AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0920520

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0920520 MtrunA17_Chr6g0476831 98.140 215 4 0 1 215 1 215 3.35e-156 432
Msa0920520 MtrunA17_Chr6g0476871 72.603 219 56 2 1 215 1 219 2.74e-96 280
Msa0920520 MtrunA17_Chr6g0452491 55.825 206 85 3 1 204 1 202 4.14e-73 220
Msa0920520 MtrunA17_Chr6g0452521 55.556 207 85 4 1 204 33 235 1.23e-70 215
Msa0920520 MtrunA17_Chr6g0477741 54.028 211 91 3 1 209 1 207 1.50e-67 206
Msa0920520 MtrunA17_Chr6g0477751 51.174 213 96 4 1 209 1 209 4.02e-64 197
Msa0920520 MtrunA17_Chr6g0476791 52.607 211 90 7 3 206 6 213 7.49e-61 189
Msa0920520 MtrunA17_Chr1g0163381 47.768 224 107 7 1 215 1 223 5.10e-60 187
Msa0920520 MtrunA17_Chr6g0476921 50.549 182 81 7 29 205 26 203 3.32e-47 154
Msa0920520 MtrunA17_Chr6g0476951 47.170 212 95 9 1 208 1 199 1.03e-40 137
Msa0920520 MtrunA17_Chr3g0104591 50.265 189 81 6 23 204 21 203 2.25e-40 137
Msa0920520 MtrunA17_Chr6g0477281 45.729 199 83 3 7 204 6 180 1.28e-39 134
Msa0920520 MtrunA17_Chr6g0476961 45.455 209 99 7 4 208 1 198 3.64e-39 134
Msa0920520 MtrunA17_Chr6g0457121 70.000 100 27 2 1 100 26 122 7.88e-38 128
Msa0920520 MtrunA17_Chr6g0467621 37.879 198 106 10 1 189 1 190 2.30e-22 90.9
Msa0920520 MtrunA17_Chr6g0467611 37.563 197 108 9 1 189 1 190 4.11e-22 90.1
Msa0920520 MtrunA17_Chr6g0467771 36.190 210 120 8 1 203 1 203 8.04e-22 89.4
Msa0920520 MtrunA17_Chr6g0481941 34.783 184 110 6 29 204 24 205 8.27e-22 89.0
Msa0920520 MtrunA17_Chr6g0467761 38.071 197 107 9 1 189 1 190 1.18e-21 89.0
Msa0920520 MtrunA17_Chr6g0481911 32.683 205 124 7 7 204 6 203 1.49e-21 88.2
Msa0920520 MtrunA17_Chr6g0467781 34.706 170 96 8 54 216 13 174 4.63e-15 70.1
Msa0920520 MtrunA17_Chr6g0476821 43.548 124 61 7 98 216 27 146 4.08e-14 67.0
Msa0920520 MtrunA17_Chr2g0314441 30.392 204 120 7 8 204 10 198 1.42e-13 66.6
Msa0920520 MtrunA17_Chr1g0173431 28.161 174 117 5 4 174 1 169 4.02e-12 62.8
Msa0920520 MtrunA17_Chr6g0482041 30.890 191 113 7 29 205 28 213 1.03e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0920520 AT1G17860.1 34.343 198 112 8 1 193 1 185 9.50e-21 86.3
Msa0920520 AT1G73260.1 30.374 214 135 9 2 208 3 209 1.50e-17 78.2
Msa0920520 AT1G73325.1 28.986 207 131 5 7 204 4 203 2.58e-13 67.0

Find 55 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTGTTGATAATGTTAT+TGG 0.155787 6_2:-55628814 Msa0920520:CDS
