AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0905250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905250 MtrunA17_Chr8g0370431 74.603 126 4 1 1 98 1 126 3.28e-54 167
Msa0905250 MtrunA17_Chr5g0407011 48.031 127 37 2 1 98 1 127 1.33e-26 97.1
Msa0905250 MtrunA17_Chr7g0242251 53.750 80 36 1 24 102 66 145 7.19e-14 64.7
Msa0905250 MtrunA17_Chr3g0143991 55.294 85 33 2 24 103 60 144 3.25e-12 60.1
Msa0905250 MtrunA17_Chr4g0052011 46.667 60 32 0 24 83 79 138 8.36e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905250 AT1G20696.3 63.855 83 29 1 24 105 8 90 8.85e-25 91.3
Msa0905250 AT1G20693.2 60.465 86 33 1 24 108 53 138 9.51e-24 90.1
Msa0905250 AT1G20696.4 63.158 76 27 1 24 98 8 83 9.74e-22 83.6
Msa0905250 AT1G20696.1 63.158 76 27 1 24 98 50 125 2.22e-21 84.0
Msa0905250 AT1G20693.3 60.526 76 29 1 24 98 53 128 1.61e-20 82.0
Msa0905250 AT1G20693.1 60.526 76 29 1 24 98 53 128 1.65e-20 82.0
Msa0905250 AT2G17560.3 45.736 129 39 4 5 103 7 134 1.15e-19 79.3
Msa0905250 AT3G51880.2 59.211 76 27 2 28 102 72 144 1.31e-19 80.5
Msa0905250 AT3G51880.5 59.211 76 27 2 28 102 72 144 1.38e-19 80.5
Msa0905250 AT3G51880.1 59.211 76 27 2 28 102 72 144 1.38e-19 80.5
Msa0905250 AT3G51880.3 59.211 76 27 2 28 102 72 144 1.38e-19 80.5
Msa0905250 AT2G17560.2 44.531 128 43 3 5 105 7 133 3.80e-19 78.2
Msa0905250 AT2G17560.1 44.531 128 43 3 5 105 7 133 3.80e-19 78.2
Msa0905250 AT3G51880.4 58.333 72 26 2 28 98 72 140 2.54e-17 73.9
Msa0905250 AT1G20696.5 63.793 58 21 0 24 81 50 107 6.26e-17 72.4
Msa0905250 AT1G20696.2 66.667 54 18 0 28 81 54 107 6.49e-17 72.8
Msa0905250 AT4G35570.1 40.000 70 42 0 31 100 56 125 3.31e-13 62.4
Msa0905250 AT4G35570.2 40.000 70 42 0 31 100 56 125 3.31e-13 62.4

