AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1435900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1435900 MtrunA17_Chr5g0446491 95.699 186 5 2 1 185 1 184 1.06e-129 361
Msa1435900 MtrunA17_Chr3g0102351 75.258 194 35 5 1 185 1 190 1.73e-84 247
Msa1435900 MtrunA17_Chr2g0290491 83.051 118 14 1 1 118 1 112 3.54e-67 202
Msa1435900 MtrunA17_Chr8g0382931 74.074 135 31 2 10 140 13 147 1.20e-64 197
Msa1435900 MtrunA17_Chr7g0263601 81.731 104 19 0 22 125 25 128 1.03e-60 186
Msa1435900 MtrunA17_Chr8g0384451 85.567 97 14 0 22 118 39 135 5.39e-59 183
Msa1435900 MtrunA17_Chr1g0185911 67.424 132 35 2 1 126 1 130 7.67e-59 181
Msa1435900 MtrunA17_Chr4g0076321 74.167 120 27 2 1 120 1 116 9.13e-59 180
Msa1435900 MtrunA17_Chr4g0076381 66.990 103 34 0 16 118 51 153 3.01e-50 162
Msa1435900 MtrunA17_Chr1g0195851 71.875 96 27 0 22 117 35 130 8.80e-50 159
Msa1435900 MtrunA17_Chr1g0165041 61.818 110 42 0 22 131 5 114 2.78e-47 153
Msa1435900 MtrunA17_Chr2g0296321 60.526 114 35 1 4 117 57 160 9.65e-47 153
Msa1435900 MtrunA17_Chr4g0067091 61.261 111 34 1 4 114 12 113 8.01e-46 150
Msa1435900 MtrunA17_Chr1g0191981 53.279 122 48 2 23 135 4 125 7.67e-40 132
Msa1435900 MtrunA17_Chr1g0159271 53.750 80 37 0 37 116 1 80 1.03e-24 92.8
Msa1435900 MtrunA17_Chr5g0446601 47.368 95 47 1 20 111 18 112 1.33e-22 89.7
Msa1435900 MtrunA17_Chr1g0159291 43.421 76 43 0 28 103 7 82 2.38e-19 78.6
Msa1435900 MtrunA17_Chr1g0158951 45.349 86 43 1 53 134 19 104 3.57e-19 78.6
Msa1435900 MtrunA17_Chr2g0307551 36.250 80 51 0 24 103 12 91 5.14e-16 71.6
Msa1435900 MtrunA17_Chr4g0062271 36.250 80 51 0 24 103 12 91 8.98e-16 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1435900 AT4G14540.1 86.777 121 14 1 1 121 1 119 2.13e-74 221
Msa1435900 AT5G47640.1 88.889 108 12 0 19 126 23 130 2.09e-67 204
Msa1435900 AT2G38880.3 70.732 123 36 0 4 126 2 124 3.84e-60 184
Msa1435900 AT2G38880.2 70.732 123 36 0 4 126 2 124 5.39e-60 184
Msa1435900 AT2G38880.1 70.732 123 36 0 4 126 2 124 5.39e-60 184
Msa1435900 AT2G38880.5 70.732 123 36 0 4 126 2 124 5.39e-60 184
Msa1435900 AT3G53340.5 59.477 153 58 2 19 170 25 174 1.65e-59 184
Msa1435900 AT3G53340.1 59.477 153 58 2 19 170 25 174 1.65e-59 184
Msa1435900 AT2G37060.2 63.087 149 45 2 6 154 15 153 3.63e-59 182
Msa1435900 AT2G37060.3 63.087 149 45 2 6 154 15 153 3.63e-59 182
Msa1435900 AT2G37060.1 63.087 149 45 2 6 154 15 153 3.63e-59 182
Msa1435900 AT2G38880.4 75.455 110 27 0 4 113 2 111 2.97e-57 176
