AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0224440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0224440 MtrunA17_Chr2g0330441 90.323 186 18 0 2 187 3 188 1.25e-120 338
Msa0224440 MtrunA17_Chr2g0330451 63.636 187 62 2 1 186 1 182 1.89e-58 181
Msa0224440 MtrunA17_Chr8g0341921 50.909 165 78 2 2 165 3 165 1.81e-45 148
Msa0224440 MtrunA17_Chr7g0260751 45.570 158 79 3 21 177 25 176 4.95e-40 135
Msa0224440 MtrunA17_Chr6g0488551 41.111 180 99 3 1 178 1 175 3.26e-38 130
Msa0224440 MtrunA17_Chr1g0184741 48.630 146 69 2 34 178 30 170 1.45e-30 110
Msa0224440 MtrunA17_Chr4g0005191 37.037 162 92 4 20 177 44 199 1.07e-27 103
Msa0224440 MtrunA17_Chr1g0190601 41.322 121 64 2 4 124 10 123 1.95e-26 99.8
Msa0224440 MtrunA17_Chr5g0437751 34.146 164 98 4 21 180 37 194 1.56e-25 97.8
Msa0224440 MtrunA17_Chr1g0187861 35.922 103 64 1 14 114 1 103 1.73e-16 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0224440 AT1G55190.1 50.000 178 82 3 1 176 1 173 2.74e-51 163
Msa0224440 AT3G13720.1 46.369 179 87 4 1 176 1 173 2.72e-44 145
Msa0224440 AT3G13710.1 41.935 186 96 4 6 185 8 187 1.04e-43 144
Msa0224440 AT1G17700.1 41.916 167 95 2 1 165 1 167 6.20e-32 114
Msa0224440 AT1G04260.1 35.714 154 98 1 19 171 4 157 4.70e-31 111
Msa0224440 AT1G08770.1 34.568 162 98 3 20 178 32 188 2.83e-29 107
Msa0224440 AT2G38360.1 35.404 161 94 4 21 177 40 194 2.90e-27 103
Msa0224440 AT5G01640.1 34.783 161 95 4 21 177 40 194 7.94e-27 102
Msa0224440 AT4G29658.2 34.270 178 111 3 1 177 1 173 3.59e-26 99.4
Msa0224440 AT1G55640.1 33.133 166 98 4 19 179 21 178 1.12e-24 95.5
Msa0224440 AT3G56110.3 33.125 160 97 4 22 177 31 184 1.21e-24 95.9
Msa0224440 AT3G56110.1 33.125 160 97 4 22 177 31 184 1.21e-24 95.9
Msa0224440 AT3G56110.2 33.125 160 97 4 22 177 31 184 1.21e-24 95.9
Msa0224440 AT3G56110.4 33.125 160 97 4 22 177 31 184 1.21e-24 95.9
Msa0224440 AT5G56230.1 31.844 179 110 5 8 180 5 177 6.66e-24 93.6
Msa0224440 AT2G40380.1 36.054 147 84 4 35 177 46 186 1.82e-23 92.8
Msa0224440 AT5G07110.1 31.013 158 99 4 27 180 36 187 4.55e-22 89.4
Msa0224440 AT5G05380.1 36.025 161 93 4 21 177 33 187 5.90e-21 86.7
Msa0224440 AT5G05380.4 36.025 161 93 4 21 177 76 230 1.35e-20 86.3
Msa0224440 AT5G05380.3 36.025 161 93 4 21 177 84 238 1.59e-20 86.3
Msa0224440 AT5G05380.2 36.025 161 93 4 21 177 100 254 2.40e-20 86.3
Msa0224440 AT4G00005.1 36.458 96 58 2 57 150 1 95 3.06e-11 58.5

