AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1415100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1415100 MtrunA17_Chr2g0333541 90.244 164 13 1 2 165 1 161 3.69e-94 274
Msa1415100 MtrunA17_Chr8g0368371 78.723 141 15 1 2 127 1 141 1.20e-73 217
Msa1415100 MtrunA17_Chr2g0333641 41.279 172 74 6 5 152 23 191 1.61e-25 99.4
Msa1415100 MtrunA17_Chr2g0333621 39.153 189 81 6 2 162 20 202 5.37e-25 98.2
Msa1415100 MtrunA17_Chr8g0336681 59.155 71 29 0 87 157 145 215 3.21e-21 88.6
Msa1415100 MtrunA17_Chr2g0333611 47.115 104 52 3 65 167 13 114 6.79e-21 85.5
Msa1415100 MtrunA17_Chr4g0002801 47.959 98 46 1 60 152 109 206 6.28e-20 84.7
Msa1415100 MtrunA17_Chr7g0249811 59.091 66 26 1 87 151 153 218 2.49e-19 83.2
Msa1415100 MtrunA17_Chr4g0002781 54.795 73 33 0 80 152 156 228 1.05e-18 81.6
Msa1415100 MtrunA17_Chr5g0400621 47.619 84 42 1 83 166 144 225 7.55e-17 76.3
Msa1415100 MtrunA17_Chr5g0400661 38.583 127 63 3 54 165 90 216 1.47e-16 75.5
Msa1415100 MtrunA17_Chr4g0054581 40.708 113 63 1 54 162 150 262 5.16e-16 74.3
Msa1415100 MtrunA17_Chr5g0400671 44.706 85 43 2 78 161 137 218 6.10e-16 73.6
Msa1415100 MtrunA17_Chr2g0280161 47.826 69 36 0 89 157 168 236 1.58e-15 72.8
Msa1415100 MtrunA17_Chr4g0033291 50.000 68 32 1 85 152 144 209 2.77e-15 72.0
Msa1415100 MtrunA17_Chr7g0225901 45.455 77 42 0 76 152 66 142 2.88e-15 70.9
Msa1415100 MtrunA17_Chr4g0033281 40.171 117 60 3 44 152 93 207 4.92e-15 71.2
Msa1415100 MtrunA17_Chr4g0033391 47.222 72 36 1 85 156 136 205 1.67e-14 69.7
Msa1415100 MtrunA17_Chr6g0468461 33.742 163 88 4 23 165 78 240 1.70e-14 69.7
Msa1415100 MtrunA17_Chr4g0049331 44.444 81 41 1 77 153 110 190 2.83e-14 68.9
Msa1415100 MtrunA17_Chr4g0054561 43.284 67 38 0 91 157 148 214 7.60e-14 67.8
Msa1415100 MtrunA17_Chr4g0054551 43.662 71 40 0 91 161 148 218 8.55e-14 67.8
Msa1415100 MtrunA17_Chr2g0307131 47.222 72 37 1 85 156 167 237 3.56e-13 66.2
Msa1415100 MtrunA17_Chr6g0468491 44.872 78 42 1 76 152 114 191 1.01e-12 64.7
Msa1415100 MtrunA17_Chr2g0307141 50.847 59 29 0 98 156 183 241 1.04e-12 64.7
Msa1415100 MtrunA17_Chr5g0400641 55.769 52 23 0 101 152 1 52 1.41e-12 62.4
Msa1415100 MtrunA17_Chr4g0054571 53.333 60 28 0 96 155 148 207 2.13e-12 63.9
Msa1415100 MtrunA17_Chr4g0054621 38.947 95 53 1 63 152 132 226 1.12e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1415100 AT4G37850.2 37.391 115 68 2 55 165 105 219 5.66e-17 77.0
Msa1415100 AT4G37850.1 37.391 115 68 2 55 165 105 219 5.66e-17 77.0
Msa1415100 AT2G22770.1 51.786 56 27 0 98 153 132 187 3.81e-13 66.2
Msa1415100 AT2G22750.1 52.727 55 26 0 91 145 119 173 6.12e-13 65.5
Msa1415100 AT2G22750.2 52.727 55 26 0 91 145 119 173 6.47e-13 65.5
Msa1415100 AT2G22750.4 52.727 55 26 0 91 145 147 201 7.41e-13 65.5
Msa1415100 AT2G22750.5 52.727 55 26 0 91 145 143 197 7.53e-13 65.5
Msa1415100 AT2G22750.3 52.727 55 26 0 91 145 147 201 7.66e-13 65.5
Msa1415100 AT2G22760.2 46.032 63 34 0 91 153 112 174 8.73e-12 62.0
Msa1415100 AT2G22760.1 46.032 63 34 0 91 153 112 174 9.32e-12 62.0
Msa1415100 AT4G09820.1 42.424 66 38 0 86 151 351 416 8.28e-11 60.1