Msa1435900 AT2G38880.7 69.919 123 35 1 4 126 2 122 5.34e-57 176
Msa1435900 AT2G38880.11 75.455 110 27 0 4 113 2 111 1.13e-56 176
Msa1435900 AT2G38880.8 75.455 110 27 0 4 113 2 111 1.13e-56 176
Msa1435900 AT2G38880.9 75.455 110 27 0 4 113 2 111 1.29e-56 176
Msa1435900 AT2G38880.10 75.455 110 27 0 4 113 2 111 1.29e-56 176
Msa1435900 AT2G38880.6 75.455 110 27 0 4 113 2 111 1.29e-56 176
Msa1435900 AT3G53340.4 80.000 95 19 0 19 113 25 119 2.05e-56 174
Msa1435900 AT3G53340.3 80.208 96 19 0 19 114 25 120 4.49e-56 174
Msa1435900 AT3G53340.2 80.208 96 19 0 19 114 25 120 4.49e-56 174
Msa1435900 AT2G13570.1 78.218 101 22 0 22 122 35 135 4.49e-56 176
Msa1435900 AT5G47670.2 50.909 165 74 3 6 163 12 176 1.23e-54 172
Msa1435900 AT5G47670.1 49.693 163 74 2 6 160 41 203 3.43e-54 172
Msa1435900 AT5G47670.3 49.693 163 74 2 6 160 41 203 3.43e-54 172
Msa1435900 AT2G47810.1 72.917 96 26 0 22 117 50 145 8.36e-50 159
Msa1435900 AT1G21970.1 63.366 101 37 0 22 122 58 158 1.07e-46 153
Msa1435900 AT1G09030.1 60.417 96 38 0 23 118 3 98 7.27e-42 137
Msa1435900 AT5G08190.2 38.272 81 50 0 23 103 11 91 7.63e-17 74.3
Msa1435900 AT5G08190.1 38.272 81 50 0 23 103 11 91 8.05e-17 74.3
Msa1435900 AT5G23090.4 37.179 78 49 0 24 101 12 89 2.23e-16 72.8
Msa1435900 AT5G23090.5 37.179 78 49 0 24 101 12 89 2.43e-16 72.8
Msa1435900 AT5G23090.2 37.179 78 49 0 24 101 12 89 2.43e-16 72.8
Msa1435900 AT5G23090.1 37.179 78 49 0 24 101 12 89 2.43e-16 72.8
Msa1435900 AT5G23090.3 35.938 64 41 0 40 103 15 78 5.60e-12 60.8

Find 47 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCGCATTAGTTTCAGCATT+AGG 0.327218 tig0027814:-31895 Msa1435900:intergenic
TTTCTCTCTCTGACACTTAT+CGG 0.341007 tig0027814:-31584 Msa1435900:intergenic
TCCTTCTTCTTCTTCGTCTT+CGG 0.344056 tig0027814:+31756 Msa1435900:CDS
AGTTTCAGCATTAGGATAAC+CGG 0.355328 tig0027814:-31887 Msa1435900:intergenic
AATAATGAAGAAGGCGTTAC+CGG 0.357624 tig0027814:+31477 Msa1435900:CDS
ATTCTGCTCACGTTTGCTAT+TGG 0.361435 tig0027814:-31457 Msa1435900:intergenic
CGGTGATAACTCGCTGTTCC+CGG 0.363693 tig0027814:-31413 Msa1435900:intergenic
CAGGGACACGTGTACGGTTC+TGG 0.366578 tig0027814:+31838 Msa1435900:CDS
AACTCGCTGTTCCCGGCGTT+CGG 0.373131 tig0027814:-31406 Msa1435900:intergenic
GGCTGATTCCGACAATGAAT+CGG 0.393443 tig0027814:+31375 Msa1435900:CDS
GCAGCATCAGCATCAGCATC+AGG 0.402922 tig0027814:+31819 Msa1435900:CDS
TCAACGGCGACGATCTACTT+TGG 0.416392 tig0027814:+31617 Msa1435900:CDS
CGGGAGGAGCACCGAACGCC+GGG 0.420650 tig0027814:+31395 Msa1435900:CDS
