AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1269810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269810 MtrunA17_Chr3g0085311 96.825 189 6 0 1 189 1 189 2.57e-135 376
Msa1269810 MtrunA17_Chr3g0085291 91.534 189 14 1 1 189 1 187 1.45e-127 356
Msa1269810 MtrunA17_Chr3g0085301 64.550 189 67 0 1 189 6 194 1.81e-88 258
Msa1269810 MtrunA17_Chr3g0085321 64.021 189 68 0 1 189 1 189 7.46e-88 256
Msa1269810 MtrunA17_Chr3g0090231 59.459 185 70 1 4 188 5 184 1.89e-78 232
Msa1269810 MtrunA17_Chr4g0040551 59.669 181 68 1 8 188 9 184 2.77e-78 231
Msa1269810 MtrunA17_Chr1g0177051 48.370 184 88 5 10 188 4 185 2.17e-53 168
Msa1269810 MtrunA17_Chr4g0005081 51.592 157 72 2 34 188 42 196 1.23e-48 157
Msa1269810 MtrunA17_Chr4g0005071 49.682 157 75 2 34 188 41 195 1.20e-46 151
Msa1269810 MtrunA17_Chr4g0005041 49.045 157 76 2 34 188 43 197 1.05e-45 149
Msa1269810 MtrunA17_Chr1g0175911 49.324 148 71 3 43 188 46 191 4.81e-45 147
Msa1269810 MtrunA17_Chr4g0005031 47.134 157 79 2 34 188 66 220 1.44e-43 144
Msa1269810 MtrunA17_Chr7g0243501 44.086 186 98 3 7 188 8 191 5.81e-42 139
Msa1269810 MtrunA17_Chr7g0259091 48.993 149 73 2 43 188 45 193 2.28e-41 138
Msa1269810 MtrunA17_Chr7g0259071 48.000 150 73 4 43 188 42 190 3.85e-41 137
Msa1269810 MtrunA17_Chr4g0037481 41.830 153 84 2 39 188 41 191 2.58e-40 135
Msa1269810 MtrunA17_Chr7g0259101 48.993 149 73 2 43 188 45 193 2.19e-38 135
Msa1269810 MtrunA17_Chr7g0259101 46.309 149 77 2 43 188 244 392 1.04e-36 131
Msa1269810 MtrunA17_Chr4g0005011 45.806 155 78 4 34 186 44 194 5.19e-38 129
Msa1269810 MtrunA17_Chr4g0005111 38.776 147 89 1 43 188 43 189 3.21e-36 125
Msa1269810 MtrunA17_Chr4g0005131 40.884 181 98 3 11 188 16 190 9.72e-36 123
Msa1269810 MtrunA17_Chr5g0446751 38.220 191 99 5 7 188 8 188 6.80e-34 119
Msa1269810 MtrunA17_Chr7g0259121 44.444 153 78 2 43 188 40 192 7.45e-33 117
Msa1269810 MtrunA17_Chr3g0136631 40.397 151 85 2 43 188 38 188 2.39e-31 112
Msa1269810 MtrunA17_Chr3g0136641 40.000 150 86 3 43 188 38 187 3.32e-30 109
Msa1269810 MtrunA17_Chr4g0024961 31.169 154 104 1 38 189 25 178 1.89e-20 84.0
Msa1269810 MtrunA17_Chr4g0024951 32.215 149 99 1 43 189 30 178 3.65e-20 83.2
Msa1269810 MtrunA17_Chr4g0068381 33.793 145 94 1 46 188 35 179 5.41e-20 82.8
Msa1269810 MtrunA17_Chr4g0068391 32.353 170 93 4 3 168 8 159 6.14e-20 82.4
Msa1269810 MtrunA17_Chr4g0005091 32.903 155 88 2 36 188 34 174 1.37e-19 81.6
Msa1269810 MtrunA17_Chr1g0169281 38.298 94 57 1 76 169 141 233 6.19e-13 65.1
Msa1269810 MtrunA17_Chr1g0169511 39.362 94 56 1 76 169 135 227 1.10e-12 64.7
Msa1269810 MtrunA17_Chr1g0169291 39.362 94 56 1 76 169 135 227 1.35e-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
Msa1269810 AT1G65870.1 49.689 161 79 2 30 188 29 189 2.59e-48 156
Msa1269810 AT5G42500.1 45.399 163 85 3 28 188 25 185 2.37e-44 145