GTATTGGCCACCGGGGAAAA+TGG 0.209848 6_2:+55629065 None:intergenic
CAGAAACATGCATCTGGATT+TGG 0.274684 6_2:-55628718 Msa0920520:CDS
TACTGGATCTCCTACTTGTT+TGG 0.292002 6_2:-55628674 Msa0920520:CDS
TCTCCTACTTGTTTGGATAT+TGG 0.304475 6_2:-55628667 Msa0920520:CDS
AATCTTACTCCTCCTCCTCC+TGG 0.306584 6_2:+55629018 None:intergenic
GAGCAAGTATTGGACATAAA+TGG 0.344000 6_2:-55629093 Msa0920520:CDS
TGACTTCTCTACGATCTTGT+AGG 0.351929 6_2:+55628959 None:intergenic
TATTGGCCACCGGGGAAAAT+GGG 0.355256 6_2:+55629066 None:intergenic
CCTCCTGGGCCGCGAAGTGC+TGG 0.371965 6_2:+55629033 None:intergenic
TCTGGATTTGGTTATCAGCT+AGG 0.385720 6_2:-55628706 Msa0920520:CDS
GTTATTGGAAAAGCTTGTAT+TGG 0.386990 6_2:-55628799 Msa0920520:CDS
CGATCTTGTAGGACGGTAAC+CGG 0.388041 6_2:+55628970 None:intergenic
CCACTCAATGTTTGCACACC+AGG 0.391509 6_2:+55628754 None:intergenic
AGGAGGAGGAGGAGTAAGAT+TGG 0.399282 6_2:-55629016 Msa0920520:CDS
TTGCCAGCACTTCGCGGCCC+AGG 0.418011 6_2:-55629036 Msa0920520:CDS
ATTATACCAGGACTTATTCC+TGG 0.426390 6_2:+55628907 None:intergenic
TGAAGTAGCTAGTGAAAGAT+TGG 0.427412 6_2:+55629125 None:intergenic
AATATTCAGAAACATGCATC+TGG 0.432525 6_2:-55628724 Msa0920520:CDS
GGAAAAGCTTGTATTGGTAT+TGG 0.433537 6_2:-55628793 Msa0920520:CDS
AACCGGTGATTTAAAGTGTC+CGG 0.436663 6_2:-55628989 Msa0920520:CDS
GTTGTGCTGCATCAACAAAA+TGG 0.440488 6_2:-55628840 Msa0920520:CDS
ATCTTACTCCTCCTCCTCCT+GGG 0.445749 6_2:+55629019 None:intergenic
CTGGATTTGGTTATCAGCTA+GGG 0.451500 6_2:-55628705 Msa0920520:CDS
CCTGGTATGGTGAATTTCAC+TGG 0.452781 6_2:+55628925 None:intergenic
CTACTTGTTTGGATATTGGA+AGG 0.460131 6_2:-55628663 Msa0920520:CDS
AAATGATGTTGAGCAAGTAT+TGG 0.462535 6_2:-55629103 Msa0920520:CDS
GCACTTCGCGGCCCAGGAGG+AGG 0.466087 6_2:-55629030 Msa0920520:CDS
CTTCGCGGCCCAGGAGGAGG+AGG 0.469024 6_2:-55629027 Msa0920520:CDS
GGAGGAGGAGGAGTAAGATT+GGG 0.488170 6_2:-55629015 Msa0920520:CDS
ACCAGGACTTATTCCTGGTA+TGG 0.501683 6_2:+55628912 None:intergenic
AACCGGACACTTTAAATCAC+CGG 0.506786 6_2:+55628987 None:intergenic
CCAGTGAAATTCACCATACC+AGG 0.517650 6_2:-55628925 Msa0920520:CDS
AAACAAAGATGAAGAAGGAA+AGG 0.526008 6_2:+55629154 None:intergenic
AGGTTTGATAATGATGAAGC+TGG 0.526396 6_2:-55628643 Msa0920520:CDS
GATGAAAACAAAGATGAAGA+AGG 0.527190 6_2:+55629149 None:intergenic
AGTCCTGGTATAATCTTCAC+TGG 0.527399 6_2:-55628898 Msa0920520:CDS
CAAAATGTAGTATTGGCCAC+CGG 0.529950 6_2:+55629056 None:intergenic