ACTAATAAGCTTGTTCTACC+TGG 0.429128 tig0027814:-31923 Msa1435900:intergenic
CGTTGAAGATAAATCTTCAA+TGG 0.432633 tig0027814:-31676 Msa1435900:intergenic
CATCAAGTGCCTGGTGGGCC+CGG 0.439513 tig0027814:+31868 Msa1435900:CDS
AGACGCGAAGGAAACAGTTC+AGG 0.459480 tig0027814:+31519 Msa1435900:CDS
CAACGGCGACGATCTACTTT+GGG 0.462526 tig0027814:+31618 Msa1435900:CDS
CTTTGGGCGATGACTACGTT+AGG 0.467469 tig0027814:+31634 Msa1435900:CDS
TGCTCCTCCCGATTCATTGT+CGG 0.482065 tig0027814:-31383 Msa1435900:intergenic
CGTTTGCTATTGGTAAGAAT+CGG 0.499147 tig0027814:-31447 Msa1435900:intergenic
GCTGATTCCGACAATGAATC+GGG 0.501404 tig0027814:+31376 Msa1435900:CDS
ACACTTATCGGAAGCTTCGC+CGG 0.521889 tig0027814:-31572 Msa1435900:intergenic
ATCTTTATCACGTGCAGCAA+CGG 0.524172 tig0027814:-31725 Msa1435900:intergenic
ACCGAAGACGAAGAAGAAGA+AGG 0.526792 tig0027814:-31757 Msa1435900:intergenic
TTAGGATAACCGGGCCCACC+AGG 0.536533 tig0027814:-31877 Msa1435900:intergenic
TATGGTGCTCCTCCTCAAGT+TGG 0.540598 tig0027814:+31787 Msa1435900:CDS
CCTAATGCTGAAACTAATGC+GGG 0.543861 tig0027814:+31895 Msa1435900:CDS
TCGGGAGGAGCACCGAACGC+CGG 0.558380 tig0027814:+31394 Msa1435900:CDS
CGTGAGCAGAATAATGAAGA+AGG 0.569587 tig0027814:+31468 Msa1435900:CDS
CAGCATCAGGGACACGTGTA+CGG 0.574817 tig0027814:+31832 Msa1435900:CDS
AACAGTTCAGGAATGTGTAT+CGG 0.575632 tig0027814:+31531 Msa1435900:CDS
GTTTCAGCATTAGGATAACC+GGG 0.577286 tig0027814:-31886 Msa1435900:intergenic
TCCTAATGCTGAAACTAATG+CGG 0.577317 tig0027814:+31894 Msa1435900:CDS
GAGAAACGAAAGACGATCAA+CGG 0.592030 tig0027814:+31601 Msa1435900:CDS
CTAATAAGCTTGTTCTACCT+GGG 0.593198 tig0027814:-31922 Msa1435900:intergenic
AAACTAATGCGGGTAGACCC+AGG 0.595538 tig0027814:+31905 Msa1435900:CDS
CAGCATCAGCATCAGCATCA+GGG 0.606009 tig0027814:+31820 Msa1435900:CDS
GAGTTCATCAGCTTCATCAC+CGG 0.608726 tig0027814:+31553 Msa1435900:CDS
TGCATGATCATTCCAACTTG+AGG 0.613313 tig0027814:-31799 Msa1435900:intergenic
GGACACGTGTACGGTTCTGG+TGG 0.628725 tig0027814:+31841 Msa1435900:CDS
GAAGATCTCGAAAGACGCGA+AGG 0.642019 tig0027814:+31507 Msa1435900:CDS
AAGAATCGGTCTTGTTCTCG+CGG 0.644860 tig0027814:-31433 Msa1435900:intergenic
CAACGATTCAGAGAGATCGA+AGG 0.645752 tig0027814:+31694 Msa1435900:CDS
ATGATCATTCCAACTTGAGG+AGG 0.658950 tig0027814:-31796 Msa1435900:intergenic
GTTGCTGCACGTGATAAAGA+TGG 0.679086 tig0027814:+31727 Msa1435900:CDS
GATTCCGACAATGAATCGGG+AGG 0.690680 tig0027814:+31379 Msa1435900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CGTTGAAGATAAATCTTCAA+TGG - tig0027814:31679-31698 Msa1435900:intergenic 30.0%