Find 42 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCGTGTTCATTCTCTTTAC+TGG 0.210912 2_1:+74352746 Msa0224440:CDS
TTGTTTGGAGCGGGGATAAT+GGG 0.296254 2_1:-74352379 None:intergenic
TTTGTTTGGAGCGGGGATAA+TGG 0.333094 2_1:-74352380 None:intergenic
ATATTAATTCGATGTTTGTT+TGG 0.375130 2_1:-74352394 None:intergenic
GATGAACCGTTTATTGTGTT+TGG 0.418366 2_1:+74352674 Msa0224440:CDS
GGAGCGGGGATAATGGGGTT+GGG 0.434955 2_1:-74352373 None:intergenic
TGGAGCGGGGATAATGGGGT+TGG 0.443483 2_1:-74352374 None:intergenic
AGTCTTCCAAACACAATAAA+CGG 0.444707 2_1:-74352680 None:intergenic
GACTGAGGAAGAGGATGATG+AGG 0.458785 2_1:-74352577 None:intergenic
ACACACACCATGACCACCTA+TGG 0.464759 2_1:+74352344 None:intergenic
AGAGATTGCGTCGTTGAAGT+TGG 0.470887 2_1:-74352504 None:intergenic
GCCAAGCTGCCATGAGTTCG+AGG 0.470906 2_1:-74352631 None:intergenic
AGGAAGATAATGAGCGAGGT+TGG 0.473123 2_1:-74352611 None:intergenic
GGAAGATAATGAGCGAGGTT+GGG 0.484643 2_1:-74352610 None:intergenic
CATTATCTTCCTCGAACTCA+TGG 0.485580 2_1:+74352622 Msa0224440:CDS
ATTCGATGTTTGTTTGGAGC+GGG 0.485718 2_1:-74352388 None:intergenic
TCCTCGAACTCATGGCAGCT+TGG 0.494425 2_1:+74352630 Msa0224440:CDS
GACGAATTTGATGCTTTCGT+TGG 0.506573 2_1:-74352423 None:intergenic
TGGTTGGAAGGTTGAATGAA+TGG 0.507523 2_1:-74352484 None:intergenic
GCAATAGAAGACTGAGGAAG+AGG 0.515654 2_1:-74352586 None:intergenic
TCATCGGAACTCGCCGTCCA+TGG 0.517352 2_1:+74352444 Msa0224440:CDS
ATTGCGTCGTTGAAGTTGGT+TGG 0.518252 2_1:-74352500 None:intergenic
GTTCATCACGGAGGAAATAG+AGG 0.522903 2_1:-74352658 None:intergenic
GGTTGGGATTGTTCCATAGG+TGG 0.525782 2_1:-74352357 None:intergenic
TGGGGTTGGGATTGTTCCAT+AGG 0.528026 2_1:-74352360 None:intergenic
TGTTTGGAGCGGGGATAATG+GGG 0.529321 2_1:-74352378 None:intergenic
CATCTCGAAGAAGCAGATGT+TGG 0.530096 2_1:-74352537 None:intergenic
CGTCGTTGAAGTTGGTTGGA+AGG 0.540011 2_1:-74352496 None:intergenic
GATTGTTCCATAGGTGGTCA+TGG 0.559749 2_1:-74352351 None:intergenic
ACTTCAACGACGCAATCTCT+CGG 0.560153 2_1:+74352507 Msa0224440:CDS
AATCTTCAACGTACTTGTTG+CGG 0.562962 2_1:+74352772 Msa0224440:CDS
ACGTTGAAGAAGAGTTTCCA+TGG 0.591174 2_1:-74352461 None:intergenic
TGAAGAAGAGTTTCCATGGA+CGG 0.608427 2_1:-74352457 None:intergenic
TTCGATGTTTGTTTGGAGCG+GGG 0.610423 2_1:-74352387 None:intergenic
AATTCGATGTTTGTTTGGAG+CGG 0.614384 2_1:-74352389 None:intergenic
