AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1043370

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1043370 MtrunA17_Chr4g0021561 98.864 88 1 0 1 88 169 256 2.33e-61 186
Msa1043370 MtrunA17_Chr2g0324181 86.364 88 12 0 1 88 30 117 2.98e-54 164
Msa1043370 MtrunA17_Chr5g0433841 69.318 88 27 0 1 88 177 264 6.95e-39 129
Msa1043370 MtrunA17_Chr3g0109801 70.455 88 26 0 1 88 197 284 5.58e-38 128
Msa1043370 MtrunA17_Chr3g0107311 61.364 88 34 0 1 88 167 254 4.10e-34 117
Msa1043370 MtrunA17_Chr3g0107291 61.364 88 34 0 1 88 173 260 4.50e-34 117
Msa1043370 MtrunA17_Chr5g0432611 59.091 88 36 0 1 88 164 251 1.99e-31 110
Msa1043370 MtrunA17_Chr3g0128801 59.091 88 36 0 1 88 166 253 1.36e-30 108
Msa1043370 MtrunA17_Chr3g0128791 59.091 88 36 0 1 88 166 253 5.25e-30 106
Msa1043370 MtrunA17_Chr3g0092071 59.091 88 36 0 1 88 160 247 7.56e-30 106
Msa1043370 MtrunA17_Chr5g0417701 56.818 88 38 0 1 88 160 247 6.00e-29 103
Msa1043370 MtrunA17_Chr4g0042521 56.818 88 38 0 1 88 160 247 1.04e-28 103
Msa1043370 MtrunA17_Chr6g0453341 54.545 88 40 0 1 88 165 252 4.77e-28 101
Msa1043370 MtrunA17_Chr7g0238681 53.409 88 41 0 1 88 169 256 2.65e-27 99.8
Msa1043370 MtrunA17_Chr7g0218751 56.471 85 37 0 1 85 163 247 5.25e-27 99.0
Msa1043370 MtrunA17_Chr2g0328261 54.545 88 40 0 1 88 171 258 8.26e-27 98.6
Msa1043370 MtrunA17_Chr5g0435311 55.682 88 39 0 1 88 219 306 1.02e-26 99.4
Msa1043370 MtrunA17_Chr7g0217661 52.273 88 42 0 1 88 153 240 1.80e-26 97.4
Msa1043370 MtrunA17_Chr7g0218761 52.326 86 41 0 1 86 124 209 6.37e-26 95.1
Msa1043370 MtrunA17_Chr8g0360041 52.941 85 40 0 1 85 166 250 1.23e-23 90.1
Msa1043370 MtrunA17_Chr4g0022841 48.235 85 44 0 1 85 32 116 1.25e-23 86.7
Msa1043370 MtrunA17_Chr8g0359971 53.947 76 34 1 10 84 2 77 2.34e-23 85.1
Msa1043370 MtrunA17_Chr7g0218741 53.409 88 40 1 1 87 164 251 1.12e-22 87.8
Msa1043370 MtrunA17_Chr4g0031621 53.409 88 41 0 1 88 169 256 6.61e-22 85.9
Msa1043370 MtrunA17_Chr8g0360721 50.000 84 42 0 1 84 133 216 8.32e-22 84.7
Msa1043370 MtrunA17_Chr1g0157061 44.186 86 48 0 1 86 153 238 4.18e-21 83.2
Msa1043370 MtrunA17_Chr1g0193631 48.276 87 44 1 1 86 168 254 2.20e-19 79.0
Msa1043370 MtrunA17_Chr7g0271001 47.059 85 44 1 1 84 165 249 2.62e-19 79.0
Msa1043370 MtrunA17_Chr4g0069711 41.379 87 50 1 1 86 196 282 6.00e-18 75.5
