AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1254190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1254190 MtrunA17_Chr8g0370711 92.771 83 6 0 17 99 85 167 9.04e-53 168
Msa1254190 MtrunA17_Chr8g0370721 90.361 83 8 0 17 99 85 167 4.96e-52 167
Msa1254190 MtrunA17_Chr3g0145171 72.449 98 24 1 2 99 73 167 7.69e-43 143
Msa1254190 MtrunA17_Chr3g0145181 70.588 85 22 2 17 99 84 167 1.05e-34 122
Msa1254190 MtrunA17_Chr3g0145201 70.588 85 22 2 17 99 719 802 1.22e-33 122
Msa1254190 MtrunA17_Chr4g0064781 54.639 97 41 1 2 98 67 160 1.10e-30 111
Msa1254190 MtrunA17_Chr7g0232161 37.736 106 52 1 16 107 90 195 3.00e-23 91.3
Msa1254190 MtrunA17_Chr7g0239071 42.857 84 48 0 12 95 26 109 8.32e-23 89.7
Msa1254190 MtrunA17_Chr8g0375641 36.634 101 64 0 2 102 72 172 3.05e-22 85.9
Msa1254190 MtrunA17_Chr8g0375661 35.354 99 64 0 2 100 72 170 4.06e-21 82.4
Msa1254190 MtrunA17_Chr7g0239821 42.500 80 46 0 16 95 94 173 6.24e-21 85.5
Msa1254190 MtrunA17_Chr7g0239111 43.590 78 44 0 16 93 85 162 1.52e-20 84.3
Msa1254190 MtrunA17_Chr7g0239101 41.250 80 47 0 16 95 85 164 4.43e-20 83.2
Msa1254190 MtrunA17_Chr7g0239121 36.170 94 59 1 16 109 81 173 5.03e-20 82.8
Msa1254190 MtrunA17_Chr2g0296371 38.298 94 58 0 2 95 70 163 7.40e-20 82.4
Msa1254190 MtrunA17_Chr8g0375671 36.735 98 62 0 2 99 72 169 8.55e-20 82.4
Msa1254190 MtrunA17_Chr5g0398291 35.870 92 57 1 9 98 74 165 6.66e-19 79.7
Msa1254190 MtrunA17_Chr3g0087031 39.796 98 57 1 2 99 78 173 2.22e-18 78.6
Msa1254190 MtrunA17_Chr8g0375601 39.286 84 51 0 16 99 81 164 5.88e-18 77.4
Msa1254190 MtrunA17_Chr8g0375701 40.816 98 57 1 2 99 71 167 7.00e-18 77.0
Msa1254190 MtrunA17_Chr8g0375681 40.964 83 49 0 17 99 15 97 1.27e-17 75.9
Msa1254190 MtrunA17_Chr3g0113641 39.080 87 53 0 16 102 84 170 1.04e-16 73.9
Msa1254190 MtrunA17_Chr3g0114871 32.673 101 66 1 1 99 55 155 2.04e-16 72.4
Msa1254190 MtrunA17_Chr5g0421011 40.260 77 46 0 16 92 77 153 2.46e-16 72.8
Msa1254190 MtrunA17_Chr5g0423251 40.476 84 50 0 16 99 77 160 4.55e-16 72.0
Msa1254190 MtrunA17_Chr4g0006371 39.286 84 51 0 16 99 96 179 1.20e-15 70.9
Msa1254190 MtrunA17_Chr2g0314401 36.782 87 55 0 16 102 83 169 1.66e-15 70.5
Msa1254190 MtrunA17_Chr2g0314391 39.286 84 51 0 16 99 102 185 3.28e-15 69.7
Msa1254190 MtrunA17_Chr7g0242551 36.905 84 53 0 16 99 88 171 3.28e-15 69.7
Msa1254190 MtrunA17_Chr2g0314371 39.506 81 49 0 16 96 84 164 3.85e-15 69.3
Msa1254190 MtrunA17_Chr5g0420981 35.714 84 54 0 16 99 84 167 2.27e-14 67.4