Find 32 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATTAGAACACGAGATTTA+TGG 0.199679 tig0024171:+34917 None:intergenic
ACTAGGCCAGTTGTGGCAAT+AGG 0.327076 tig0024171:+35421 None:intergenic
CTTCTTCAATCCAGGTATAA+AGG 0.361311 tig0024171:+35162 None:intergenic
AAGTAAGATCATAGAACTTT+CGG 0.375512 tig0024171:-35185 Msa1415100:CDS
ACATAATGTCGGAGAGGAAT+AGG 0.390434 tig0024171:-35222 Msa1415100:CDS
GAACTTTCGGCCTTTATACC+TGG 0.434477 tig0024171:-35172 Msa1415100:CDS
TGATGGATGAGTTGTTTACT+AGG 0.442805 tig0024171:+35404 None:intergenic
CTAGGCCAGTTGTGGCAATA+GGG 0.443059 tig0024171:+35422 None:intergenic
GATCTTGTGGAGTCTGATAC+AGG 0.452617 tig0024171:+35455 None:intergenic
AGTTGAATGTGACACATTGA+TGG 0.456224 tig0024171:+35387 None:intergenic
CTTTATACCTGGATTGAAGA+AGG 0.465281 tig0024171:-35161 Msa1415100:intron
AATGGCTGTGTAGATTGATA+AGG 0.480377 tig0024171:-35042 Msa1415100:intron
ATACTAACCTTCTTCAATCC+AGG 0.486683 tig0024171:+35154 None:intergenic
AGTGTCCCTATTGCCACAAC+TGG 0.491296 tig0024171:-35427 Msa1415100:CDS
GACATTAAGAAGAAAGATGC+AGG 0.492316 tig0024171:-34951 Msa1415100:CDS
TCATGGTGTTGTTCAATTGT+TGG 0.495507 tig0024171:+35325 None:intergenic
AATGTCTCAGAAGCGCTTCG+AGG 0.506140 tig0024171:+35250 None:intergenic
GCTTCTTTGAATTCGACCCT+TGG 0.521451 tig0024171:+35272 None:intergenic
ATGACAAAGGCAAAGAATCA+TGG 0.529186 tig0024171:+35308 None:intergenic
GGTATTGATAATGAGTTGGT+TGG 0.541397 tig0024171:+35346 None:intergenic
TTTGCCTTTGTCATCATCAA+CGG 0.545210 tig0024171:-35299 Msa1415100:CDS
TGTTGGTATTGATAATGAGT+TGG 0.562767 tig0024171:+35342 None:intergenic
TGATAAGGTTCATGTGGTAA+CGG 0.571985 tig0024171:-35027 Msa1415100:CDS
GACATTAGATCACATAATGT+CGG 0.591474 tig0024171:-35233 Msa1415100:CDS
GGGACACTGAATTGATCTTG+TGG 0.603401 tig0024171:+35442 None:intergenic
GTTGTTTACTAGGCCAGTTG+TGG 0.626590 tig0024171:+35414 None:intergenic
TCATCATCAACGGATAACCA+AGG 0.662866 tig0024171:-35289 Msa1415100:CDS
CATCATCAACGGATAACCAA+GGG 0.664890 tig0024171:-35288 Msa1415100:CDS
TTATCCGTTGATGATGACAA+AGG 0.681037 tig0024171:+35295 None:intergenic
TAGATCACATAATGTCGGAG+AGG 0.685140 tig0024171:-35228 Msa1415100:CDS
GTAGATTGATAAGGTTCATG+TGG 0.700450 tig0024171:-35033 Msa1415100:intron
TCTGATACAGGATATCTCTG+AGG 0.706562 tig0024171:+35467 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATATTATATTAAACC+TGG - tig0024171:35308-35327 Msa1415100:CDS 10.0%
!! AATAAAAATGATCTAATTAA+TGG - tig0024171:35377-35396 Msa1415100:CDS 10.0%
!!! ATTTTTATAGTCGTTATCAT+TGG - tig0024171:35343-35362 Msa1415100:CDS 20.0%
! AAGTAAGATCATAGAACTTT+CGG - tig0024171:35252-35271 Msa1415100:CDS 25.0%
! AAAAATTTACTCATTCATCC+AGG + tig0024171:35329-35348 None:intergenic 25.0%
!! TGTTGGTATTGATAATGAGT+TGG + tig0024171:35098-35117 None:intergenic 30.0%
GACATTAGATCACATAATGT+CGG - tig0024171:35204-35223 Msa1415100:CDS 30.0%
! TGATGGATGAGTTGTTTACT+AGG + tig0024171:35036-35055 None:intergenic 35.0%
AGTTGAATGTGACACATTGA+TGG + tig0024171:35053-35072 None:intergenic 35.0%
!! GGTATTGATAATGAGTTGGT+TGG + tig0024171:35094-35113 None:intergenic 35.0%
!! TCATGGTGTTGTTCAATTGT+TGG + tig0024171:35115-35134 None:intergenic 35.0%
ATGACAAAGGCAAAGAATCA+TGG + tig0024171:35132-35151 None:intergenic 35.0%
TTTGCCTTTGTCATCATCAA+CGG - tig0024171:35138-35157 Msa1415100:intron 35.0%
!! TTATCCGTTGATGATGACAA+AGG + tig0024171:35145-35164 None:intergenic 35.0%
CTTCTTCAATCCAGGTATAA+AGG + tig0024171:35278-35297 None:intergenic 35.0%
CTTTATACCTGGATTGAAGA+AGG - tig0024171:35276-35295 Msa1415100:CDS 35.0%
ATACTAACCTTCTTCAATCC+AGG + tig0024171:35286-35305 None:intergenic 35.0%
AATGGCTGTGTAGATTGATA+AGG - tig0024171:35395-35414 Msa1415100:CDS 35.0%
GTAGATTGATAAGGTTCATG+TGG - tig0024171:35404-35423 Msa1415100:CDS 35.0%
TGATAAGGTTCATGTGGTAA+CGG - tig0024171:35410-35429 Msa1415100:CDS 35.0%
GACATTAAGAAGAAAGATGC+AGG - tig0024171:35486-35505 Msa1415100:CDS 35.0%
TCTGATACAGGATATCTCTG+AGG + tig0024171:34973-34992 None:intergenic 40.0%
TCATCATCAACGGATAACCA+AGG - tig0024171:35148-35167 Msa1415100:intron 40.0%
CATCATCAACGGATAACCAA+GGG - tig0024171:35149-35168 Msa1415100:intron 40.0%
TAGATCACATAATGTCGGAG+AGG - tig0024171:35209-35228 Msa1415100:CDS 40.0%
ACATAATGTCGGAGAGGAAT+AGG - tig0024171:35215-35234 Msa1415100:CDS 40.0%
GATCTTGTGGAGTCTGATAC+AGG + tig0024171:34985-35004 None:intergenic 45.0%
GGGACACTGAATTGATCTTG+TGG + tig0024171:34998-35017 None:intergenic 45.0%
GTTGTTTACTAGGCCAGTTG+TGG + tig0024171:35026-35045 None:intergenic 45.0%
GCTTCTTTGAATTCGACCCT+TGG + tig0024171:35168-35187 None:intergenic 45.0%
GAACTTTCGGCCTTTATACC+TGG - tig0024171:35265-35284 Msa1415100:CDS 45.0%
AGTGTCCCTATTGCCACAAC+TGG - tig0024171:35010-35029 Msa1415100:CDS 50.0%
CTAGGCCAGTTGTGGCAATA+GGG + tig0024171:35018-35037 None:intergenic 50.0%
ACTAGGCCAGTTGTGGCAAT+AGG + tig0024171:35019-35038 None:intergenic 50.0%
!! AATGTCTCAGAAGCGCTTCG+AGG + tig0024171:35190-35209 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0024171 gene 34920 35539 34920 ID=Msa1415100;Name=Msa1415100
tig0024171 mRNA 34920 35539 34920 ID=Msa1415100-mRNA-1;Parent=Msa1415100;Name=Msa1415100-mRNA-1;_AED=0.12;_eAED=0.15;_QI=0|0|0|1|1|1|2|0|169
tig0024171 exon 35162 35539 35162 ID=Msa1415100-mRNA-1:exon:22182;Parent=Msa1415100-mRNA-1
tig0024171 exon 34920 35051 34920 ID=Msa1415100-mRNA-1:exon:22181;Parent=Msa1415100-mRNA-1
tig0024171 CDS 35162 35539 35162 ID=Msa1415100-mRNA-1:cds;Parent=Msa1415100-mRNA-1
tig0024171 CDS 34920 35051 34920 ID=Msa1415100-mRNA-1:cds;Parent=Msa1415100-mRNA-1
Gene Sequence