TTTGTTGATGCAGCACAACT+AGG 0.536918 6_2:+55628844 None:intergenic
GTGCTGGCAAAATGTAGTAT+TGG 0.538469 6_2:+55629049 None:intergenic
AAAATGTAGTATTGGCCACC+GGG 0.543213 6_2:+55629057 None:intergenic
AACAAAGATGAAGAAGGAAA+GGG 0.548845 6_2:+55629155 None:intergenic
TTTGTGTACTCGATCTCAAG+TGG 0.551167 6_2:+55628871 None:intergenic
CCAGCACTTCGCGGCCCAGG+AGG 0.557692 6_2:-55629033 Msa0920520:CDS
ACCATACCAGGAATAAGTCC+TGG 0.563380 6_2:-55628913 Msa0920520:CDS
AAAGCTTGTATTGGTATTGG+TGG 0.570948 6_2:-55628790 Msa0920520:CDS
TTTGAATTTGACTGAACATG+AGG 0.576045 6_2:-55628614 Msa0920520:CDS
CTTCCAATATCCAAACAAGT+AGG 0.582048 6_2:+55628664 None:intergenic
ATTGGCCACCGGGGAAAATG+GGG 0.604953 6_2:+55629067 None:intergenic
CACTCAATGTTTGCACACCA+GGG 0.607129 6_2:+55628755 None:intergenic
TTCTCTACGATCTTGTAGGA+CGG 0.636262 6_2:+55628963 None:intergenic
GTACCAGTGAAGATTATACC+AGG 0.672259 6_2:+55628895 None:intergenic
GGTGGTCCTGAAAATTACCC+TGG 0.679018 6_2:-55628772 Msa0920520:CDS
CCTGGTGTGCAAACATTGAG+TGG 0.686652 6_2:-55628754 Msa0920520:CDS
AAATGTAGTATTGGCCACCG+GGG 0.732042 6_2:+55629058 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTTTGTTGATAATGTTAT+TGG - chr6_2:55628912-55628931 Msa0920520:CDS 20.0%
AACAAAGATGAAGAAGGAAA+GGG + chr6_2:55628574-55628593 None:intergenic 30.0%
AAACAAAGATGAAGAAGGAA+AGG + chr6_2:55628575-55628594 None:intergenic 30.0%
GATGAAAACAAAGATGAAGA+AGG + chr6_2:55628580-55628599 None:intergenic 30.0%
AAATGATGTTGAGCAAGTAT+TGG - chr6_2:55628623-55628642 Msa0920520:CDS 30.0%
GTTATTGGAAAAGCTTGTAT+TGG - chr6_2:55628927-55628946 Msa0920520:CDS 30.0%
AATATTCAGAAACATGCATC+TGG - chr6_2:55629002-55629021 Msa0920520:CDS 30.0%
TTTGAATTTGACTGAACATG+AGG - chr6_2:55629112-55629131 Msa0920520:CDS 30.0%
TGAAGTAGCTAGTGAAAGAT+TGG + chr6_2:55628604-55628623 None:intergenic 35.0%
!! GAGCAAGTATTGGACATAAA+TGG - chr6_2:55628633-55628652 Msa0920520:CDS 35.0%
GATCGTAGAGAAGTCAAAAA+TGG - chr6_2:55628774-55628793 Msa0920520:CDS 35.0%
ATTATACCAGGACTTATTCC+TGG + chr6_2:55628822-55628841 None:intergenic 35.0%
! GGAAAAGCTTGTATTGGTAT+TGG - chr6_2:55628933-55628952 Msa0920520:CDS 35.0%
! AAAGCTTGTATTGGTATTGG+TGG - chr6_2:55628936-55628955 Msa0920520:CDS 35.0%
TCTCCTACTTGTTTGGATAT+TGG - chr6_2:55629059-55629078 Msa0920520:CDS 35.0%
CTTCCAATATCCAAACAAGT+AGG + chr6_2:55629065-55629084 None:intergenic 35.0%
CTACTTGTTTGGATATTGGA+AGG - chr6_2:55629063-55629082 Msa0920520:CDS 35.0%