!! CGTTTGCTATTGGTAAGAAT+CGG - tig0027814:31450-31469 Msa1435900:intergenic 35.0%
!! AATAATGAAGAAGGCGTTAC+CGG + tig0027814:31477-31496 Msa1435900:CDS 35.0%
AACAGTTCAGGAATGTGTAT+CGG + tig0027814:31531-31550 Msa1435900:CDS 35.0%
TTTCTCTCTCTGACACTTAT+CGG - tig0027814:31587-31606 Msa1435900:intergenic 35.0%
AGTTTCAGCATTAGGATAAC+CGG - tig0027814:31890-31909 Msa1435900:intergenic 35.0%
TCCTAATGCTGAAACTAATG+CGG + tig0027814:31894-31913 Msa1435900:CDS 35.0%
!! ATTCTGCTCACGTTTGCTAT+TGG - tig0027814:31460-31479 Msa1435900:intergenic 40.0%
CGTGAGCAGAATAATGAAGA+AGG + tig0027814:31468-31487 Msa1435900:CDS 40.0%
GAGAAACGAAAGACGATCAA+CGG + tig0027814:31601-31620 Msa1435900:CDS 40.0%
ATCTTTATCACGTGCAGCAA+CGG - tig0027814:31728-31747 Msa1435900:intergenic 40.0%
TCCTTCTTCTTCTTCGTCTT+CGG + tig0027814:31756-31775 Msa1435900:CDS 40.0%
! TCGTCTTCGGTTTTCGATTA+TGG + tig0027814:31769-31788 Msa1435900:CDS 40.0%
ATGATCATTCCAACTTGAGG+AGG - tig0027814:31799-31818 Msa1435900:intergenic 40.0%
TGCATGATCATTCCAACTTG+AGG - tig0027814:31802-31821 Msa1435900:intergenic 40.0%
GTTTCAGCATTAGGATAACC+GGG - tig0027814:31889-31908 Msa1435900:intergenic 40.0%
CCTAATGCTGAAACTAATGC+GGG + tig0027814:31895-31914 Msa1435900:CDS 40.0%
! GGCTGATTCCGACAATGAAT+CGG + tig0027814:31375-31394 Msa1435900:CDS 45.0%
! GCTGATTCCGACAATGAATC+GGG + tig0027814:31376-31395 Msa1435900:CDS 45.0%
!! AAGAATCGGTCTTGTTCTCG+CGG - tig0027814:31436-31455 Msa1435900:intergenic 45.0%
GAGTTCATCAGCTTCATCAC+CGG + tig0027814:31553-31572 Msa1435900:CDS 45.0%
CAACGATTCAGAGAGATCGA+AGG + tig0027814:31694-31713 Msa1435900:CDS 45.0%
GTTGCTGCACGTGATAAAGA+TGG + tig0027814:31727-31746 Msa1435900:CDS 45.0%
ACCGAAGACGAAGAAGAAGA+AGG - tig0027814:31760-31779 Msa1435900:intergenic 45.0%
! GTTTTCATCAAGTGCCTGGT+GGG + tig0027814:31863-31882 Msa1435900:CDS 45.0%
! CCCGCATTAGTTTCAGCATT+AGG - tig0027814:31898-31917 Msa1435900:intergenic 45.0%
GATTCCGACAATGAATCGGG+AGG + tig0027814:31379-31398 Msa1435900:CDS 50.0%
TGCTCCTCCCGATTCATTGT+CGG - tig0027814:31386-31405 Msa1435900:intergenic 50.0%
GAAGATCTCGAAAGACGCGA+AGG + tig0027814:31507-31526 Msa1435900:CDS 50.0%
AGACGCGAAGGAAACAGTTC+AGG + tig0027814:31519-31538 Msa1435900:CDS 50.0%
ACACTTATCGGAAGCTTCGC+CGG - tig0027814:31575-31594 Msa1435900:intergenic 50.0%
TCAACGGCGACGATCTACTT+TGG + tig0027814:31617-31636 Msa1435900:CDS 50.0%
CAACGGCGACGATCTACTTT+GGG + tig0027814:31618-31637 Msa1435900:CDS 50.0%
