msa0492560:CDS
AACCTGTTGGTAGGGCCCAA+GGG 0.564840 3_4:+16361894 Msa0492560:CDS
TTGGCATCTTTGCATGATCG+TGG 0.594187 3_4:+16361926 Msa0492560:CDS
ATCTTTGCATGATCGTGGAA+TGG 0.599273 3_4:+16361931 Msa0492560:CDS
TTGTTCGGAGAACAAACCAT+TGG 0.604047 3_4:-16361675 None:intergenic
CTTAGAAGGTAAAGATCCAA+CGG 0.624749 3_4:+16361772 Msa0492560:CDS
CCATCAACTAATTCACCAAG+TGG 0.625731 3_4:+16361812 Msa0492560:CDS
GAGAAAGAAGAACCTAAGAG+AGG 0.627560 3_4:-16361615 None:intergenic
GGCGTGTTTAGGTTTGCTAG+AGG 0.642316 3_4:+16362070 Msa0492560:CDS
AAGGAATCCTGTTCAAGACA+CGG 0.674439 3_4:+16362018 Msa0492560:CDS
AATGTTGTTCCAAATCCACT+TGG 0.683285 3_4:-16361827 None:intergenic
AGAGAACTGCCTATTGTCGG+CGG 0.685485 3_4:+16362043 Msa0492560:CDS
TCTAGCAAACCTAAACACGC+CGG 0.719035 3_4:-16362068 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAACATTATGTTGGATTGTT+CGG - chr3_4:16361693-16361712 None:intergenic 25.0%
!!! ATTTGTTGGTAACATTATGT+TGG - chr3_4:16361702-16361721 None:intergenic 25.0%
!! TCAGTGCTTTGTTTATTTGT+TGG - chr3_4:16361716-16361735 None:intergenic 30.0%
! ATGGTAAAAAAAGTGCAAGT+GGG - chr3_4:16361747-16361766 None:intergenic 30.0%
! TTTTACCATGACATCTTAGA+AGG + chr3_4:16361758-16361777 Msa0492560:CDS 30.0%
! TCTATAATTTGTACAACCGT+TGG - chr3_4:16361791-16361810 None:intergenic 30.0%
! ATTTGGAACAACATTCATGA+TGG + chr3_4:16361835-16361854 Msa0492560:CDS 30.0%
ATTAATCTTGCTTTCACTGA+AGG + chr3_4:16361962-16361981 Msa0492560:CDS 30.0%
! GCTCAATTTTTCACTACCAA+TGG + chr3_4:16361659-16361678 Msa0492560:CDS 35.0%
! CATGGTAAAAAAAGTGCAAG+TGG - chr3_4:16361748-16361767 None:intergenic 35.0%
!! CTTTACCTTCTAAGATGTCA+TGG - chr3_4:16361766-16361785 None:intergenic 35.0%
CTTAGAAGGTAAAGATCCAA+CGG + chr3_4:16361772-16361791 Msa0492560:CDS 35.0%
! ACTAATTCACCAAGTGGATT+TGG + chr3_4:16361818-16361837 Msa0492560:CDS 35.0%
AATGTTGTTCCAAATCCACT+TGG - chr3_4:16361830-16361849 None:intergenic 35.0%
GTTCTTGTTCTTCAGTTAAG+AGG - chr3_4:16361865-16361884 None:intergenic 35.0%
GAACTAACATCAAAACCTGT+TGG + chr3_4:16361881-16361900 Msa0492560:CDS 35.0%
TAACATCAAAACCTGTTGGT+AGG + chr3_4:16361885-16361904 Msa0492560:CDS 35.0%
AACATCAAAACCTGTTGGTA+GGG + chr3_4:16361886-16361905 Msa0492560:CDS 35.0%
GAGAAAGAAGAACCTAAGAG+AGG - chr3_4:16361618-16361637 None:intergenic 40.0%
TTGTTCGGAGAACAAACCAT+TGG - chr3_4:16361678-16361697 None:intergenic 40.0%
! CCACTTGGTGAATTAGTTGA+TGG - chr3_4:16361815-16361834 None:intergenic 40.0%
CCATCAACTAATTCACCAAG+TGG + chr3_4:16361812-16361831 Msa0492560:CDS 40.0%
ATCTTTGCATGATCGTGGAA+TGG + chr3_4:16361931-16361950 Msa0492560:CDS 40.0%
! TTCACTGAAGGTGATTTTGC+TGG + chr3_4:16361974-16361993 Msa0492560:CDS 40.0%
GGTAGTACTCTTAGTATGCT+TGG + chr3_4:16361995-16362014 Msa0492560:CDS 40.0%
GTACTCTTAGTATGCTTGGA+AGG + chr3_4:16361999-16362018 Msa0492560:CDS 40.0%
AAGGAATCCTGTTCAAGACA+CGG + chr3_4:16362018-16362037 Msa0492560:CDS 40.0%
GTTAGAGAACTGCCTATTGT+CGG + chr3_4:16362040-16362059 Msa0492560:CDS 40.0%
ATGCTACTGCTAAGAGTCTT+TGG + chr3_4:16362095-16362114 Msa0492560:CDS 40.0%
TGCTACTGCTAAGAGTCTTT+GGG + chr3_4:16362096-16362115 Msa0492560:CDS 40.0%
TGCCAAACCAAACATCCCTT+GGG - chr3_4:16361912-16361931 None:intergenic 45.0%
ATGCCAAACCAAACATCCCT+TGG - chr3_4:16361913-16361932 None:intergenic 45.0%
TTGGCATCTTTGCATGATCG+TGG + chr3_4:16361926-16361945 Msa0492560:CDS 45.0%
TCTCTAACCGTGTCTTGAAC+AGG - chr3_4:16362028-16362047 None:intergenic 45.0%
TCTAGCAAACCTAAACACGC+CGG - chr3_4:16362071-16362090 None:intergenic 45.0%
AGAGAACTGCCTATTGTCGG+CGG + chr3_4:16362043-16362062 Msa0492560:CDS 50.0%
!! GGCGTGTTTAGGTTTGCTAG+AGG + chr3_4:16362070-16362089 Msa0492560:CDS 50.0%
! AAACCTGTTGGTAGGGCCCA+AGG + chr3_4:16361893-16361912 Msa0492560:CDS 55.0%
! AACCTGTTGGTAGGGCCCAA+GGG + chr3_4:16361894-16361913 Msa0492560:CDS 55.0%
GGCCCAAGGGATGTTTGGTT+TGG + chr3_4:16361907-16361926 Msa0492560:CDS 55.0%
ATCCCTTGGGCCCTACCAAC+AGG - chr3_4:16361899-16361918 None:intergenic 60.0%
GGTAGGGCCCAAGGGATGTT+TGG + chr3_4:16361902-16361921 Msa0492560:CDS 60.0%
CTGCCTATTGTCGGCGGCAC+CGG + chr3_4:16362049-16362068 Msa0492560:CDS 65.0%
!! ACGCCGGTGCCGCCGACAAT+AGG - chr3_4:16362055-16362074 None:intergenic 70.0%
!! TCGGCGGCACCGGCGTGTTT+AGG + chr3_4:16362059-16362078 Msa0492560:CDS 70.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 16361608 16362177 16361608 ID=Msa0492560;Name=Msa0492560
chr3_4 mRNA 16361608 16362177 16361608 ID=Msa0492560-mRNA-1;Parent=Msa0492560;Name=Msa0492560-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|189
chr3_4 exon 16361608 16362177 16361608 ID=Msa0492560-mRNA-1:exon:4721;Parent=Msa0492560-mRNA-1
chr3_4 CDS 16361608 16362177 16361608 ID=Msa0492560-mRNA-1:cds;Parent=Msa0492560-mRNA-1
Gene Sequence

