AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0206370

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0206370 MtrunA17_Chr2g0322861 67.717 127 2 1 1 88 124 250 1.77e-52 168
Msa0206370 MtrunA17_Chr4g0024121 47.727 132 29 2 1 92 64 195 5.66e-32 114
Msa0206370 MtrunA17_Chr1g0157051 41.406 128 34 3 1 88 61 187 1.29e-25 97.4
Msa0206370 MtrunA17_Chr7g0268501 45.238 126 31 2 1 88 62 187 1.55e-25 97.1
Msa0206370 MtrunA17_Chr7g0268521 45.238 126 31 2 1 88 62 187 1.55e-25 97.1
Msa0206370 MtrunA17_Chr2g0292241 42.105 133 36 2 1 92 66 198 6.94e-25 95.9
Msa0206370 MtrunA17_Chr2g0292211 41.353 133 37 2 1 92 77 209 4.14e-24 94.0
Msa0206370 MtrunA17_Chr2g0292181 41.353 133 37 2 1 92 75 207 1.09e-23 92.8
Msa0206370 MtrunA17_Chr2g0292091 40.602 133 38 2 1 92 61 193 1.67e-23 92.0
Msa0206370 MtrunA17_Chr5g0405991 40.625 128 35 3 1 88 60 186 3.08e-23 90.9
Msa0206370 MtrunA17_Chr2g0292261 40.602 133 38 2 1 92 66 198 3.38e-23 91.3
Msa0206370 MtrunA17_Chr2g0292101 39.850 133 39 2 1 92 62 194 4.11e-23 90.9
Msa0206370 MtrunA17_Chr8g0371381 39.062 128 37 3 1 88 63 189 5.00e-23 90.5
Msa0206370 MtrunA17_Chr3g0106921 39.552 134 39 3 1 92 62 195 7.99e-23 89.7
Msa0206370 MtrunA17_Chr2g0292251 42.105 133 36 3 1 92 65 197 1.88e-22 89.4
Msa0206370 MtrunA17_Chr2g0291751 39.850 133 39 2 1 92 66 198 1.14e-21 87.0
Msa0206370 MtrunA17_Chr3g0114451 39.850 133 39 3 1 92 63 195 1.48e-21 86.7
Msa0206370 MtrunA17_Chr1g0204011 40.625 128 35 3 1 88 64 190 1.70e-21 86.3
Msa0206370 MtrunA17_Chr2g0320071 37.984 129 39 2 1 88 62 190 2.19e-21 85.9
Msa0206370 MtrunA17_Chr2g0320061 38.760 129 38 2 1 88 62 190 2.53e-21 85.9
Msa0206370 MtrunA17_Chr2g0292111 39.850 133 39 2 1 92 66 198 2.63e-21 86.3
Msa0206370 MtrunA17_Chr2g0299691 38.281 128 38 2 1 88 93 219 3.13e-21 85.9
Msa0206370 MtrunA17_Chr2g0320051 37.984 129 39 2 1 88 62 190 4.66e-21 85.1
Msa0206370 MtrunA17_Chr8g0372601 39.535 129 37 2 1 88 67 195 5.29e-21 85.1
Msa0206370 MtrunA17_Chr2g0292151 39.098 133 40 2 1 92 66 198 5.38e-21 85.5
Msa0206370 MtrunA17_Chr2g0320101 37.209 129 40 2 1 88 62 190 8.39e-21 84.3
Msa0206370 MtrunA17_Chr2g0292271 38.760 129 38 2 1 88 66 194 2.03e-20 84.0
Msa0206370 MtrunA17_Chr5g0404721 37.984 129 39 2 1 88 67 195 3.09e-20 83.2
Msa0206370 MtrunA17_Chr4g0043391 35.659 129 42 2 1 88 64 192 5.52e-20 82.4
Msa0206370 MtrunA17_Chr5g0402571 36.090 133 43 3 1 92 64 195 7.89e-20 82.0
Msa0206370 MtrunA17_Chr5g0400331 38.760 129 38 2 1 88 63 191 8.68e-20 82.0
Msa0206370 MtrunA17_Chr3g0129061 38.346 133 41 2 1 92 65 197 1.03e-19 81.6