GAAAGCATCAAATTCGTCAT+CGG 0.623282 2_1:+74352428 Msa0224440:CDS
ACACAATAAACGGTTCATCA+CGG 0.644664 2_1:-74352670 None:intergenic
TTCGAGGAAGATAATGAGCG+AGG 0.673485 2_1:-74352615 None:intergenic
TTGGGTGCAATAGAAGACTG+AGG 0.727799 2_1:-74352592 None:intergenic
ACGACGGTGAGAATCAACAT+CGG 0.750572 2_1:-74352728 None:intergenic
CAATAAACGGTTCATCACGG+AGG 0.762564 2_1:-74352667 None:intergenic
AGTAAAGAGAATGAACACGA+CGG 0.782861 2_1:-74352744 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAATTCGATGTTTGTT+TGG - chr2_1:74352397-74352416 None:intergenic 20.0%
AGTCTTCCAAACACAATAAA+CGG - chr2_1:74352683-74352702 None:intergenic 30.0%
AATTCGATGTTTGTTTGGAG+CGG - chr2_1:74352392-74352411 None:intergenic 35.0%
!! GAAAGCATCAAATTCGTCAT+CGG + chr2_1:74352428-74352447 Msa0224440:CDS 35.0%
ACACAATAAACGGTTCATCA+CGG - chr2_1:74352673-74352692 None:intergenic 35.0%
GATGAACCGTTTATTGTGTT+TGG + chr2_1:74352674-74352693 Msa0224440:CDS 35.0%
AGTAAAGAGAATGAACACGA+CGG - chr2_1:74352747-74352766 None:intergenic 35.0%
! AATCTTCAACGTACTTGTTG+CGG + chr2_1:74352772-74352791 Msa0224440:CDS 35.0%
! ATTCGATGTTTGTTTGGAGC+GGG - chr2_1:74352391-74352410 None:intergenic 40.0%
GACGAATTTGATGCTTTCGT+TGG - chr2_1:74352426-74352445 None:intergenic 40.0%
TGAAGAAGAGTTTCCATGGA+CGG - chr2_1:74352460-74352479 None:intergenic 40.0%
ACGTTGAAGAAGAGTTTCCA+TGG - chr2_1:74352464-74352483 None:intergenic 40.0%
TGGTTGGAAGGTTGAATGAA+TGG - chr2_1:74352487-74352506 None:intergenic 40.0%
CATTATCTTCCTCGAACTCA+TGG + chr2_1:74352622-74352641 Msa0224440:CDS 40.0%
GTCGTGTTCATTCTCTTTAC+TGG + chr2_1:74352746-74352765 Msa0224440:CDS 40.0%
! TTGTTTGGAGCGGGGATAAT+GGG - chr2_1:74352382-74352401 None:intergenic 45.0%
! TTTGTTTGGAGCGGGGATAA+TGG - chr2_1:74352383-74352402 None:intergenic 45.0%
! TTCGATGTTTGTTTGGAGCG+GGG - chr2_1:74352390-74352409 None:intergenic 45.0%
! ATTGCGTCGTTGAAGTTGGT+TGG - chr2_1:74352503-74352522 None:intergenic 45.0%
AGAGATTGCGTCGTTGAAGT+TGG - chr2_1:74352507-74352526 None:intergenic 45.0%
ACTTCAACGACGCAATCTCT+CGG + chr2_1:74352507-74352526 Msa0224440:CDS 45.0%
CATCTCGAAGAAGCAGATGT+TGG - chr2_1:74352540-74352559 None:intergenic 45.0%
GCAATAGAAGACTGAGGAAG+AGG - chr2_1:74352589-74352608 None:intergenic 45.0%
TTGGGTGCAATAGAAGACTG+AGG - chr2_1:74352595-74352614 None:intergenic 45.0%
GGAAGATAATGAGCGAGGTT+GGG - chr2_1:74352613-74352632 None:intergenic 45.0%