Msa1269810 AT2G21100.1 42.500 160 87 2 31 188 31 187 2.25e-42 140
Msa1269810 AT2G21100.2 42.500 160 87 2 31 188 31 187 2.25e-42 140
Msa1269810 AT1G22900.1 46.452 155 79 3 36 188 41 193 2.30e-42 141
Msa1269810 AT5G42510.1 44.516 155 82 2 36 188 30 182 5.61e-41 137
Msa1269810 AT3G13650.1 43.151 146 82 1 43 188 41 185 2.19e-40 135
Msa1269810 AT1G55210.1 44.966 149 81 1 40 188 39 186 2.13e-39 133
Msa1269810 AT1G55210.2 44.966 149 81 1 40 188 39 186 2.13e-39 133
Msa1269810 AT1G58170.1 38.947 190 108 3 1 188 1 184 1.51e-38 131
Msa1269810 AT5G49040.1 44.295 149 79 3 43 188 43 190 1.92e-38 130
Msa1269810 AT5G49030.3 47.656 128 65 1 43 168 43 170 2.36e-34 128
Msa1269810 AT3G13662.1 46.825 126 66 1 43 168 40 164 2.44e-34 120
Msa1269810 AT4G38700.1 41.772 158 84 3 39 188 32 189 3.20e-32 115
Msa1269810 AT3G58090.1 51.402 107 52 0 82 188 165 271 2.12e-31 115
Msa1269810 AT2G21110.1 34.536 194 112 4 1 188 1 185 4.15e-29 107
Msa1269810 AT3G13660.1 40.650 123 73 0 66 188 2 124 9.96e-28 101
Msa1269810 AT4G11210.1 29.032 186 125 4 1 186 1 179 3.38e-18 78.6
Msa1269810 AT4G23690.1 31.293 147 93 4 45 186 40 183 5.86e-13 64.7
Msa1269810 AT4G11190.1 29.286 140 97 2 47 186 42 179 3.08e-11 60.1

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTTGTTCCTCAGTTAAA+AGG 0.268043 8_3:+3110966 None:intergenic
ATGCCACTGCTAAGAGTCTT+TGG 0.283577 8_3:-3110733 Msa1269810:CDS
ACTAATTCACCAAGTGGATT+TGG 0.298818 8_3:-3111010 Msa1269810:CDS
TCAGTGCTTTGTTTATTTGT+TGG 0.319384 8_3:+3111115 None:intergenic
TTCAAATGGCTACCTCTCTT+AGG 0.324065 8_3:-3111225 None:intergenic
GGTAGGGCCCAAGGGATGTT+TGG 0.361631 8_3:-3110926 Msa1269810:CDS
CCACTTGGTGAATTAGTTGA+TGG 0.386177 8_3:+3111016 None:intergenic
ATCCCTTGGGCCCTACCAAC+AGG 0.403996 8_3:+3110932 None:intergenic
TAACAGTATGTTGGATTGTT+CGG 0.420769 8_3:+3111138 None:intergenic
TCTCTAACAGTGTCTTGAAC+AGG 0.431116 8_3:+3110803 None:intergenic
TGCCACTGCTAAGAGTCTTT+GGG 0.436210 8_3:-3110732 Msa1269810:CDS
ATTTGGAACAACATTTATGA+TGG 0.441085 8_3:-3110993 Msa1269810:CDS
CTGCCTATTGTTGGTGGCAC+GGG 0.441961 8_3:-3110779 Msa1269810:CDS
ACTCCCGTGCCACCAACAAT+AGG 0.455127 8_3:+3110776 None:intergenic
ATTAATCTTGCTTTCACTGA+AGG 0.457487 8_3:-3110866 Msa1269810:CDS
ATTTGTTGGTAACAGTATGT+TGG 0.458738 8_3:+3111129 None:intergenic
GGTAGTACTCTTAGTATGCT+TGG 0.469670 8_3:-3110833 Msa1269810:CDS
TTGGTGGCACGGGAGTGTTT+AGG 0.470502 8_3:-3110769 Msa1269810:CDS
TCTATAATTTGTACAACCGT+TGG 0.476718 8_3:+3111040 None:intergenic
ATGCTAAACCAAACATCCCT+TGG 0.482775 8_3:+3110918 None:intergenic
TGCTAAACCAAACATCCCTT+GGG 0.511527 8_3:+3110919 None:intergenic
GTTAGAGAACTGCCTATTGT+TGG 0.513260 8_3:-3110788 Msa1269810:CDS
AAACCTGTTGGTAGGGCCCA+AGG 0.521091 8_3:-3110935 Msa1269810:CDS
TAACATCAAAACCTGTTGGT+AGG 0.522247 8_3:-3110943 Msa1269810:CDS
