AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0078290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0078290 MtrunA17_Chr5g0420351 61.538 117 45 0 1 117 1 117 8.85e-47 148
Msa0078290 MtrunA17_Chr4g0012761 50.314 159 55 1 1 135 1 159 8.08e-42 136
Msa0078290 MtrunA17_Chr7g0218151 49.057 159 57 1 1 135 1 159 1.41e-41 135
Msa0078290 MtrunA17_Chr1g0197461 50.388 129 62 1 3 129 2 130 5.44e-40 131
Msa0078290 MtrunA17_Chr1g0193311 57.025 121 52 0 1 121 1 121 2.01e-39 130
Msa0078290 MtrunA17_Chr1g0188661 47.170 159 60 1 1 135 1 159 4.61e-39 129
Msa0078290 MtrunA17_Chr1g0188681 42.675 157 66 1 1 133 1 157 3.40e-37 124
Msa0078290 MtrunA17_Chr1g0188651 46.497 157 62 2 1 135 1 157 5.61e-37 123
Msa0078290 MtrunA17_Chr1g0197321 47.934 121 63 0 1 121 1 121 3.31e-36 121
Msa0078290 MtrunA17_Chr1g0197261 47.934 121 63 0 1 121 1 121 7.68e-34 115
Msa0078290 MtrunA17_Chr4g0013041 36.441 118 72 2 1 117 1 116 8.97e-24 91.3
Msa0078290 MtrunA17_Chr4g0014321 35.593 118 75 1 1 117 1 118 6.48e-22 87.0
Msa0078290 MtrunA17_Chr3g0110131 41.525 118 68 1 1 117 1 118 1.82e-20 83.6
Msa0078290 MtrunA17_Chr3g0107381 36.441 118 74 1 1 117 1 118 3.35e-20 82.4
Msa0078290 MtrunA17_Chr3g0107331 38.168 131 78 2 3 132 2 130 4.16e-20 80.9
Msa0078290 MtrunA17_Chr4g0014031 35.766 137 85 2 1 134 1 137 8.27e-20 81.6
Msa0078290 MtrunA17_Chr8g0351751 34.965 143 82 3 1 135 1 140 2.43e-19 80.5
Msa0078290 MtrunA17_Chr3g0107351 36.207 116 73 1 3 117 2 117 1.00e-17 74.7
Msa0078290 MtrunA17_Chr2g0296831 34.746 118 76 1 1 117 1 118 1.30e-17 73.2
Msa0078290 MtrunA17_Chr5g0432691 36.275 102 64 1 1 101 1 102 3.54e-17 73.2
Msa0078290 MtrunA17_Chr4g0014131 38.686 137 81 2 1 134 1 137 7.33e-17 73.9
Msa0078290 MtrunA17_Chr4g0014121 38.406 138 82 2 1 135 29 166 8.08e-17 72.8
Msa0078290 MtrunA17_Chr3g0107341 33.621 116 76 1 3 117 2 117 4.94e-16 70.1
Msa0078290 MtrunA17_Chr3g0107361 35.345 116 74 1 3 117 2 117 5.73e-16 70.1
Msa0078290 MtrunA17_Chr3g0107461 30.973 113 77 1 1 112 1 113 3.89e-15 67.8
Msa0078290 MtrunA17_Chr2g0283941 33.898 118 77 1 1 118 1 117 5.90e-13 63.5
Msa0078290 MtrunA17_Chr4g0008701 26.772 127 90 2 3 126 6 132 2.88e-11 59.7
Msa0078290 MtrunA17_Chr7g0267601 27.778 108 77 1 3 109 6 113 6.14e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0078290 AT5G27960.1 39.474 114 68 1 5 117 3 116 5.87e-21 86.7
Msa0078290 AT5G26630.1 37.313 134 75 2 1 133 1 126 8.53e-21 84.3
Msa0078290 AT1G65330.1 34.677 124 80 1 3 125 2 125 1.32e-19 82.4
Msa0078290 AT5G26650.1 37.719 114 70 1 5 117 3 116 1.55e-19 83.2
Msa0078290 AT1G65300.1 34.167 120 78 1 3 121 2 121 2.61e-19 81.6
Msa0078290 AT3G05860.2 33.333 138 83 4 1 135 1 132 1.05e-16 73.2
Msa0078290 AT3G05860.3 33.333 138 83 4 1 135 1 132 2.51e-16 73.2
Msa0078290 AT1G31630.1 32.759 116 76 2 3 117 2 116 2.54e-16 73.9
Msa0078290 AT3G05860.1 33.333 138 83 4 1 135 1 132 3.14e-16 72.8
Msa0078290 AT5G48670.1 35.593 118 75 1 1 117 1 118 3.88e-16 73.6
Msa0078290 AT1G31640.1 32.174 115 76 2 3 116 2 115 1.97e-14 68.9
Msa0078290 AT5G26580.1 34.746 118 62 3 1 117 1 104 1.71e-12 63.5
Msa0078290 AT2G28700.1 30.303 132 85 2 1 128 1 129 1.43e-11 60.8
Msa0078290 AT1G22590.2 27.778 126 90 1 1 126 1 125 1.62e-11 58.9
Msa0078290 AT5G27810.1 30.682 88 60 1 31 117 3 90 2.03e-11 57.4