>Msa0492560

ATGGCTACCTCTCTTAGGTTCTTCTTTCTCTTCACTCTCACTCTCATATTTGCTCAATTTTTCACTACCAATGGTTTGTTCTCCGAACAATCCAACATAATGTTACCAACAAATAAACAAAGCACTGAAAAATTAACCCACTTGCACTTTTTTTACCATGACATCTTAGAAGGTAAAGATCCAACGGTTGTACAAATTATAGATCCATCAACTAATTCACCAAGTGGATTTGGAACAACATTCATGATGGACAACCTCTTAACTGAAGAACAAGAACTAACATCAAAACCTGTTGGTAGGGCCCAAGGGATGTTTGGTTTGGCATCTTTGCATGATCGTGGAATGGTTATGTTAATTAATCTTGCTTTCACTGAAGGTGATTTTGCTGGTAGTACTCTTAGTATGCTTGGAAGGAATCCTGTTCAAGACACGGTTAGAGAACTGCCTATTGTCGGCGGCACCGGCGTGTTTAGGTTTGCTAGAGGATATGCTACTGCTAAGAGTCTTTGGGAGATTTCAACTTCTGAACATTTTGTTGTTGAGTATGATGTCACTGTTTCTCATCCATAG
Protein sequence

>Msa0492560

MATSLRFFFLFTLTLIFAQFFTTNGLFSEQSNIMLPTNKQSTEKLTHLHFFYHDILEGKDPTVVQIIDPSTNSPSGFGTTFMMDNLLTEEQELTSKPVGRAQGMFGLASLHDRGMVMLINLAFTEGDFAGSTLSMLGRNPVQDTVRELPIVGGTGVFRFARGYATAKSLWEISTSEHFVVEYDVTVSHP*