AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1356980

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1356980 MtrunA17_Chr1g0193311 94.872 156 8 0 1 156 1 156 2.88e-99 282
Msa1356980 MtrunA17_Chr5g0420351 85.897 156 22 0 1 156 1 156 7.12e-95 271
Msa1356980 MtrunA17_Chr7g0218151 78.205 156 34 0 1 156 1 156 1.44e-79 232
Msa1356980 MtrunA17_Chr4g0012761 76.923 156 36 0 1 156 1 156 3.99e-78 229
Msa1356980 MtrunA17_Chr1g0188661 75.641 156 38 0 1 156 1 156 1.59e-77 227
Msa1356980 MtrunA17_Chr1g0188681 69.231 156 48 0 1 156 1 156 2.40e-75 221
Msa1356980 MtrunA17_Chr1g0188651 73.718 156 39 1 1 156 1 154 8.80e-69 205
Msa1356980 MtrunA17_Chr1g0197461 63.399 153 56 0 3 155 2 154 3.32e-65 196
Msa1356980 MtrunA17_Chr1g0197261 59.355 155 63 0 1 155 1 155 1.55e-63 192
Msa1356980 MtrunA17_Chr1g0197321 58.333 156 64 1 1 155 1 156 4.96e-62 188
Msa1356980 MtrunA17_Chr3g0107381 46.104 154 82 1 1 153 1 154 1.78e-42 140
Msa1356980 MtrunA17_Chr3g0110131 50.641 156 76 1 1 155 1 156 5.30e-42 140
Msa1356980 MtrunA17_Chr4g0014321 39.355 155 92 2 1 153 1 155 1.42e-40 135
Msa1356980 MtrunA17_Chr4g0013041 39.610 154 89 3 1 152 1 152 4.45e-36 124
Msa1356980 MtrunA17_Chr8g0351751 40.881 159 90 2 1 155 1 159 4.39e-35 122
Msa1356980 MtrunA17_Chr5g0432691 37.821 156 96 1 1 155 1 156 2.16e-34 118
Msa1356980 MtrunA17_Chr3g0107351 42.208 154 88 1 3 155 2 155 6.21e-34 117
Msa1356980 MtrunA17_Chr4g0014031 42.308 156 88 2 1 154 1 156 8.95e-34 118
Msa1356980 MtrunA17_Chr3g0107331 41.558 154 89 1 3 155 2 155 1.50e-33 115
Msa1356980 MtrunA17_Chr3g0107361 40.260 154 91 1 3 155 2 155 4.23e-32 112
Msa1356980 MtrunA17_Chr3g0107341 39.610 154 92 1 3 155 2 155 1.08e-30 108
Msa1356980 MtrunA17_Chr4g0014131 43.590 156 86 2 1 154 1 156 2.97e-30 109
Msa1356980 MtrunA17_Chr4g0014121 42.949 156 87 2 1 154 29 184 7.75e-30 107
Msa1356980 MtrunA17_Chr3g0107461 35.443 158 98 3 1 155 1 157 1.08e-28 103
Msa1356980 MtrunA17_Chr2g0296831 44.628 121 66 1 1 120 1 121 1.13e-28 102
Msa1356980 MtrunA17_Chr2g0283941 37.748 151 92 2 1 149 1 151 2.72e-28 104
Msa1356980 MtrunA17_Chr4g0031421 36.508 126 78 2 29 152 1 126 2.14e-22 87.0
Msa1356980 MtrunA17_Chr2g0296861 34.194 155 101 1 1 154 1 155 3.39e-22 86.7
Msa1356980 MtrunA17_Chr3g0105791 35.714 126 79 2 29 152 1 126 8.03e-22 85.5
Msa1356980 MtrunA17_Chr3g0106421 33.333 129 84 2 29 155 1 129 1.77e-19 81.3
Msa1356980 MtrunA17_Chr4g0008701 37.903 124 69 3 1 120 1 120 1.99e-19 84.0
Msa1356980 MtrunA17_Chr1g0162261 46.237 93 49 1 64 155 22 114 5.67e-19 77.4