Msa1254190 MtrunA17_Chr5g0437181 35.632 87 56 0 16 102 83 169 2.48e-14 67.0
Msa1254190 MtrunA17_Chr5g0421041 36.905 84 53 0 16 99 75 158 2.66e-14 67.0
Msa1254190 MtrunA17_Chr2g0314381 35.714 84 54 0 16 99 109 192 3.09e-14 67.0
Msa1254190 MtrunA17_Chr5g0424201 31.313 99 66 1 3 99 59 157 3.93e-14 66.6
Msa1254190 MtrunA17_Chr5g0423201 37.647 85 52 1 16 99 77 161 5.47e-14 66.2
Msa1254190 MtrunA17_Chr5g0421101 32.632 95 63 1 6 99 66 160 5.85e-14 66.2
Msa1254190 MtrunA17_Chr5g0423221 33.684 95 62 1 6 99 90 184 2.12e-13 64.7
Msa1254190 MtrunA17_Chr5g0420941 38.095 84 52 0 16 99 75 158 3.15e-13 63.9
Msa1254190 MtrunA17_Chr3g0114861 30.000 100 65 2 2 99 56 152 4.81e-13 63.5
Msa1254190 MtrunA17_Chr8g0365241 31.579 95 64 1 6 99 77 171 5.43e-13 63.5
Msa1254190 MtrunA17_Chr5g0423191 34.524 84 55 0 16 99 77 160 1.11e-12 62.4
Msa1254190 MtrunA17_Chr8g0375571 34.524 84 55 0 16 99 79 162 1.64e-12 62.0
Msa1254190 MtrunA17_Chr5g0421091 35.632 87 56 0 16 102 75 161 5.63e-12 60.5
Msa1254190 MtrunA17_Chr5g0424211 29.703 101 67 1 3 99 57 157 1.06e-11 59.7
Msa1254190 MtrunA17_Chr5g0420891 32.353 102 65 2 2 102 65 163 1.35e-11 57.8
Msa1254190 MtrunA17_Chr5g0420951 32.143 84 57 0 16 99 84 167 3.32e-11 58.5
Msa1254190 MtrunA17_Chr7g0239091 32.911 79 46 1 16 94 190 261 8.62e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1254190 AT1G49390.1 53.608 97 45 0 2 98 64 160 1.97e-35 124
Msa1254190 AT1G49390.2 59.259 81 33 0 18 98 1 81 2.73e-33 116
Msa1254190 AT5G20550.1 50.000 98 49 0 2 99 64 161 6.60e-33 117
Msa1254190 AT5G54000.2 50.000 98 49 0 2 99 65 162 7.57e-33 117
Msa1254190 AT5G20400.1 48.980 98 50 0 2 99 64 161 1.57e-32 116
Msa1254190 AT5G54000.1 53.659 82 38 0 18 99 1 82 3.60e-30 108
Msa1254190 AT3G21420.1 50.000 80 40 0 16 95 89 168 1.09e-20 85.1
Msa1254190 AT1G17020.1 45.238 84 46 0 16 99 85 168 1.67e-19 82.0
Msa1254190 AT2G38240.1 42.857 84 48 0 16 99 77 160 1.35e-18 79.3
Msa1254190 AT4G25300.1 39.796 98 59 0 2 99 70 167 1.77e-18 79.0
Msa1254190 AT1G17010.1 41.667 84 49 0 16 99 86 169 2.86e-17 75.9
Msa1254190 AT4G22880.1 34.831 89 56 1 12 98 77 165 2.40e-16 73.2
Msa1254190 AT4G22880.2 34.831 89 56 1 12 98 77 165 2.40e-16 73.2
Msa1254190 AT4G22880.3 34.831 89 56 1 12 98 77 165 2.40e-16 73.2
Msa1254190 AT1G78550.2 41.176 85 50 0 15 99 6 90 5.48e-16 71.6
Msa1254190 AT4G25310.2 41.667 84 46 1 16 99 84 164 7.81e-16 71.6
Msa1254190 AT4G25310.1 41.667 84 46 1 16 99 84 164 9.79e-16 71.6