!! AGGTTTGATAATGATGAAGC+TGG - chr6_2:55629083-55629102 Msa0920520:CDS 35.0%
!! AAAATGTAGTATTGGCCACC+GGG + chr6_2:55628672-55628691 None:intergenic 40.0%
!! CAAAATGTAGTATTGGCCAC+CGG + chr6_2:55628673-55628692 None:intergenic 40.0%
! GTGCTGGCAAAATGTAGTAT+TGG + chr6_2:55628680-55628699 None:intergenic 40.0%
GGAGTAAGATTGGGAAAAAC+CGG - chr6_2:55628720-55628739 Msa0920520:CDS 40.0%
! AACCGGTGATTTAAAGTGTC+CGG - chr6_2:55628737-55628756 Msa0920520:CDS 40.0%
AACCGGACACTTTAAATCAC+CGG + chr6_2:55628742-55628761 None:intergenic 40.0%
TTCTCTACGATCTTGTAGGA+CGG + chr6_2:55628766-55628785 None:intergenic 40.0%
TGACTTCTCTACGATCTTGT+AGG + chr6_2:55628770-55628789 None:intergenic 40.0%
AGTCCTGGTATAATCTTCAC+TGG - chr6_2:55628828-55628847 Msa0920520:CDS 40.0%
GTACCAGTGAAGATTATACC+AGG + chr6_2:55628834-55628853 None:intergenic 40.0%
TTTGTGTACTCGATCTCAAG+TGG + chr6_2:55628858-55628877 None:intergenic 40.0%
TTTGTTGATGCAGCACAACT+AGG + chr6_2:55628885-55628904 None:intergenic 40.0%
GTTGTGCTGCATCAACAAAA+TGG - chr6_2:55628886-55628905 Msa0920520:CDS 40.0%
CAGAAACATGCATCTGGATT+TGG - chr6_2:55629008-55629027 Msa0920520:CDS 40.0%
! TCTGGATTTGGTTATCAGCT+AGG - chr6_2:55629020-55629039 Msa0920520:CDS 40.0%
! CTGGATTTGGTTATCAGCTA+GGG - chr6_2:55629021-55629040 Msa0920520:CDS 40.0%
TACTGGATCTCCTACTTGTT+TGG - chr6_2:55629052-55629071 Msa0920520:CDS 40.0%
! AATGGTAACCCCATTTTCCC+CGG - chr6_2:55628651-55628670 Msa0920520:CDS 45.0%
!! AAATGTAGTATTGGCCACCG+GGG + chr6_2:55628671-55628690 None:intergenic 45.0%
! TACATTTTGCCAGCACTTCG+CGG - chr6_2:55628684-55628703 Msa0920520:CDS 45.0%
CCTGGTATGGTGAATTTCAC+TGG + chr6_2:55628804-55628823 None:intergenic 45.0%
CCAGTGAAATTCACCATACC+AGG - chr6_2:55628801-55628820 Msa0920520:CDS 45.0%
ACCATACCAGGAATAAGTCC+TGG - chr6_2:55628813-55628832 Msa0920520:CDS 45.0%
ACCAGGACTTATTCCTGGTA+TGG + chr6_2:55628817-55628836 None:intergenic 45.0%
! TGCACACCAGGGTAATTTTC+AGG + chr6_2:55628963-55628982 None:intergenic 45.0%
CACTCAATGTTTGCACACCA+GGG + chr6_2:55628974-55628993 None:intergenic 45.0%
!! CAGCTAGGGTTTTGTGTTAC+TGG - chr6_2:55629035-55629054 Msa0920520:CDS 45.0%
TATTGGCCACCGGGGAAAAT+GGG + chr6_2:55628663-55628682 None:intergenic 50.0%
ATCTTACTCCTCCTCCTCCT+GGG + chr6_2:55628710-55628729 None:intergenic 50.0%
AATCTTACTCCTCCTCCTCC+TGG + chr6_2:55628711-55628730 None:intergenic 50.0%
AGGAGGAGGAGGAGTAAGAT+TGG - chr6_2:55628710-55628729 Msa0920520:CDS 50.0%