Msa1356980 MtrunA17_Chr3g0106501 34.109 129 83 2 29 155 1 129 1.17e-18 77.4
Msa1356980 MtrunA17_Chr7g0267601 37.168 113 67 2 1 109 1 113 2.98e-18 80.5
Msa1356980 MtrunA17_Chr1g0161931 45.000 100 54 1 57 155 21 120 2.66e-17 73.2
Msa1356980 MtrunA17_Chr1g0162181 45.556 90 48 1 64 152 22 111 3.82e-16 70.1
Msa1356980 MtrunA17_Chr6g0449861 31.818 110 69 3 1 104 9 118 1.82e-13 66.6
Msa1356980 MtrunA17_Chr3g0128721 28.571 133 89 2 3 134 6 133 2.42e-13 66.2
Msa1356980 MtrunA17_Chr6g0457851 29.091 110 72 3 1 104 11 120 2.64e-12 63.2
Msa1356980 MtrunA17_Chr1g0212151 28.182 110 73 2 1 104 1 110 1.82e-11 60.8
Msa1356980 MtrunA17_Chr5g0427401 29.221 154 85 5 1 148 1 136 9.18e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1356980 AT5G26630.1 44.872 156 85 1 1 155 1 156 9.14e-38 129
Msa1356980 AT5G48670.1 46.795 156 82 1 1 155 1 156 2.48e-35 125
Msa1356980 AT3G05860.2 40.268 149 88 1 1 148 1 149 4.53e-33 116
Msa1356980 AT1G65330.1 40.909 154 90 1 3 155 2 155 5.72e-33 118
Msa1356980 AT3G05860.3 40.268 149 88 1 1 148 1 149 1.84e-32 115
Msa1356980 AT3G05860.1 40.268 149 88 1 1 148 1 149 2.81e-32 115
Msa1356980 AT1G65300.1 38.312 154 94 1 3 155 2 155 3.40e-31 113
Msa1356980 AT5G26650.1 35.948 153 97 1 4 155 2 154 2.80e-27 104
Msa1356980 AT5G27960.1 34.641 153 99 1 4 155 2 154 3.58e-25 98.6
Msa1356980 AT1G31630.1 30.464 151 103 2 3 152 2 151 1.87e-24 97.1
Msa1356980 AT1G22590.2 32.051 156 102 2 1 155 1 153 3.27e-24 92.4
Msa1356980 AT1G31640.1 34.459 148 95 2 3 149 2 148 7.70e-23 93.6
Msa1356980 AT5G27810.1 44.444 90 49 1 29 117 1 90 7.92e-21 82.4
Msa1356980 AT2G28700.1 34.746 118 76 1 1 117 1 118 4.31e-20 85.1
Msa1356980 AT5G26580.1 32.903 155 91 2 1 155 1 142 1.79e-19 83.6
Msa1356980 AT5G06500.1 36.301 146 80 5 1 141 1 138 8.38e-18 77.8
Msa1356980 AT2G40210.1 34.884 129 81 2 1 127 1 128 5.09e-14 68.6
Msa1356980 AT5G55690.1 26.582 158 95 3 1 151 1 144 3.69e-12 62.8
Msa1356980 AT5G55690.2 26.582 158 95 3 1 151 1 144 3.69e-12 62.8
Msa1356980 AT1G47760.1 33.333 111 67 3 1 110 1 105 7.50e-12 60.8
Msa1356980 AT5G58890.1 34.234 111 65 3 1 104 1 110 1.00e-11 61.6

Find 25 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGATGTTCCCTAGCTT+TGG 0.376916 tig0015879:-52022 None:intergenic
GCCGGATGGTTTGACCGTTT+CGG 0.379706 tig0015879:+52116 Msa1356980:CDS
TGTTTAGCCTTCTCTAGATC+TGG 0.403006 tig0015879:-51916 None:intergenic
CTTTGGTAATCCTCTGCAAT+AGG 0.405146 tig0015879:-52005 None:intergenic
AGATCTAGAGAAGGCTAAAC+AGG 0.406038 tig0015879:+51918 Msa1356980:CDS