AGGAAGATAATGAGCGAGGT+TGG - chr2_1:74352614-74352633 None:intergenic 45.0%
TTCGAGGAAGATAATGAGCG+AGG - chr2_1:74352618-74352637 None:intergenic 45.0%
GTTCATCACGGAGGAAATAG+AGG - chr2_1:74352661-74352680 None:intergenic 45.0%
CAATAAACGGTTCATCACGG+AGG - chr2_1:74352670-74352689 None:intergenic 45.0%
ACGACGGTGAGAATCAACAT+CGG - chr2_1:74352731-74352750 None:intergenic 45.0%
GGTTGGGATTGTTCCATAGG+TGG - chr2_1:74352360-74352379 None:intergenic 50.0%
TGGGGTTGGGATTGTTCCAT+AGG - chr2_1:74352363-74352382 None:intergenic 50.0%
! TGTTTGGAGCGGGGATAATG+GGG - chr2_1:74352381-74352400 None:intergenic 50.0%
! CGTCGTTGAAGTTGGTTGGA+AGG - chr2_1:74352499-74352518 None:intergenic 50.0%
GACTGAGGAAGAGGATGATG+AGG - chr2_1:74352580-74352599 None:intergenic 50.0%
TCCTCGAACTCATGGCAGCT+TGG + chr2_1:74352630-74352649 Msa0224440:CDS 55.0%
!! GGAGCGGGGATAATGGGGTT+GGG - chr2_1:74352376-74352395 None:intergenic 60.0%
!! TGGAGCGGGGATAATGGGGT+TGG - chr2_1:74352377-74352396 None:intergenic 60.0%
TCATCGGAACTCGCCGTCCA+TGG + chr2_1:74352444-74352463 Msa0224440:CDS 60.0%
GCCAAGCTGCCATGAGTTCG+AGG - chr2_1:74352634-74352653 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 74352353 74352916 74352353 ID=Msa0224440;Name=Msa0224440
chr2_1 mRNA 74352353 74352916 74352353 ID=Msa0224440-mRNA-1;Parent=Msa0224440;Name=Msa0224440-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|187
chr2_1 exon 74352353 74352916 74352353 ID=Msa0224440-mRNA-1:exon:22000;Parent=Msa0224440-mRNA-1
chr2_1 CDS 74352353 74352916 74352353 ID=Msa0224440-mRNA-1:cds;Parent=Msa0224440-mRNA-1
Gene Sequence

>Msa0224440

ATGACCACCTATGGAACAATCCCAACCCCATTATCCCCGCTCCAAACAAACATCGAATTAATATCACGTACCAACGAAAGCATCAAATTCGTCATCGGAACTCGCCGTCCATGGAAACTCTTCTTCAACGTCCATTCATTCAACCTTCCAACCAACTTCAACGACGCAATCTCTCGGTACAAAACCAACATCTGCTTCTTCGAGATGAACTACACTATCATACTCCTCATCATCCTCTTCCTCAGTCTTCTATTGCACCCAACCTCGCTCATTATCTTCCTCGAACTCATGGCAGCTTGGCTCTTCCTCTATTTCCTCCGTGATGAACCGTTTATTGTGTTTGGAAGACTCATCAATGATCGTGTTGTTGTTTTTCCGATGTTGATTCTCACCGTCGTGTTCATTCTCTTTACTGGCACAATCTTCAACGTACTTGTTGCGGTTTTGATCTGTGTTGTTATTCTTCTTCACGCTGCTTTCAGAAACACGAATGATTATTCTATAGCTGATCTATTTATTGATGAAGAAGATGTAATTTCGTTTTCTCATCCAAATGTCTCATAA
Protein sequence

>Msa0224440

MTTYGTIPTPLSPLQTNIELISRTNESIKFVIGTRRPWKLFFNVHSFNLPTNFNDAISRYKTNICFFEMNYTIILLIILFLSLLLHPTSLIIFLELMAAWLFLYFLRDEPFIVFGRLINDRVVVFPMLILTVVFILFTGTIFNVLVAVLICVVILLHAAFRNTNDYSIADLFIDEEDVISFSHPNVS*