Find 43 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCCTCCAGTTTCTTGTTGT+AGG 0.290827 6_2:+3272524 None:intergenic
CAAGCGGTTATCAGCGGGTT+TGG 0.326315 6_2:+3272728 None:intergenic
TCCATGGGTTGAATGAAATT+AGG 0.332045 6_2:+3272378 None:intergenic
GCGGCAACGGATTTGTTGTT+AGG 0.341320 6_2:+3272657 None:intergenic
CGCTTGAAGCGCAAAGGTGC+TGG 0.364891 6_2:-3272711 Msa0905250:CDS
TTGGAACCAGCTTTAACTTT+CGG 0.369853 6_2:+3272747 None:intergenic
TGGGTTGTGGTTTAGATCCA+TGG 0.370651 6_2:+3272362 None:intergenic
ACAAGCCTACAACAAGAAAC+TGG 0.408473 6_2:-3272529 Msa0905250:CDS
CGCTTCAAGCGGTTATCAGC+GGG 0.418583 6_2:+3272723 None:intergenic
TTCTTTCTTCTTCAATGCCC+TGG 0.433917 6_2:+3272569 None:intergenic
TTCAATGCCCTGGCAGCATA+AGG 0.436854 6_2:+3272579 None:intergenic
CGGGTTAAACCCATGGGTTG+TGG 0.457300 6_2:+3272349 None:intergenic
AGGGAGTCTTTCCTTTGTGT+TGG 0.462918 6_2:-3272432 Msa0905250:CDS
GGATGACGATGAGGAGAAGA+GGG 0.483736 6_2:-3272451 Msa0905250:CDS
TCCTAATTTCATTCAACCCA+TGG 0.487638 6_2:-3272379 Msa0905250:CDS
ACAAGGCTCCTTATGCTGCC+AGG 0.494207 6_2:-3272587 Msa0905250:CDS
AACAAATCCGTTGCCGCTGT+CGG 0.503516 6_2:-3272651 Msa0905250:CDS
AGGATGACGATGAGGAGAAG+AGG 0.508159 6_2:-3272452 Msa0905250:CDS
CAGCACCTTTGCGCTTCAAG+CGG 0.509228 6_2:+3272712 None:intergenic
AGAACTCGCACGTTTCTTGA+AGG 0.509887 6_2:+3272406 None:intergenic
GGGTTGTGGTTTAGATCCAT+GGG 0.520582 6_2:+3272363 None:intergenic
GAAAAGCTTGCGGTGAAGCA+TGG 0.538505 6_2:-3272629 Msa0905250:CDS
TGGATCTAAACCACAACCCA+TGG 0.540187 6_2:-3272359 Msa0905250:CDS
GTGCTGGAGCTGAAAGGAAA+CGG 0.543202 6_2:-3272695 Msa0905250:CDS
GTCATCCTCATCATTGACTT+CGG 0.548182 6_2:+3272467 None:intergenic
CAAGGCTCCTTATGCTGCCA+GGG 0.553485 6_2:-3272586 Msa0905250:CDS
ACCAGCTTTAACTTTCGGCA+TGG 0.554492 6_2:+3272752 None:intergenic
GCCATGCCGAAAGTTAAAGC+TGG 0.556061 6_2:-3272753 Msa0905250:CDS
GAGGGAAAAGACGAGGAAGA+TGG 0.572307 6_2:-3272507 Msa0905250:CDS
GCGCTTCAAGCGGTTATCAG+CGG 0.585968 6_2:+3272722 None:intergenic
TGGGTTGAATGAAATTAGGA+TGG 0.587262 6_2:+3272382 None:intergenic
GATAACCGCTTGAAGCGCAA+AGG 0.598359 6_2:-3272717 Msa0905250:CDS
GCCGCTGTCGGAAAAGCTTG+CGG 0.599478 6_2:-3272639 Msa0905250:CDS
GCAAAGGTGCTGGAGCTGAA+AGG 0.614876 6_2:-3272701 Msa0905250:CDS
GCGGGTCGGGTTAAACCCAT+GGG 0.615854 6_2:+3272343 None:intergenic
GGATCTAAACCACAACCCAT+GGG 0.631282 6_2:-3272358 Msa0905250:CDS
ATCGATGTCTGAAGAAGACA+AGG 0.632956 6_2:-3272604 Msa0905250:CDS
GCCTACAACAAGAAACTGGA+GGG 0.637058 6_2:-3272525 Msa0905250:CDS
CAATGATGAGGATGACGATG+AGG 0.661967 6_2:-3272460 Msa0905250:CDS
AGCCTACAACAAGAAACTGG+AGG 0.670368 6_2:-3272526 Msa0905250:CDS
GAAATCCGAAGTCAATGATG+AGG 0.674597 6_2:-3272472 Msa0905250:CDS
CTTGAAGGAAACCAACACAA+AGG 0.675285 6_2:+3272421 None:intergenic
GAAACTGGAGGGAAAAGACG+AGG 0.680761 6_2:-3272514 Msa0905250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGGAACCAGCTTTAACTTT+CGG + chr6_2:3272359-3272378 None:intergenic 35.0%
! TGGGTTGAATGAAATTAGGA+TGG + chr6_2:3272724-3272743 None:intergenic 35.0%
TCCTAATTTCATTCAACCCA+TGG - chr6_2:3272724-3272743 Msa0905250:CDS 35.0%
! TCCATGGGTTGAATGAAATT+AGG + chr6_2:3272728-3272747 None:intergenic 35.0%
ATCGATGTCTGAAGAAGACA+AGG - chr6_2:3272499-3272518 Msa0905250:CDS 40.0%
TTCTTTCTTCTTCAATGCCC+TGG + chr6_2:3272537-3272556 None:intergenic 40.0%
ACAAGCCTACAACAAGAAAC+TGG - chr6_2:3272574-3272593 Msa0905250:CDS 40.0%
GAAATCCGAAGTCAATGATG+AGG - chr6_2:3272631-3272650 Msa0905250:CDS 40.0%
!! GTCATCCTCATCATTGACTT+CGG + chr6_2:3272639-3272658 None:intergenic 40.0%
CTTGAAGGAAACCAACACAA+AGG + chr6_2:3272685-3272704 None:intergenic 40.0%
AGCCTACAACAAGAAACTGG+AGG - chr6_2:3272577-3272596 Msa0905250:CDS 45.0%
GCCTACAACAAGAAACTGGA+GGG - chr6_2:3272578-3272597 Msa0905250:CDS 45.0%
! TCCCTCCAGTTTCTTGTTGT+AGG + chr6_2:3272582-3272601 None:intergenic 45.0%
CAATGATGAGGATGACGATG+AGG - chr6_2:3272643-3272662 Msa0905250:CDS 45.0%
AGGGAGTCTTTCCTTTGTGT+TGG - chr6_2:3272671-3272690 Msa0905250:CDS 45.0%
AGAACTCGCACGTTTCTTGA+AGG + chr6_2:3272700-3272719 None:intergenic 45.0%
GGGTTGTGGTTTAGATCCAT+GGG + chr6_2:3272743-3272762 None:intergenic 45.0%
TGGGTTGTGGTTTAGATCCA+TGG + chr6_2:3272744-3272763 None:intergenic 45.0%
TGGATCTAAACCACAACCCA+TGG - chr6_2:3272744-3272763 Msa0905250:CDS 45.0%
GGATCTAAACCACAACCCAT+GGG - chr6_2:3272745-3272764 Msa0905250:CDS 45.0%
GATAACCGCTTGAAGCGCAA+AGG - chr6_2:3272386-3272405 Msa0905250:CDS 50.0%
GTGCTGGAGCTGAAAGGAAA+CGG - chr6_2:3272408-3272427 Msa0905250:CDS 50.0%
!! GCGGCAACGGATTTGTTGTT+AGG + chr6_2:3272449-3272468 None:intergenic 50.0%
AACAAATCCGTTGCCGCTGT+CGG - chr6_2:3272452-3272471 Msa0905250:CDS 50.0%
GAAAAGCTTGCGGTGAAGCA+TGG - chr6_2:3272474-3272493 Msa0905250:CDS 50.0%
TTCAATGCCCTGGCAGCATA+AGG + chr6_2:3272527-3272546 None:intergenic 50.0%
GAAACTGGAGGGAAAAGACG+AGG - chr6_2:3272589-3272608 Msa0905250:CDS 50.0%
GAGGGAAAAGACGAGGAAGA+TGG - chr6_2:3272596-3272615 Msa0905250:CDS 50.0%
AGGATGACGATGAGGAGAAG+AGG - chr6_2:3272651-3272670 Msa0905250:CDS 50.0%
GGATGACGATGAGGAGAAGA+GGG - chr6_2:3272652-3272671 Msa0905250:CDS 50.0%
! CAAGCGGTTATCAGCGGGTT+TGG + chr6_2:3272378-3272397 None:intergenic 55.0%
CGCTTCAAGCGGTTATCAGC+GGG + chr6_2:3272383-3272402 None:intergenic 55.0%
GCGCTTCAAGCGGTTATCAG+CGG + chr6_2:3272384-3272403 None:intergenic 55.0%
CAGCACCTTTGCGCTTCAAG+CGG + chr6_2:3272394-3272413 None:intergenic 55.0%
!! GCAAAGGTGCTGGAGCTGAA+AGG - chr6_2:3272402-3272421 Msa0905250:CDS 55.0%
! AGCTTTTCCGACAGCGGCAA+CGG + chr6_2:3272462-3272481 None:intergenic 55.0%
! ACCGCAAGCTTTTCCGACAG+CGG + chr6_2:3272468-3272487 None:intergenic 55.0%
ACAAGGCTCCTTATGCTGCC+AGG - chr6_2:3272516-3272535 Msa0905250:CDS 55.0%
CAAGGCTCCTTATGCTGCCA+GGG - chr6_2:3272517-3272536 Msa0905250:CDS 55.0%
! CGCTTGAAGCGCAAAGGTGC+TGG - chr6_2:3272392-3272411 Msa0905250:CDS 60.0%
GCCGCTGTCGGAAAAGCTTG+CGG - chr6_2:3272464-3272483 Msa0905250:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 3272353 3272772 3272353 ID=Msa0905250;Name=Msa0905250
chr6_2 mRNA 3272353 3272772 3272353 ID=Msa0905250-mRNA-1;Parent=Msa0905250;Name=Msa0905250-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|-1|0|1|-1|1|1|0|139
chr6_2 exon 3272353 3272772 3272353 ID=Msa0905250-mRNA-1:exon:1011;Parent=Msa0905250-mRNA-1
chr6_2 CDS 3272353 3272772 3272353 ID=Msa0905250-mRNA-1:cds;Parent=Msa0905250-mRNA-1
Gene Sequence