GGAGGAGGAGGAGTAAGATT+GGG - chr6_2:55628711-55628730 Msa0920520:CDS 50.0%
CGATCTTGTAGGACGGTAAC+CGG + chr6_2:55628759-55628778 None:intergenic 50.0%
GGTGGTCCTGAAAATTACCC+TGG - chr6_2:55628954-55628973 Msa0920520:CDS 50.0%
CCACTCAATGTTTGCACACC+AGG + chr6_2:55628975-55628994 None:intergenic 50.0%
CCTGGTGTGCAAACATTGAG+TGG - chr6_2:55628972-55628991 Msa0920520:CDS 50.0%
ATTGGCCACCGGGGAAAATG+GGG + chr6_2:55628662-55628681 None:intergenic 55.0%
! GTATTGGCCACCGGGGAAAA+TGG + chr6_2:55628664-55628683 None:intergenic 55.0%
! GGTAACCCCATTTTCCCCGG+TGG - chr6_2:55628654-55628673 Msa0920520:CDS 60.0%
TTGCCAGCACTTCGCGGCCC+AGG - chr6_2:55628690-55628709 Msa0920520:CDS 70.0%
CCTCCTGGGCCGCGAAGTGC+TGG + chr6_2:55628696-55628715 None:intergenic 75.0%
CCAGCACTTCGCGGCCCAGG+AGG - chr6_2:55628693-55628712 Msa0920520:CDS 75.0%
GCACTTCGCGGCCCAGGAGG+AGG - chr6_2:55628696-55628715 Msa0920520:CDS 75.0%
CTTCGCGGCCCAGGAGGAGG+AGG - chr6_2:55628699-55628718 Msa0920520:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 55628549 55629199 55628549 ID=Msa0920520;Name=Msa0920520
chr6_2 mRNA 55628549 55629199 55628549 ID=Msa0920520-mRNA-1;Parent=Msa0920520;Name=Msa0920520-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|216
chr6_2 exon 55628549 55629199 55628549 ID=Msa0920520-mRNA-1:exon:8269;Parent=Msa0920520-mRNA-1
chr6_2 CDS 55628549 55629199 55628549 ID=Msa0920520-mRNA-1:cds;Parent=Msa0920520-mRNA-1
Gene Sequence

>Msa0920520

ATGAAGCATCTTTTATCACTAACCCTTTCCTTCTTCATCTTTGTTTTCATCACCAATCTTTCACTAGCTACTTCAAATGATGTTGAGCAAGTATTGGACATAAATGGTAACCCCATTTTCCCCGGTGGCCAATACTACATTTTGCCAGCACTTCGCGGCCCAGGAGGAGGAGGAGTAAGATTGGGAAAAACCGGTGATTTAAAGTGTCCGGTTACCGTCCTACAAGATCGTAGAGAAGTCAAAAATGGTCTACCAGTGAAATTCACCATACCAGGAATAAGTCCTGGTATAATCTTCACTGGTACACCACTTGAGATCGAGTACACAAAAAAACCTAGTTGTGCTGCATCAACAAAATGGTTAATCTTTGTTGATAATGTTATTGGAAAAGCTTGTATTGGTATTGGTGGTCCTGAAAATTACCCTGGTGTGCAAACATTGAGTGGTAAATTTAATATTCAGAAACATGCATCTGGATTTGGTTATCAGCTAGGGTTTTGTGTTACTGGATCTCCTACTTGTTTGGATATTGGAAGGTTTGATAATGATGAAGCTGGAAGACGTTTGAATTTGACTGAACATGAGGTTTATCATGTTGTGTTTGTTGATGCTGCTACTTATGAAGCTGAGTATATTAAGTCTGTTGTTTGA
Protein sequence

>Msa0920520

MKHLLSLTLSFFIFVFITNLSLATSNDVEQVLDINGNPIFPGGQYYILPALRGPGGGGVRLGKTGDLKCPVTVLQDRREVKNGLPVKFTIPGISPGIIFTGTPLEIEYTKKPSCAASTKWLIFVDNVIGKACIGIGGPENYPGVQTLSGKFNIQKHASGFGYQLGFCVTGSPTCLDIGRFDNDEAGRRLNLTEHEVYHVVFVDAATYEAEYIKSVV*