Msa1043370 MtrunA17_Chr5g0398271 43.529 85 47 1 3 86 175 259 1.17e-16 72.0
Msa1043370 MtrunA17_Chr4g0057091 44.578 83 45 1 3 84 174 256 5.52e-16 70.1
Msa1043370 MtrunA17_Chr1g0193571 51.852 54 26 0 33 86 4 57 2.52e-13 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1043370 AT4G38210.1 69.318 88 27 0 1 88 167 254 1.88e-40 134
Msa1043370 AT3G03220.1 64.773 88 31 0 1 88 176 263 1.79e-36 124
Msa1043370 AT2G03090.1 56.818 88 38 0 1 88 165 252 4.73e-28 102
Msa1043370 AT5G05290.1 56.180 89 38 1 1 88 167 255 9.15e-28 101
Msa1043370 AT2G40610.1 56.180 89 38 1 1 88 165 253 1.57e-27 100
Msa1043370 AT1G26770.1 54.545 88 40 0 1 88 161 248 1.97e-27 100
Msa1043370 AT1G26770.2 54.545 88 40 0 1 88 171 258 2.16e-27 100
Msa1043370 AT3G55500.1 55.682 88 39 0 1 88 171 258 4.86e-27 99.4
Msa1043370 AT5G56320.1 53.409 88 41 0 1 88 164 251 7.04e-27 99.0
Msa1043370 AT5G56320.2 53.409 88 41 0 1 88 164 251 7.04e-27 99.0
Msa1043370 AT3G29030.1 54.545 88 40 0 1 88 166 253 1.18e-26 98.6
Msa1043370 AT1G69530.2 56.818 88 38 0 1 88 162 249 1.26e-26 98.2
Msa1043370 AT1G69530.1 56.818 88 38 0 1 88 162 249 1.26e-26 98.2
Msa1043370 AT2G39700.1 54.545 88 40 0 1 88 168 255 1.37e-26 98.2
Msa1043370 AT5G56320.3 53.409 88 41 0 1 88 164 251 1.97e-26 98.6
Msa1043370 AT2G37640.2 53.409 88 41 0 1 88 148 235 6.40e-26 96.3
Msa1043370 AT2G37640.1 53.409 88 41 0 1 88 173 260 1.07e-25 95.9
Msa1043370 AT5G02260.1 52.273 88 42 0 1 88 169 256 1.56e-25 95.5
Msa1043370 AT1G69530.3 57.831 83 35 0 1 83 162 244 6.42e-25 94.4
Msa1043370 AT5G39270.1 51.765 85 41 0 2 86 192 276 2.27e-22 87.8
Msa1043370 AT5G39280.1 51.190 84 41 0 3 86 189 272 3.15e-22 87.0
Msa1043370 AT5G39300.1 51.190 84 41 0 3 86 190 273 4.07e-22 87.0
Msa1043370 AT5G39290.1 50.588 85 42 0 2 86 192 276 1.15e-21 85.9
Msa1043370 AT1G20190.2 45.238 84 46 0 1 84 105 188 3.67e-21 82.8
Msa1043370 AT1G20190.1 45.238 84 46 0 1 84 164 247 7.61e-21 83.2
Msa1043370 AT5G39260.1 46.512 86 46 0 1 86 174 259 1.30e-20 82.8
Msa1043370 AT2G28950.1 51.136 88 43 0 1 88 168 255 2.57e-20 82.0
Msa1043370 AT3G15370.1 48.352 91 44 2 1 88 161 251 1.37e-19 79.7
Msa1043370 AT3G15370.2 48.352 91 44 2 1 88 191 281 2.06e-19 79.7
Msa1043370 AT1G12560.1 44.578 83 45 1 3 84 174 256 1.21e-17 74.7
Msa1043370 AT5G39310.1 44.828 87 47 1 1 86 223 309 1.34e-17 75.5