Msa0206370 MtrunA17_Chr5g0402581 37.594 133 41 4 1 92 64 195 1.10e-19 81.6
Msa0206370 MtrunA17_Chr3g0129041 37.594 133 42 2 1 92 65 197 1.17e-19 81.3
Msa0206370 MtrunA17_Chr1g0175561 35.821 134 44 2 1 92 61 194 1.30e-19 81.3
Msa0206370 MtrunA17_Chr1g0155611 36.842 133 43 2 1 92 83 215 1.64e-19 81.3
Msa0206370 MtrunA17_Chr3g0129051 37.594 133 42 2 1 92 65 197 2.60e-19 80.5
Msa0206370 MtrunA17_Chr5g0432441 38.060 134 41 3 1 92 67 200 4.54e-19 79.7
Msa0206370 MtrunA17_Chr4g0068621 36.842 133 43 2 1 92 75 207 7.05e-19 79.3
Msa0206370 MtrunA17_Chr4g0070951 37.500 128 39 2 1 88 65 191 1.15e-18 79.0
Msa0206370 MtrunA17_Chr2g0320091 37.209 129 40 2 1 88 62 190 1.50e-18 78.2
Msa0206370 MtrunA17_Chr2g0296621 36.800 125 41 3 1 88 87 210 1.91e-18 78.2
Msa0206370 MtrunA17_Chr5g0421411 33.333 129 45 2 1 88 18 146 2.13e-18 77.4
Msa0206370 MtrunA17_Chr4g0076211 36.800 125 41 3 1 88 78 201 1.12e-17 76.3
Msa0206370 MtrunA17_Chr2g0320031 34.586 133 46 2 1 92 63 195 1.39e-17 75.9
Msa0206370 MtrunA17_Chr7g0258811 35.821 134 44 2 1 92 106 239 1.41e-17 76.3
Msa0206370 MtrunA17_Chr2g0292291 36.434 129 41 2 1 88 67 195 1.23e-16 73.6
Msa0206370 MtrunA17_Chr3g0114461 55.932 59 26 0 34 92 10 68 4.23e-16 70.1
Msa0206370 MtrunA17_Chr4g0053871 34.559 136 45 2 1 92 64 199 5.49e-16 71.2
Msa0206370 MtrunA17_Chr4g0013811 49.091 55 28 0 33 87 5 59 2.18e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0206370 AT3G21770.1 53.435 131 22 1 1 92 66 196 1.27e-38 131
Msa0206370 AT4G11290.1 54.264 129 18 2 1 88 62 190 8.58e-38 129
Msa0206370 AT1G05260.1 53.435 131 22 1 1 92 63 193 4.21e-37 127
Msa0206370 AT1G05240.1 44.882 127 31 1 1 88 63 189 2.54e-29 107
Msa0206370 AT1G05250.1 44.882 127 31 1 1 88 63 189 2.54e-29 107
Msa0206370 AT5G15180.1 42.857 133 37 1 1 94 69 201 1.26e-27 103
Msa0206370 AT1G49570.1 39.161 143 44 3 1 100 85 227 1.25e-24 95.5
Msa0206370 AT3G01190.1 43.307 127 31 2 1 88 63 187 1.79e-24 94.7
Msa0206370 AT2G18150.1 39.583 144 45 3 1 103 73 215 7.66e-24 93.2
Msa0206370 AT4G36430.1 39.583 144 45 3 1 103 67 209 8.40e-24 93.2
Msa0206370 AT5G42180.1 40.625 128 35 3 1 88 60 186 1.11e-23 92.4
Msa0206370 AT2G38390.1 41.045 134 37 3 1 92 68 201 5.67e-22 88.2
Msa0206370 AT2G38380.1 41.045 134 37 3 1 92 68 201 6.68e-22 88.2
Msa0206370 AT5G66390.1 38.519 135 42 2 1 94 70 204 1.09e-21 87.4
Msa0206370 AT5G51890.1 39.062 128 37 3 1 88 63 189 1.26e-21 87.0
Msa0206370 AT5G06730.1 37.594 133 42 2 1 92 70 202 3.06e-21 86.3
Msa0206370 AT1G44970.1 38.760 129 38 2 1 88 82 210 1.58e-20 84.3