>Msa1415100

GAAATGGAAGAACATTTGTGTCACACAAACAGCACATTTGATGAAGAGTTCCTCAGAGATATCCTGTATCAGACTCCACAAGATCAATTCAGTGTCCCTATTGCCACAACTGGCCTAGTAAACAACTCATCCATCAATGTGTCACATTCAACTCAACATGCTGAAGAAAATCCAACCAACTCATTATCAATACCAACAATTGAACAACACCATGATTCTTTGCCTTTGTCATCATCAACGGATAACCAAGGGTCGAATTCAAAGAAGCCTCGAAGCGCTTCTGAGACATTAGATCACATAATGTCGGAGAGGAATAGGAGACAACTACTTACAAGTAAGATCATAGAACTTTCGGCCTTTATACCTGGATTGAAGAAGATTGATAAGGTTCATGTGGTAACGGAAGCTATCAATTACGTGAAACATCTTGAAGAACGTTTGAAAGAGCTAGAAGAAGACATTAAGAAGAAAGATGCAGGATCATTGAGCACCATAAATCTCGTGTTCTAA
Protein sequence

>Msa1415100

EMEEHLCHTNSTFDEEFLRDILYQTPQDQFSVPIATTGLVNNSSINVSHSTQHAEENPTNSLSIPTIEQHHDSLPLSSSTDNQGSNSKKPRSASETLDHIMSERNRRQLLTSKIIELSAFIPGLKKIDKVHVVTEAINYVKHLEERLKELEEDIKKKDAGSLSTINLVF*