Msa1043370 AT4G01630.1 44.706 85 46 1 1 84 166 250 1.77e-17 74.3
Msa1043370 AT1G62980.1 42.353 85 48 1 3 86 169 253 1.11e-16 72.4
Msa1043370 AT1G69530.4 39.773 88 23 1 1 88 162 219 6.17e-12 58.9
Msa1043370 AT1G69530.5 60.000 45 18 0 1 45 162 206 4.33e-11 57.0

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCACCTCCAAACTGGCAATT+TGG 0.255098 7_2:-1575574 Msa1043370:CDS
GGATACCAATGGCAAGGAAT+TGG 0.318465 7_2:-1575693 Msa1043370:CDS
GTTTGTCCAAATTGCCAGTT+TGG 0.334344 7_2:+1575568 None:intergenic
GATACCAATGGCAAGGAATT+GGG 0.350848 7_2:-1575692 Msa1043370:CDS
ACATCAGCCTTTGTCCTTTG+AGG 0.354377 7_2:-1575638 Msa1043370:CDS
CAATTTGGACAAACATTTGA+AGG 0.398107 7_2:-1575559 Msa1043370:CDS
CAAGGAATTGGGGAATGAAT+TGG 0.429950 7_2:-1575681 Msa1043370:CDS
ATAACTAATGTGGGGTTAGA+TGG 0.442300 7_2:-1575757 Msa1043370:CDS
ACAATGTAGCACCTCCAAAC+TGG 0.451802 7_2:-1575582 Msa1043370:CDS
ATTCCCCAATTCCTTGCCAT+TGG 0.501334 7_2:+1575688 None:intergenic
AAAGTGAAGGGATCTAGAAC+AGG 0.502893 7_2:-1575718 Msa1043370:CDS
CAAGTTCTGATAACTAATGT+GGG 0.508543 7_2:-1575766 Msa1043370:CDS
TCAAGTTCTGATAACTAATG+TGG 0.509065 7_2:-1575767 Msa1043370:CDS
AGGACAAAGGCTGATGTTGA+AGG 0.517191 7_2:+1575644 None:intergenic
TGTCCAAATTGCCAGTTTGG+AGG 0.539604 7_2:+1575571 None:intergenic
TTTGAGGTAACTAGCAGCAC+TGG 0.546125 7_2:-1575622 Msa1043370:CDS
GGGTTGAAATTCACAATGAG+TGG 0.572612 7_2:-1575805 None:intergenic
ATACCAATGGCAAGGAATTG+GGG 0.587228 7_2:-1575691 Msa1043370:CDS
TGAAGGGATCTAGAACAGGA+TGG 0.625878 7_2:-1575714 Msa1043370:CDS
CAGGATGGATACCAATGGCA+AGG 0.630186 7_2:-1575699 Msa1043370:CDS
CTAGTTACCTCAAAGGACAA+AGG 0.637645 7_2:+1575631 None:intergenic
TAGAACAGGATGGATACCAA+TGG 0.662207 7_2:-1575704 Msa1043370:CDS
AGTGCTGCTAGTTACCTCAA+AGG 0.674064 7_2:+1575624 None:intergenic
AAGTTCTGATAACTAATGTG+GGG 0.688292 7_2:-1575765 Msa1043370:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCAAGTTCTGATAACTAATG+TGG - chr7_2:1575569-1575588 Msa1043370:CDS 30.0%
! CAAGTTCTGATAACTAATGT+GGG - chr7_2:1575570-1575589 Msa1043370:CDS 30.0%
! AAGTTCTGATAACTAATGTG+GGG - chr7_2:1575571-1575590 Msa1043370:CDS 30.0%
CAATTTGGACAAACATTTGA+AGG - chr7_2:1575777-1575796 Msa1043370:CDS 30.0%
ATAACTAATGTGGGGTTAGA+TGG - chr7_2:1575579-1575598 Msa1043370:CDS 35.0%