CTCTGATGATTCGGCAAGAA+AGG 0.409977 tig0015879:+51774 Msa1356980:CDS
TTTCACCTTCTTCCTAGTCA+TGG 0.473113 tig0015879:-51740 None:intergenic
TCCGAAACGGTCAAACCATC+CGG 0.476793 tig0015879:-52117 None:intergenic
TCTGCAATAGGAAGCTCTCT+TGG 0.511328 tig0015879:-51993 None:intergenic
AGCTGGAATACCGCATAGAA+TGG 0.529502 tig0015879:-51848 None:intergenic
TTGGAAATTATAGCACAAGC+TGG 0.550429 tig0015879:-51865 None:intergenic
TTGCATTGCAAGCCATGACT+AGG 0.554602 tig0015879:+51728 None:intergenic
GCAAGCCATGACTAGGAAGA+AGG 0.558932 tig0015879:+51735 None:intergenic
AAACTCTTTCAAATCCGAAA+CGG 0.563009 tig0015879:-52130 None:intergenic
TGCAGAGGATTACCAAAGCT+AGG 0.568390 tig0015879:+52010 Msa1356980:CDS
GCAGAGGATTACCAAAGCTA+GGG 0.571791 tig0015879:+52011 Msa1356980:CDS
GGGAACATCTTCAAAAGCAA+AGG 0.603982 tig0015879:+52031 Msa1356980:CDS
TGAGAGGTATCAAAATTCAT+CGG 0.625826 tig0015879:+51945 Msa1356980:CDS
AAGAGAGCTTCCTATTGCAG+AGG 0.626560 tig0015879:+51995 Msa1356980:CDS
AGGCTAAACAGGTGATTGAG+AGG 0.629216 tig0015879:+51929 Msa1356980:CDS
TTGATTCTAAAACAGAGGTG+TGG 0.633348 tig0015879:+51893 Msa1356980:CDS
AAGGCACGACAATCGTGAGA+AGG 0.638977 tig0015879:+52050 Msa1356980:CDS
GGTGTGGCCAGATCTAGAGA+AGG 0.655354 tig0015879:+51909 Msa1356980:CDS
GATAACAAGATTGATGCACT+CGG 0.692256 tig0015879:+52186 Msa1356980:CDS
AGCGAACTCACCATTCTATG+CGG 0.710886 tig0015879:+51838 Msa1356980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACCTATAAGAAAAGAAAAA+AGG + tig0015879:51798-51817 Msa1356980:CDS 20.0%
!! ACCTATAAGAAAAGAAAAAA+GGG + tig0015879:51799-51818 Msa1356980:CDS 20.0%
!!! ACCCTTTTTTCTTTTCTTAT+AGG - tig0015879:51803-51822 None:intergenic 25.0%
!!! AAAAAAGGGTATCATCAAAA+AGG + tig0015879:51813-51832 Msa1356980:CDS 25.0%
!!! TGTTTTAGAATCAAAAGGAT+TGG - tig0015879:51887-51906 None:intergenic 25.0%
! GCTAATTGAGAAAAATATGA+AGG + tig0015879:52158-52177 Msa1356980:CDS 25.0%
! TGCTTTTATCTCTGATGATT+CGG + tig0015879:51765-51784 Msa1356980:CDS 30.0%
!!! TCCTTTTGATTCTAAAACAG+AGG + tig0015879:51888-51907 Msa1356980:CDS 30.0%
!!! ACCTCTGTTTTAGAATCAAA+AGG - tig0015879:51892-51911 None:intergenic 30.0%
!! TGAGAGGTATCAAAATTCAT+CGG + tig0015879:51945-51964 Msa1356980:CDS 30.0%
AAACTCTTTCAAATCCGAAA+CGG - tig0015879:52133-52152 None:intergenic 30.0%
TTGGAAATTATAGCACAAGC+TGG - tig0015879:51868-51887 None:intergenic 35.0%
!! TTGATTCTAAAACAGAGGTG+TGG + tig0015879:51893-51912 Msa1356980:CDS 35.0%
CATGAAAAACAAAAAGCTGC+CGG + tig0015879:52098-52117 Msa1356980:CDS 35.0%