Msa1254190 AT1G78550.1 41.667 84 49 0 16 99 85 168 1.71e-15 70.9
Msa1254190 AT5G08640.2 33.721 86 55 1 16 99 71 156 5.47e-15 69.3
Msa1254190 AT5G08640.1 33.721 86 55 1 16 99 71 156 5.47e-15 69.3
Msa1254190 AT3G55970.2 33.333 84 56 0 16 99 86 169 5.14e-14 66.2
Msa1254190 AT3G11180.2 38.095 84 52 0 16 99 125 208 1.01e-13 65.9
Msa1254190 AT3G55970.1 33.333 84 56 0 16 99 86 169 1.02e-13 65.9
Msa1254190 AT3G11180.1 38.095 84 52 0 16 99 125 208 1.15e-13 65.9
Msa1254190 AT5G05600.2 34.524 84 55 0 16 99 96 179 5.11e-13 63.5
Msa1254190 AT5G05600.1 34.524 84 55 0 16 99 96 179 6.13e-13 63.5
Msa1254190 AT5G63600.2 30.303 99 65 2 1 99 46 140 9.90e-13 63.2
Msa1254190 AT5G63600.1 30.303 99 65 2 1 99 46 140 1.01e-12 62.8
Msa1254190 AT5G63580.2 31.111 90 58 2 12 99 43 130 1.41e-12 62.0
Msa1254190 AT5G63580.1 31.111 90 58 2 12 99 43 130 1.58e-12 62.0
Msa1254190 AT5G63590.1 30.435 92 62 1 9 98 35 126 5.27e-12 60.8
Msa1254190 AT5G63595.1 32.558 86 50 2 16 99 53 132 3.24e-11 58.5
Msa1254190 AT5G43935.1 31.765 85 53 2 16 98 47 128 3.82e-11 58.5

Find 15 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAATTCCTTTGATCTTC+AGG 0.217680 8_2:-52224350 None:intergenic
CAAAACAATATTGAAGGATA+TGG 0.284911 8_2:+52224260 Msa1254190:CDS
CAGAAAATCAAATGCTTGAT+TGG 0.314111 8_2:+52224300 Msa1254190:CDS
ATCAAAGGAATTTCAAACTT+TGG 0.350874 8_2:+52224357 Msa1254190:CDS
GAATTTATACCTGTAATCAA+TGG 0.398773 8_2:-52224390 None:intergenic
AATTTATACCTGTAATCAAT+GGG 0.465506 8_2:-52224389 None:intergenic
AGGGAACAAAACAATATTGA+AGG 0.499241 8_2:+52224254 Msa1254190:CDS
CCTGAATAGCTGAAAACAGT+TGG 0.540739 8_2:-52224133 None:intergenic
GCTCGTTTCTTGACAAAGTG+AGG 0.541459 8_2:+52224177 Msa1254190:CDS
CTGAATAGCTGAAAACAGTT+GGG 0.543716 8_2:-52224132 None:intergenic
CTCGTTTCTTGACAAAGTGA+GGG 0.576302 8_2:+52224178 Msa1254190:CDS
GAAACGAGCTTGTCATCCCA+TGG 0.585363 8_2:-52224163 None:intergenic
GCTATTCAGGTGATAAACCA+TGG 0.588359 8_2:+52224146 Msa1254190:CDS
AGGTACATCCTGAAGATCAA+AGG 0.594954 8_2:+52224342 Msa1254190:CDS
CTATTCAGGTGATAAACCAT+GGG 0.622367 8_2:+52224147 Msa1254190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTATACCTGTAATCAAT+GGG - chr8_2:52224392-52224411 None:intergenic 20.0%
!!! TATTTTTGCTTTTCTTCCTT+TGG - chr8_2:52224230-52224249 None:intergenic 25.0%
! AAGAAAAGCAAAAATATGCA+AGG + chr8_2:52224234-52224253 Msa1254190:CDS 25.0%
! AGAAAAGCAAAAATATGCAA+GGG + chr8_2:52224235-52224254 Msa1254190:CDS 25.0%
! CAAAACAATATTGAAGGATA+TGG + chr8_2:52224260-52224279 Msa1254190:CDS 25.0%