!! AGTTTTTGCTGTGAAAGTGA+AGG - chr7_2:1575605-1575624 Msa1043370:CDS 35.0%
!! GTTTTTGCTGTGAAAGTGAA+GGG - chr7_2:1575606-1575625 Msa1043370:CDS 35.0%
! AAAGTGAAGGGATCTAGAAC+AGG - chr7_2:1575618-1575637 Msa1043370:CDS 40.0%
TAGAACAGGATGGATACCAA+TGG - chr7_2:1575632-1575651 Msa1043370:CDS 40.0%
GATACCAATGGCAAGGAATT+GGG - chr7_2:1575644-1575663 Msa1043370:CDS 40.0%
ATACCAATGGCAAGGAATTG+GGG - chr7_2:1575645-1575664 Msa1043370:CDS 40.0%
CAAGGAATTGGGGAATGAAT+TGG - chr7_2:1575655-1575674 Msa1043370:CDS 40.0%
CTAGTTACCTCAAAGGACAA+AGG + chr7_2:1575708-1575727 None:intergenic 40.0%
GTTTGTCCAAATTGCCAGTT+TGG + chr7_2:1575771-1575790 None:intergenic 40.0%
! TGAAGGGATCTAGAACAGGA+TGG - chr7_2:1575622-1575641 Msa1043370:CDS 45.0%
GGATACCAATGGCAAGGAAT+TGG - chr7_2:1575643-1575662 Msa1043370:CDS 45.0%
ATTCCCCAATTCCTTGCCAT+TGG + chr7_2:1575651-1575670 None:intergenic 45.0%
AGGACAAAGGCTGATGTTGA+AGG + chr7_2:1575695-1575714 None:intergenic 45.0%
ACATCAGCCTTTGTCCTTTG+AGG - chr7_2:1575698-1575717 Msa1043370:CDS 45.0%
! AGTGCTGCTAGTTACCTCAA+AGG + chr7_2:1575715-1575734 None:intergenic 45.0%
! TTTGAGGTAACTAGCAGCAC+TGG - chr7_2:1575714-1575733 Msa1043370:CDS 45.0%
ACAATGTAGCACCTCCAAAC+TGG - chr7_2:1575754-1575773 Msa1043370:CDS 45.0%
TGTCCAAATTGCCAGTTTGG+AGG + chr7_2:1575768-1575787 None:intergenic 45.0%
CAGGATGGATACCAATGGCA+AGG - chr7_2:1575637-1575656 Msa1043370:CDS 50.0%
GCACCTCCAAACTGGCAATT+TGG - chr7_2:1575762-1575781 Msa1043370:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 1575546 1575812 1575546 ID=Msa1043370;Name=Msa1043370
chr7_2 mRNA 1575546 1575812 1575546 ID=Msa1043370-mRNA-1;Parent=Msa1043370;Name=Msa1043370-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|-1|0|1|-1|1|1|0|88
chr7_2 exon 1575546 1575812 1575546 ID=Msa1043370-mRNA-1:exon:258;Parent=Msa1043370-mRNA-1
chr7_2 CDS 1575546 1575812 1575546 ID=Msa1043370-mRNA-1:cds;Parent=Msa1043370-mRNA-1
Gene Sequence

>Msa1043370

ATGAGTGGAAGTTCTCATTTCTATCAAGTTCTGATAACTAATGTGGGGTTAGATGGTGAAGTTTTTGCTGTGAAAGTGAAGGGATCTAGAACAGGATGGATACCAATGGCAAGGAATTGGGGAATGAATTGGCATTGCAATGTCAACCTTCAACATCAGCCTTTGTCCTTTGAGGTAACTAGCAGCACTGGAAAAACACTCACATCTTACAATGTAGCACCTCCAAACTGGCAATTTGGACAAACATTTGAAGGAAAACAATTTTAG
Protein sequence

>Msa1043370

MSGSSHFYQVLITNVGLDGEVFAVKVKGSRTGWIPMARNWGMNWHCNVNLQHQPLSFEVTSSTGKTLTSYNVAPPNWQFGQTFEGKQF*