Find 25 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTATCATTGATGAATTT+TGG 0.169071 1_2:-55676270 None:intergenic
AGCTTTCCTTGCTAAATATT+TGG 0.216107 1_2:-55676092 None:intergenic
ACCTCTGTTTCGGAATTAAA+AGG 0.225174 1_2:-55676205 None:intergenic
TGCTAAATATTTGGAGATAA+AGG 0.240702 1_2:-55676083 None:intergenic
GTAGCTCTTAAGACCTTGTT+TGG 0.358470 1_2:-55676248 None:intergenic
ATCTGGCCACACCTCTGTTT+CGG 0.384477 1_2:-55676215 None:intergenic
TATGATTCTTGAACTTAAGA+AGG 0.409403 1_2:+55676402 Msa0078290:CDS
TGTTTCGGAATTAAAAGGAT+TGG 0.421452 1_2:-55676200 None:intergenic
TGTTTGGCACCCTCTAGATC+TGG 0.457133 1_2:-55676232 None:intergenic
CAAGGCCATGGCTAGGAGTA+AGG 0.469639 1_2:+55676051 None:intergenic
TAAGTTCAAGAATCATAAGA+AGG 0.499644 1_2:-55676396 None:intergenic
GCAGAAGATTACTGAAGCCA+AGG 0.517795 1_2:+55676327 Msa0078290:CDS
AGACAATCATGAGAAGAAGT+TGG 0.529577 1_2:+55676372 Msa0078290:CDS
TTATCTCCAAATATTTAGCA+AGG 0.539762 1_2:+55676086 Msa0078290:CDS
AGAGAACTCACAATTCTTTG+TGG 0.541082 1_2:+55676154 Msa0078290:CDS
GATCTAGAGGGTGCCAAACA+AGG 0.565612 1_2:+55676235 Msa0078290:CDS
AAAGAATGCTCTCTTTGAGA+AGG 0.568994 1_2:+55676129 Msa0078290:CDS
AGAGGTGTGGCCAGATCTAG+AGG 0.570284 1_2:+55676222 Msa0078290:CDS
TGCATTGCAAGGCCATGGCT+AGG 0.571000 1_2:+55676044 None:intergenic
TTTCACCTTACTCCTAGCCA+TGG 0.587383 1_2:-55676056 None:intergenic
TAAGAAGGTAATTGATGACA+AGG 0.625288 1_2:+55676417 Msa0078290:CDS
AGCATTCTTTCTCCGCATGT+AGG 0.642073 1_2:-55676116 None:intergenic
CAAGGAAAGCTGCCTACATG+CGG 0.644135 1_2:+55676104 Msa0078290:CDS
TTAATTCCGAAACAGAGGTG+TGG 0.655386 1_2:+55676209 Msa0078290:CDS
GAGGTGTGGCCAGATCTAGA+GGG 0.694385 1_2:+55676223 Msa0078290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTAAATATTTGGAGATAA+AGG - chr1_2:55676086-55676105 None:intergenic 25.0%
! TTATCTCCAAATATTTAGCA+AGG + chr1_2:55676086-55676105 Msa0078290:CDS 25.0%
! TAAGTTCAAGAATCATAAGA+AGG - chr1_2:55676399-55676418 None:intergenic 25.0%
! TATGATTCTTGAACTTAAGA+AGG + chr1_2:55676402-55676421 Msa0078290:CDS 25.0%
AGCTTTCCTTGCTAAATATT+TGG - chr1_2:55676095-55676114 None:intergenic 30.0%
TGTTTCGGAATTAAAAGGAT+TGG - chr1_2:55676203-55676222 None:intergenic 30.0%
! CAGCTATCATTGATGAATTT+TGG - chr1_2:55676273-55676292 None:intergenic 30.0%
! TAAGAAGGTAATTGATGACA+AGG + chr1_2:55676417-55676436 Msa0078290:CDS 30.0%