>Msa0905250

ATGCCGAAAGTTAAAGCTGGTTCCAAACCCGCTGATAACCGCTTGAAGCGCAAAGGTGCTGGAGCTGAAAGGAAACGGACGAAGAAAGATCATCCTAACAACAAATCCGTTGCCGCTGTCGGAAAAGCTTGCGGTGAAGCATGGAAATCGATGTCTGAAGAAGACAAGGCTCCTTATGCTGCCAGGGCATTGAAGAAGAAAGAAGAGTATGAAGCTGCTACACAAGCCTACAACAAGAAACTGGAGGGAAAAGACGAGGAAGATGGTTCTGACAAGTCGAAATCCGAAGTCAATGATGAGGATGACGATGAGGAGAAGAGGGAGTCTTTCCTTTGTGTTGGTTTCCTTCAAGAAACGTGCGAGTTCTTCCATCCTAATTTCATTCAACCCATGGATCTAAACCACAACCCATGGGTTTAA
Protein sequence

>Msa0905250

MPKVKAGSKPADNRLKRKGAGAERKRTKKDHPNNKSVAAVGKACGEAWKSMSEEDKAPYAARALKKKEEYEAATQAYNKKLEGKDEEDGSDKSKSEVNDEDDDEEKRESFLCVGFLQETCEFFHPNFIQPMDLNHNPWV*