CTTTACCTTCTAAGATGTCA+TGG 0.530269 8_3:+3111065 None:intergenic
AACATCAAAACCTGTTGGTA+GGG 0.532522 8_3:-3110942 Msa1269810:CDS
ATCTTTGCATGACCGTGGAA+TGG 0.552546 8_3:-3110897 Msa1269810:CDS
GAACTAACATCAAAACCTGT+TGG 0.553309 8_3:-3110947 Msa1269810:CDS
AACCTGTTGGTAGGGCCCAA+GGG 0.564840 8_3:-3110934 Msa1269810:CDS
ACTGCCTATTGTTGGTGGCA+CGG 0.589836 8_3:-3110780 Msa1269810:CDS
AGAGAACTGCCTATTGTTGG+TGG 0.596697 8_3:-3110785 Msa1269810:CDS
TTGTTCGGAGAACAAACCAT+TGG 0.604047 8_3:+3111153 None:intergenic
AATGTTGTTCCAAATCCACT+TGG 0.620374 8_3:+3111001 None:intergenic
TTAGCATCTTTGCATGACCG+TGG 0.623261 8_3:-3110902 Msa1269810:CDS
TAATTAGCATAACCATTCCA+CGG 0.624255 8_3:+3110885 None:intergenic
CTTAGAAGGTAAAGATCCAA+CGG 0.624749 8_3:-3111056 Msa1269810:CDS
CCATCAACTAATTCACCAAG+TGG 0.625731 8_3:-3111016 Msa1269810:CDS
GAGAAAGAAGAACCTAAGAG+AGG 0.627560 8_3:+3111213 None:intergenic
GGAGTGTTTAGGTTTGCTAG+AGG 0.636893 8_3:-3110758 Msa1269810:CDS
CTCCCAAAGACTCTTAGCAG+TGG 0.646686 8_3:+3110730 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTGGAACAACATTTATGA+TGG - chr8_3:3110900-3110919 Msa1269810:CDS 25.0%
TAACAGTATGTTGGATTGTT+CGG + chr8_3:3110758-3110777 None:intergenic 30.0%
!! ATTTGTTGGTAACAGTATGT+TGG + chr8_3:3110767-3110786 None:intergenic 30.0%
!! TCAGTGCTTTGTTTATTTGT+TGG + chr8_3:3110781-3110800 None:intergenic 30.0%
! ATGGTAAAAAAAGTGCAAGT+GGG + chr8_3:3110812-3110831 None:intergenic 30.0%
! TTTTACCATGACATCTTAGA+AGG - chr8_3:3110823-3110842 Msa1269810:CDS 30.0%
! TCTATAATTTGTACAACCGT+TGG + chr8_3:3110856-3110875 None:intergenic 30.0%
TAATTAGCATAACCATTCCA+CGG + chr8_3:3111011-3111030 None:intergenic 30.0%
ATTAATCTTGCTTTCACTGA+AGG - chr8_3:3111027-3111046 Msa1269810:CDS 30.0%
! GCTCAATTTTTCACTACCAA+TGG - chr8_3:3110724-3110743 Msa1269810:CDS 35.0%
! CATGGTAAAAAAAGTGCAAG+TGG + chr8_3:3110813-3110832 None:intergenic 35.0%
!! CTTTACCTTCTAAGATGTCA+TGG + chr8_3:3110831-3110850 None:intergenic 35.0%
CTTAGAAGGTAAAGATCCAA+CGG - chr8_3:3110837-3110856 Msa1269810:CDS 35.0%
! ACTAATTCACCAAGTGGATT+TGG - chr8_3:3110883-3110902 Msa1269810:CDS 35.0%
AATGTTGTTCCAAATCCACT+TGG + chr8_3:3110895-3110914 None:intergenic 35.0%
GTTCTTGTTCCTCAGTTAAA+AGG + chr8_3:3110930-3110949 None:intergenic 35.0%
GAACTAACATCAAAACCTGT+TGG - chr8_3:3110946-3110965 Msa1269810:CDS 35.0%
TAACATCAAAACCTGTTGGT+AGG - chr8_3:3110950-3110969 Msa1269810:CDS 35.0%
AACATCAAAACCTGTTGGTA+GGG - chr8_3:3110951-3110970 Msa1269810:CDS 35.0%
GAGAAAGAAGAACCTAAGAG+AGG + chr8_3:3110683-3110702 None:intergenic 40.0%
TTGTTCGGAGAACAAACCAT+TGG + chr8_3:3110743-3110762 None:intergenic 40.0%
! CCACTTGGTGAATTAGTTGA+TGG + chr8_3:3110880-3110899 None:intergenic 40.0%
CCATCAACTAATTCACCAAG+TGG - chr8_3:3110877-3110896 Msa1269810:CDS 40.0%
!! GATGGACAACCTTTTAACTG+AGG - chr8_3:3110918-3110937 Msa1269810:CDS 40.0%