! AAAGAATGCTCTCTTTGAGA+AGG + chr1_2:55676129-55676148 Msa0078290:CDS 35.0%
AGAGAACTCACAATTCTTTG+TGG + chr1_2:55676154-55676173 Msa0078290:CDS 35.0%
!! TCCTTTTAATTCCGAAACAG+AGG + chr1_2:55676204-55676223 Msa0078290:CDS 35.0%
ACCTCTGTTTCGGAATTAAA+AGG - chr1_2:55676208-55676227 None:intergenic 35.0%
!!! TGTCTTGTTTCAGCATTTTC+AGG - chr1_2:55676357-55676376 None:intergenic 35.0%
AGACAATCATGAGAAGAAGT+TGG + chr1_2:55676372-55676391 Msa0078290:CDS 35.0%
TTAATTCCGAAACAGAGGTG+TGG + chr1_2:55676209-55676228 Msa0078290:CDS 40.0%
GTAGCTCTTAAGACCTTGTT+TGG - chr1_2:55676251-55676270 None:intergenic 40.0%
!!! CAGCATTTTCAGGTTTTCCT+TGG - chr1_2:55676347-55676366 None:intergenic 40.0%
AGCATTCTTTCTCCGCATGT+AGG - chr1_2:55676119-55676138 None:intergenic 45.0%
GCAGAAGATTACTGAAGCCA+AGG + chr1_2:55676327-55676346 Msa0078290:CDS 45.0%
CAAGGAAAGCTGCCTACATG+CGG + chr1_2:55676104-55676123 Msa0078290:CDS 50.0%
ATCTGGCCACACCTCTGTTT+CGG - chr1_2:55676218-55676237 None:intergenic 50.0%
TGTTTGGCACCCTCTAGATC+TGG - chr1_2:55676235-55676254 None:intergenic 50.0%
!! GATCTAGAGGGTGCCAAACA+AGG + chr1_2:55676235-55676254 Msa0078290:CDS 50.0%
! AGAGGTGTGGCCAGATCTAG+AGG + chr1_2:55676222-55676241 Msa0078290:CDS 55.0%
GAGGTGTGGCCAGATCTAGA+GGG + chr1_2:55676223-55676242 Msa0078290:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 55676058 55676465 55676058 ID=Msa0078290;Name=Msa0078290
chr1_2 mRNA 55676058 55676465 55676058 ID=Msa0078290-mRNA-1;Parent=Msa0078290;Name=Msa0078290-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|-1|0|1|-1|1|1|0|135
chr1_2 exon 55676058 55676465 55676058 ID=Msa0078290-mRNA-1:exon:17337;Parent=Msa0078290-mRNA-1
chr1_2 CDS 55676058 55676465 55676058 ID=Msa0078290-mRNA-1:cds;Parent=Msa0078290-mRNA-1
Gene Sequence

>Msa0078290

ATGGCTAGGAGTAAGGTGAAACTTGCCTTTATCTCCAAATATTTAGCAAGGAAAGCTGCCTACATGCGGAGAAAGAATGCTCTCTTTGAGAAGGTGAGAGAACTCACAATTCTTTGTGGTATTTCAGCTTTTGTTGTAATTTCCAATCCTTTTAATTCCGAAACAGAGGTGTGGCCAGATCTAGAGGGTGCCAAACAAGGTCTTAAGAGCTACCAAAATTCATCAATGATAGCTGAGACAAATGATATGAACGAAGAAAGTCTTCTTTTGCAGAAGATTACTGAAGCCAAGGAAAACCTGAAAATGCTGAAACAAGACAATCATGAGAAGAAGTTGGACCTTCTTATGATTCTTGAACTTAAGAAGGTAATTGATGACAAGGTTGCTGCACTCAATTTATCAAATTGA
Protein sequence

>Msa0078290

MARSKVKLAFISKYLARKAAYMRRKNALFEKVRELTILCGISAFVVISNPFNSETEVWPDLEGAKQGLKSYQNSSMIAETNDMNEESLLLQKITEAKENLKMLKQDNHEKKLDLLMILELKKVIDDKVAALNLSN*