Msa0206370 AT3G03670.1 37.500 128 40 2 1 88 60 187 3.79e-20 83.2
Msa0206370 AT5G06720.1 36.842 133 43 2 1 92 69 201 3.84e-20 83.2
Msa0206370 AT2G18140.1 35.417 144 51 3 1 103 72 214 4.55e-20 83.2
Msa0206370 AT2G39040.1 38.806 134 40 2 1 92 83 216 2.00e-19 81.3
Msa0206370 AT3G32980.1 38.806 134 40 3 1 92 68 201 2.87e-19 80.9
Msa0206370 AT2G35380.1 35.659 129 42 2 1 88 67 195 1.46e-18 79.0
Msa0206370 AT3G49110.1 39.552 134 39 3 1 92 70 203 2.36e-18 78.6
Msa0206370 AT3G50990.1 35.556 135 46 2 1 94 78 212 2.57e-18 78.2
Msa0206370 AT4G08770.1 38.060 134 41 3 1 92 61 194 7.85e-18 77.0
Msa0206370 AT3G49120.1 38.806 134 40 3 1 92 69 202 9.93e-18 76.6
Msa0206370 AT5G17820.1 36.220 127 38 3 1 88 61 183 3.40e-17 75.1
Msa0206370 AT5G17820.2 36.220 127 38 3 1 88 114 236 8.45e-17 74.3
Msa0206370 AT5G19890.1 33.846 130 47 3 1 92 67 195 8.55e-16 71.2
Msa0206370 AT2G35380.2 49.123 57 29 0 32 88 51 107 1.01e-11 59.7
Msa0206370 AT4G31760.1 35.433 127 41 5 1 88 66 190 2.05e-11 59.3

Find 25 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGATTGGCAAAGAGAGTT+TGG 0.269943 2_1:+35639047 None:intergenic
ACTTTCATGATTGCTTTGTT+AGG 0.271511 2_1:-35639608 Msa0206370:CDS
CTTTCATGATTGCTTTGTTA+GGG 0.352765 2_1:-35639607 Msa0206370:intron
AGTTTGGAGGGTGGTGAAGT+TGG 0.356287 2_1:+35639063 None:intergenic
AAAGACTTAGTCCTCCTATC+TGG 0.364479 2_1:-35639013 Msa0206370:CDS
GGAAAGTTCCAACAGGTAGA+AGG 0.373285 2_1:-35639141 Msa0206370:CDS
GATTTCAGGGTGGTCCATAT+TGG 0.381350 2_1:-35639162 Msa0206370:intron
CCTGTTGGAACTTTCCAATA+TGG 0.384950 2_1:+35639148 None:intergenic
AAGCCTCTAACAGTAAGATT+TGG 0.388544 2_1:+35639427 None:intergenic
AGGGTGGTGAAGTTGGAAAA+TGG 0.423456 2_1:+35639070 None:intergenic
GTTGGTTTGTTGAGTTCAAA+AGG 0.425359 2_1:+35639470 None:intergenic
CAAACTCTCTTTGCCAATCA+AGG 0.450028 2_1:-35639046 Msa0206370:CDS
CCTCTAACAGTAAGATTTGG+AGG 0.486565 2_1:+35639430 None:intergenic
TGGAGTCGTATCGAATTTGT+TGG 0.490287 2_1:-35639116 Msa0206370:CDS
CCATATTGGAAAGTTCCAAC+AGG 0.513974 2_1:-35639148 Msa0206370:CDS
TGAATGTAATAATACCAGAT+AGG 0.531919 2_1:+35638999 None:intergenic
GACGAAAGTGCTTAATGCTA+AGG 0.539713 2_1:+35638969 None:intergenic
GTGAAGTTGGAAAATGGAGC+AGG 0.550766 2_1:+35639076 None:intergenic
ACTCCATCCCTTCTACCTGT+TGG 0.553125 2_1:+35639133 None:intergenic
GAAAGTTCCAACAGGTAGAA+GGG 0.557568 2_1:-35639140 Msa0206370:CDS
GTTCCAACAGGTAGAAGGGA+TGG 0.566917 2_1:-35639136 Msa0206370:CDS
GATTGGCAAAGAGAGTTTGG+AGG 0.571052 2_1:+35639050 None:intergenic