TGCTAAACCAAACATCCCTT+GGG + chr8_3:3110977-3110996 None:intergenic 40.0%
ATGCTAAACCAAACATCCCT+TGG + chr8_3:3110978-3110997 None:intergenic 40.0%
! TTCACTGAAGGTGATTTTGC+TGG - chr8_3:3111039-3111058 Msa1269810:CDS 40.0%
GGTAGTACTCTTAGTATGCT+TGG - chr8_3:3111060-3111079 Msa1269810:CDS 40.0%
TCTCTAACAGTGTCTTGAAC+AGG + chr8_3:3111093-3111112 None:intergenic 40.0%
GTTAGAGAACTGCCTATTGT+TGG - chr8_3:3111105-3111124 Msa1269810:CDS 40.0%
TTAGCATCTTTGCATGACCG+TGG - chr8_3:3110991-3111010 Msa1269810:CDS 45.0%
ATCTTTGCATGACCGTGGAA+TGG - chr8_3:3110996-3111015 Msa1269810:CDS 45.0%
AGAGAACTGCCTATTGTTGG+TGG - chr8_3:3111108-3111127 Msa1269810:CDS 45.0%
!! GGAGTGTTTAGGTTTGCTAG+AGG - chr8_3:3111135-3111154 Msa1269810:CDS 45.0%
ATGCCACTGCTAAGAGTCTT+TGG - chr8_3:3111160-3111179 Msa1269810:CDS 45.0%
TGCCACTGCTAAGAGTCTTT+GGG - chr8_3:3111161-3111180 Msa1269810:CDS 45.0%
!! ACTGCCTATTGTTGGTGGCA+CGG - chr8_3:3111113-3111132 Msa1269810:CDS 50.0%
CTCCCAAAGACTCTTAGCAG+TGG + chr8_3:3111166-3111185 None:intergenic 50.0%
! AAACCTGTTGGTAGGGCCCA+AGG - chr8_3:3110958-3110977 Msa1269810:CDS 55.0%
! AACCTGTTGGTAGGGCCCAA+GGG - chr8_3:3110959-3110978 Msa1269810:CDS 55.0%
!! CTGCCTATTGTTGGTGGCAC+GGG - chr8_3:3111114-3111133 Msa1269810:CDS 55.0%
ACTCCCGTGCCACCAACAAT+AGG + chr8_3:3111120-3111139 None:intergenic 55.0%
!! TTGGTGGCACGGGAGTGTTT+AGG - chr8_3:3111124-3111143 Msa1269810:CDS 55.0%
ATCCCTTGGGCCCTACCAAC+AGG + chr8_3:3110964-3110983 None:intergenic 60.0%
GGTAGGGCCCAAGGGATGTT+TGG - chr8_3:3110967-3110986 Msa1269810:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 3110673 3111242 3110673 ID=Msa1269810;Name=Msa1269810
chr8_3 mRNA 3110673 3111242 3110673 ID=Msa1269810-mRNA-1;Parent=Msa1269810;Name=Msa1269810-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|189
chr8_3 exon 3110673 3111242 3110673 ID=Msa1269810-mRNA-1:exon:1013;Parent=Msa1269810-mRNA-1
chr8_3 CDS 3110673 3111242 3110673 ID=Msa1269810-mRNA-1:cds;Parent=Msa1269810-mRNA-1
Gene Sequence

>Msa1269810

ATGGCTACCTCTCTTAGGTTCTTCTTTCTCTTCACTCTCACTCTCATATTTGCTCAATTTTTCACTACCAATGGTTTGTTCTCCGAACAATCCAACATACTGTTACCAACAAATAAACAAAGCACTGAAAAATTAACCCACTTGCACTTTTTTTACCATGACATCTTAGAAGGTAAAGATCCAACGGTTGTACAAATTATAGATCCATCAACTAATTCACCAAGTGGATTTGGAACAACATTTATGATGGACAACCTTTTAACTGAGGAACAAGAACTAACATCAAAACCTGTTGGTAGGGCCCAAGGGATGTTTGGTTTAGCATCTTTGCATGACCGTGGAATGGTTATGCTAATTAATCTTGCTTTCACTGAAGGTGATTTTGCTGGTAGTACTCTTAGTATGCTTGGAAGAAATCCTGTTCAAGACACTGTTAGAGAACTGCCTATTGTTGGTGGCACGGGAGTGTTTAGGTTTGCTAGAGGATATGCCACTGCTAAGAGTCTTTGGGAGATTTCAACTTCTGAACATTTTGTTGTTGAGTATGATGTCACTGTTTCTCATCCATAG
Protein sequence

>Msa1269810

MATSLRFFFLFTLTLIFAQFFTTNGLFSEQSNILLPTNKQSTEKLTHLHFFYHDILEGKDPTVVQIIDPSTNSPSGFGTTFMMDNLLTEEQELTSKPVGRAQGMFGLASLHDRGMVMLINLAFTEGDFAGSTLSMLGRNPVQDTVRELPIVGGTGVFRFARGYATAKSLWEISTSEHFVVEYDVTVSHP*