! ATCAAAGGAATTTCAAACTT+TGG + chr8_2:52224357-52224376 Msa1254190:CDS 25.0%
! GAATTTATACCTGTAATCAA+TGG - chr8_2:52224393-52224412 None:intergenic 25.0%
!!! GCAATTTTTTGAACTTCCAA+AGG + chr8_2:52224211-52224230 Msa1254190:CDS 30.0%
AGGGAACAAAACAATATTGA+AGG + chr8_2:52224254-52224273 Msa1254190:CDS 30.0%
CAGAAAATCAAATGCTTGAT+TGG + chr8_2:52224300-52224319 Msa1254190:CDS 30.0%
!! GTGTGACAGAATATTTTTGA+AGG + chr8_2:52224322-52224341 Msa1254190:CDS 30.0%
TTGAAATTCCTTTGATCTTC+AGG - chr8_2:52224353-52224372 None:intergenic 30.0%
CTGAATAGCTGAAAACAGTT+GGG - chr8_2:52224135-52224154 None:intergenic 35.0%
CTATTCAGGTGATAAACCAT+GGG + chr8_2:52224147-52224166 Msa1254190:CDS 35.0%
!! CTGTAATCAATGGGTTTTTG+GGG - chr8_2:52224383-52224402 None:intergenic 35.0%
!! CCTGTAATCAATGGGTTTTT+GGG - chr8_2:52224384-52224403 None:intergenic 35.0%
!! ACCTGTAATCAATGGGTTTT+TGG - chr8_2:52224385-52224404 None:intergenic 35.0%
CCTGAATAGCTGAAAACAGT+TGG - chr8_2:52224136-52224155 None:intergenic 40.0%
! CCAACTGTTTTCAGCTATTC+AGG + chr8_2:52224133-52224152 Msa1254190:CDS 40.0%
GCTATTCAGGTGATAAACCA+TGG + chr8_2:52224146-52224165 Msa1254190:CDS 40.0%
CTCGTTTCTTGACAAAGTGA+GGG + chr8_2:52224178-52224197 Msa1254190:CDS 40.0%
AGGTACATCCTGAAGATCAA+AGG + chr8_2:52224342-52224361 Msa1254190:CDS 40.0%
! CCCAAAAACCCATTGATTAC+AGG + chr8_2:52224381-52224400 Msa1254190:CDS 40.0%
GCTCGTTTCTTGACAAAGTG+AGG + chr8_2:52224177-52224196 Msa1254190:CDS 45.0%
GAAACGAGCTTGTCATCCCA+TGG - chr8_2:52224166-52224185 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 52224107 52224436 52224107 ID=Msa1254190;Name=Msa1254190
chr8_2 mRNA 52224107 52224436 52224107 ID=Msa1254190-mRNA-1;Parent=Msa1254190;Name=Msa1254190-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|109
chr8_2 exon 52224107 52224436 52224107 ID=Msa1254190-mRNA-1:exon:15982;Parent=Msa1254190-mRNA-1
chr8_2 CDS 52224107 52224436 52224107 ID=Msa1254190-mRNA-1:cds;Parent=Msa1254190-mRNA-1
Gene Sequence

>Msa1254190

ATGTTAAACAAAGCATTTTCACATGCCCAACTGTTTTCAGCTATTCAGGTGATAAACCATGGGATGACAAGCTCGTTTCTTGACAAAGTGAGGGAAGTTTCAAAGCAATTTTTTGAACTTCCAAAGGAAGAAAAGCAAAAATATGCAAGGGAACAAAACAATATTGAAGGATATGGAAATGATACAATATATTCAGAAAATCAAATGCTTGATTGGTGTGACAGAATATTTTTGAAGGTACATCCTGAAGATCAAAGGAATTTCAAACTTTGGCCCCAAAAACCCATTGATTACAGGTATAAATTCTTATCGTCACTAAGTTCTCAATAA
Protein sequence

>Msa1254190

MLNKAFSHAQLFSAIQVINHGMTSSFLDKVREVSKQFFELPKEEKQKYAREQNNIEGYGNDTIYSENQMLDWCDRIFLKVHPEDQRNFKLWPQKPIDYRYKFLSSLSSQ*