ATTGGCAAAGAGAGTTTGGA+GGG 0.582534 2_1:+35639051 None:intergenic
GGCAAAGAGAGTTTGGAGGG+TGG 0.591559 2_1:+35639054 None:intergenic
ATGTAATAATACCAGATAGG+AGG 0.629799 2_1:+35639002 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATACTTTCATTTCATTTT+TGG - chr2_1:35639012-35639031 Msa0206370:CDS 15.0%
!!! AACATTAAGCATTTTGATTT+AGG - chr2_1:35639061-35639080 Msa0206370:CDS 20.0%
!!! ACATTAAGCATTTTGATTTA+GGG - chr2_1:35639062-35639081 Msa0206370:CDS 20.0%
! ATTCTATCTTTAACAGACTA+AGG - chr2_1:35639283-35639302 Msa0206370:intron 25.0%
! TATCTATCTACTGATACATT+TGG - chr2_1:35639377-35639396 Msa0206370:intron 25.0%
!! TTTTAAATCAAGTCCTTGAT+TGG + chr2_1:35639540-35639559 None:intergenic 25.0%
! TGAATGTAATAATACCAGAT+AGG + chr2_1:35639574-35639593 None:intergenic 25.0%
! ACTTTCATGATTGCTTTGTT+AGG - chr2_1:35638962-35638981 Msa0206370:CDS 30.0%
! CTTTCATGATTGCTTTGTTA+GGG - chr2_1:35638963-35638982 Msa0206370:CDS 30.0%
!!! ATTTTGATTTAGGGATGTGA+TGG - chr2_1:35639071-35639090 Msa0206370:CDS 30.0%
ATAGAATTGAGTACTTACTG+TGG + chr2_1:35639270-35639289 None:intergenic 30.0%
TTAAATAAGCCAATCCAAAC+AGG + chr2_1:35639309-35639328 None:intergenic 30.0%
! ATTTGGTGATTTGTGATTTC+AGG - chr2_1:35639394-35639413 Msa0206370:intron 30.0%
! TTTGGTGATTTGTGATTTCA+GGG - chr2_1:35639395-35639414 Msa0206370:intron 30.0%
ATGTAATAATACCAGATAGG+AGG + chr2_1:35639571-35639590 None:intergenic 30.0%
!! GTTGGTTTGTTGAGTTCAAA+AGG + chr2_1:35639103-35639122 None:intergenic 35.0%
!!! GAGCATTTTTTTCAGCTTGT+TGG + chr2_1:35639121-35639140 None:intergenic 35.0%
AAGCCTCTAACAGTAAGATT+TGG + chr2_1:35639146-35639165 None:intergenic 35.0%
CCTCTAACAGTAAGATTTGG+AGG + chr2_1:35639143-35639162 None:intergenic 40.0%
CCTCCAAATCTTACTGTTAG+AGG - chr2_1:35639140-35639159 Msa0206370:CDS 40.0%
TTAACAGACTAAGGCCTGTT+TGG - chr2_1:35639292-35639311 Msa0206370:intron 40.0%
CCTGTTGGAACTTTCCAATA+TGG + chr2_1:35639425-35639444 None:intergenic 40.0%
CCATATTGGAAAGTTCCAAC+AGG - chr2_1:35639422-35639441 Msa0206370:intron 40.0%
GAAAGTTCCAACAGGTAGAA+GGG - chr2_1:35639430-35639449 Msa0206370:intron 40.0%
TGGAGTCGTATCGAATTTGT+TGG - chr2_1:35639454-35639473 Msa0206370:CDS 40.0%
ATTGGCAAAGAGAGTTTGGA+GGG + chr2_1:35639522-35639541 None:intergenic 40.0%
CTTGATTGGCAAAGAGAGTT+TGG + chr2_1:35639526-35639545 None:intergenic 40.0%
CAAACTCTCTTTGCCAATCA+AGG - chr2_1:35639524-35639543 Msa0206370:intron 40.0%
AAAGACTTAGTCCTCCTATC+TGG - chr2_1:35639557-35639576 Msa0206370:intron 40.0%
!! GACGAAAGTGCTTAATGCTA+AGG + chr2_1:35639604-35639623 None:intergenic 40.0%