CTTTGGGCGATGACTACGTT+AGG + tig0027814:31634-31653 Msa1435900:CDS 50.0%
TATGGTGCTCCTCCTCAAGT+TGG + tig0027814:31787-31806 Msa1435900:CDS 50.0%
CAGCATCAGCATCAGCATCA+GGG + tig0027814:31820-31839 Msa1435900:CDS 50.0%
! GGTGGTTTTCATCAAGTGCC+TGG + tig0027814:31859-31878 Msa1435900:CDS 50.0%
! GGTTTTCATCAAGTGCCTGG+TGG + tig0027814:31862-31881 Msa1435900:CDS 50.0%
AAACTAATGCGGGTAGACCC+AGG + tig0027814:31905-31924 Msa1435900:CDS 50.0%
CGGTGATAACTCGCTGTTCC+CGG - tig0027814:31416-31435 Msa1435900:intergenic 55.0%
TTCGAGATCTTCGCGTTCGC+CGG - tig0027814:31499-31518 Msa1435900:intergenic 55.0%
GCAGCATCAGCATCAGCATC+AGG + tig0027814:31819-31838 Msa1435900:CDS 55.0%
CAGCATCAGGGACACGTGTA+CGG + tig0027814:31832-31851 Msa1435900:CDS 55.0%
AACTCGCTGTTCCCGGCGTT+CGG - tig0027814:31409-31428 Msa1435900:intergenic 60.0%
CAGGGACACGTGTACGGTTC+TGG + tig0027814:31838-31857 Msa1435900:CDS 60.0%
! GGACACGTGTACGGTTCTGG+TGG + tig0027814:31841-31860 Msa1435900:CDS 60.0%
TTAGGATAACCGGGCCCACC+AGG - tig0027814:31880-31899 Msa1435900:intergenic 60.0%
! CATCAAGTGCCTGGTGGGCC+CGG + tig0027814:31868-31887 Msa1435900:CDS 65.0%
!! TCGGGAGGAGCACCGAACGC+CGG + tig0027814:31394-31413 Msa1435900:CDS 70.0%
!! CGGGAGGAGCACCGAACGCC+GGG + tig0027814:31395-31414 Msa1435900:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0027814 gene 31373 31930 31373 ID=Msa1435900;Name=Msa1435900
tig0027814 mRNA 31373 31930 31373 ID=Msa1435900-mRNA-1;Parent=Msa1435900;Name=Msa1435900-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|185
tig0027814 exon 31373 31930 31373 ID=Msa1435900-mRNA-1:exon:9943;Parent=Msa1435900-mRNA-1
tig0027814 CDS 31373 31930 31373 ID=Msa1435900-mRNA-1:cds;Parent=Msa1435900-mRNA-1
Gene Sequence

>Msa1435900

ATGGCTGATTCCGACAATGAATCGGGAGGAGCACCGAACGCCGGGAACAGCGAGTTATCACCGCGAGAACAAGACCGATTCTTACCAATAGCAAACGTGAGCAGAATAATGAAGAAGGCGTTACCGGCGAACGCGAAGATCTCGAAAGACGCGAAGGAAACAGTTCAGGAATGTGTATCGGAGTTCATCAGCTTCATCACCGGCGAAGCTTCCGATAAGTGTCAGAGAGAGAAACGAAAGACGATCAACGGCGACGATCTACTTTGGGCGATGACTACGTTAGGATTTGAAGAGTACGTTGAACCATTGAAGATTTATCTTCAACGATTCAGAGAGATCGAAGGTGAGAAAACCGTTGCTGCACGTGATAAAGATGGTGTTGCTCCTTCTTCTTCTTCGTCTTCGGTTTTCGATTATGGTGCTCCTCCTCAAGTTGGAATGATCATGCAGCATCAGCATCAGCATCAGGGACACGTGTACGGTTCTGGTGGTTTTCATCAAGTGCCTGGTGGGCCCGGTTATCCTAATGCTGAAACTAATGCGGGTAGACCCAGGTAG
Protein sequence

>Msa1435900

MADSDNESGGAPNAGNSELSPREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKIYLQRFREIEGEKTVAARDKDGVAPSSSSSSVFDYGAPPQVGMIMQHQHQHQGHVYGSGGFHQVPGGPGYPNAETNAGRPR*