GATAACAAGATTGATGCACT+CGG + tig0015879:52186-52205 Msa1356980:CDS 35.0%
! TGTTTAGCCTTCTCTAGATC+TGG - tig0015879:51919-51938 None:intergenic 40.0%
AGATCTAGAGAAGGCTAAAC+AGG + tig0015879:51918-51937 Msa1356980:CDS 40.0%
! CTTTGGTAATCCTCTGCAAT+AGG - tig0015879:52008-52027 None:intergenic 40.0%
TTGAAGATGTTCCCTAGCTT+TGG - tig0015879:52025-52044 None:intergenic 40.0%
GGGAACATCTTCAAAAGCAA+AGG + tig0015879:52031-52050 Msa1356980:CDS 40.0%
AAAAACAAAAAGCTGCCGGA+TGG + tig0015879:52102-52121 Msa1356980:CDS 40.0%
! CTCTGATGATTCGGCAAGAA+AGG + tig0015879:51774-51793 Msa1356980:CDS 45.0%
AGCGAACTCACCATTCTATG+CGG + tig0015879:51838-51857 Msa1356980:CDS 45.0%
AGCTGGAATACCGCATAGAA+TGG - tig0015879:51851-51870 None:intergenic 45.0%
AGGCTAAACAGGTGATTGAG+AGG + tig0015879:51929-51948 Msa1356980:CDS 45.0%
TCTGCAATAGGAAGCTCTCT+TGG - tig0015879:51996-52015 None:intergenic 45.0%
AAGAGAGCTTCCTATTGCAG+AGG + tig0015879:51995-52014 Msa1356980:CDS 45.0%
TGCAGAGGATTACCAAAGCT+AGG + tig0015879:52010-52029 Msa1356980:CDS 45.0%
GCAGAGGATTACCAAAGCTA+GGG + tig0015879:52011-52030 Msa1356980:CDS 45.0%
AAGGCACGACAATCGTGAGA+AGG + tig0015879:52050-52069 Msa1356980:CDS 50.0%
TCCGAAACGGTCAAACCATC+CGG - tig0015879:52120-52139 None:intergenic 50.0%
GGTGTGGCCAGATCTAGAGA+AGG + tig0015879:51909-51928 Msa1356980:CDS 55.0%
GCCGGATGGTTTGACCGTTT+CGG + tig0015879:52116-52135 Msa1356980:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0015879 gene 51742 52212 51742 ID=Msa1356980;Name=Msa1356980
tig0015879 mRNA 51742 52212 51742 ID=Msa1356980-mRNA-1;Parent=Msa1356980;Name=Msa1356980-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|156
tig0015879 exon 51742 52212 51742 ID=Msa1356980-mRNA-1:exon:10220;Parent=Msa1356980-mRNA-1
tig0015879 CDS 51742 52212 51742 ID=Msa1356980-mRNA-1:cds;Parent=Msa1356980-mRNA-1
Gene Sequence

>Msa1356980

ATGACTAGGAAGAAGGTGAAACTTGCTTTTATCTCTGATGATTCGGCAAGAAAGGCAACCTATAAGAAAAGAAAAAAGGGTATCATCAAAAAGGTGAGCGAACTCACCATTCTATGCGGTATTCCAGCTTGTGCTATAATTTCCAATCCTTTTGATTCTAAAACAGAGGTGTGGCCAGATCTAGAGAAGGCTAAACAGGTGATTGAGAGGTATCAAAATTCATCGGTGAAAGATGAAACAAAGAATGTGAACCAAGAGAGCTTCCTATTGCAGAGGATTACCAAAGCTAGGGAACATCTTCAAAAGCAAAGGCACGACAATCGTGAGAAGGAGTTGAACGTTCTTATGATTGAGTACATGAAAAACAAAAAGCTGCCGGATGGTTTGACCGTTTCGGATTTGAAAGAGTTTGATAAGCTAATTGAGAAAAATATGAAGGAGATTGATAACAAGATTGATGCACTCGGTTGA
Protein sequence

>Msa1356980

MTRKKVKLAFISDDSARKATYKKRKKGIIKKVSELTILCGIPACAIISNPFDSKTEVWPDLEKAKQVIERYQNSSVKDETKNVNQESFLLQRITKAREHLQKQRHDNREKELNVLMIEYMKNKKLPDGLTVSDLKEFDKLIEKNMKEIDNKIDALG*