CAGCACAAGAAACAACACCA+GGG + chr2_1:35639211-35639230 None:intergenic 45.0%
TCAGCACAAGAAACAACACC+AGG + chr2_1:35639212-35639231 None:intergenic 45.0%
AGACTAAGGCCTGTTTGGAT+TGG - chr2_1:35639297-35639316 Msa0206370:intron 45.0%
! GGTGATTTGTGATTTCAGGG+TGG - chr2_1:35639398-35639417 Msa0206370:intron 45.0%
GATTTCAGGGTGGTCCATAT+TGG - chr2_1:35639408-35639427 Msa0206370:intron 45.0%
GGAAAGTTCCAACAGGTAGA+AGG - chr2_1:35639429-35639448 Msa0206370:intron 45.0%
GTGAAGTTGGAAAATGGAGC+AGG + chr2_1:35639497-35639516 None:intergenic 45.0%
AGGGTGGTGAAGTTGGAAAA+TGG + chr2_1:35639503-35639522 None:intergenic 45.0%
GATTGGCAAAGAGAGTTTGG+AGG + chr2_1:35639523-35639542 None:intergenic 45.0%
! CAGGGCATTCAGCTTCAACA+AGG + chr2_1:35639193-35639212 None:intergenic 50.0%
CTTGTTGAAGCTGAATGCCC+TGG - chr2_1:35639191-35639210 Msa0206370:intron 50.0%
TGTGGCTGCAATAGAGTCTC+TGG + chr2_1:35639252-35639271 None:intergenic 50.0%
GTTCCAACAGGTAGAAGGGA+TGG - chr2_1:35639434-35639453 Msa0206370:intron 50.0%
ACTCCATCCCTTCTACCTGT+TGG + chr2_1:35639440-35639459 None:intergenic 50.0%
AGTTTGGAGGGTGGTGAAGT+TGG + chr2_1:35639510-35639529 None:intergenic 50.0%
GGCAAAGAGAGTTTGGAGGG+TGG + chr2_1:35639519-35639538 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 35638958 35639634 35638958 ID=Msa0206370;Name=Msa0206370
chr2_1 mRNA 35638958 35639634 35638958 ID=Msa0206370-mRNA-1;Parent=Msa0206370;Name=Msa0206370-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|1|0.5|0.66|3|0|105
chr2_1 exon 35639608 35639634 35639608 ID=Msa0206370-mRNA-1:exon:11731;Parent=Msa0206370-mRNA-1
chr2_1 exon 35639438 35639509 35639438 ID=Msa0206370-mRNA-1:exon:11730;Parent=Msa0206370-mRNA-1
chr2_1 exon 35638958 35639176 35638958 ID=Msa0206370-mRNA-1:exon:11729;Parent=Msa0206370-mRNA-1
chr2_1 CDS 35639608 35639634 35639608 ID=Msa0206370-mRNA-1:cds;Parent=Msa0206370-mRNA-1
chr2_1 CDS 35639438 35639509 35639438 ID=Msa0206370-mRNA-1:cds;Parent=Msa0206370-mRNA-1
chr2_1 CDS 35638958 35639176 35638958 ID=Msa0206370-mRNA-1:cds;Parent=Msa0206370-mRNA-1
Gene Sequence

>Msa0206370

ATGCACTTTCATGATTGCTTTGTTAGGGGATGTGATGGATCAGTCCTTTTGAACTCAACAAACCAACAAGCTGAAAAAAATGCTCCTCCAAATCTTACTGGTGGTCCATATTGGAAAGTTCCAACAGGTAGAAGGGATGGAGTCGTATCGAATTTGTTGGAAGCAAATCAAAACATTCCTGCTCCATTTTCCAACTTCACCACCCTCCAAACTCTCTTTGCCAATCAAGGACTTGATTTAAAAGACTTAGTCCTCCTATCTGGTATTATTACATTCAACAATTTCCTTAGCATTAAGCACTTTCGTCGTGCACGCTAA
Protein sequence

>Msa0206370

MHFHDCFVRGCDGSVLLNSTNQQAEKNAPPNLTGGPYWKVPTGRRDGVVSNLLEANQNIPAPFSNFTTLQTLFANQGLDLKDLVLLSGIITFNNFLSIKHFRRAR*