AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1339240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1339240 MtrunA17_Chr4g0031671 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa1339240 MtrunA17_Chr4g0031631 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa1339240 MtrunA17_Chr4g0030941 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa1339240 MtrunA17_Chr4g0035061 99.324 148 1 0 1 148 1 148 6.48e-102 288
Msa1339240 MtrunA17_Chr4g0035631 99.324 148 1 0 1 148 1 148 6.48e-102 288
Msa1339240 MtrunA17_Chr4g0031061 98.649 148 2 0 1 148 1 148 2.95e-101 286
Msa1339240 MtrunA17_Chr4g0032321 98.649 148 2 0 1 148 1 148 2.95e-101 286
Msa1339240 MtrunA17_Chr4g0035071 97.973 148 3 0 1 148 1 148 3.19e-100 284
Msa1339240 MtrunA17_Chr4g0030981 98.649 148 1 1 1 148 1 147 8.74e-100 283
Msa1339240 MtrunA17_Chr4g0030951 99.306 144 1 0 5 148 4 147 3.68e-99 281
Msa1339240 MtrunA17_Chr4g0046191 93.919 148 4 1 1 148 1 143 6.30e-89 255
Msa1339240 MtrunA17_Chr1g0197451 88.514 148 6 3 1 148 1 137 1.28e-78 229
Msa1339240 MtrunA17_Chr1g0198251 87.838 148 7 3 1 148 1 137 6.33e-78 227
Msa1339240 MtrunA17_Chr1g0182361 92.793 111 4 1 38 148 30 136 2.58e-64 192
Msa1339240 MtrunA17_Chr7g0263031 92.793 111 5 1 38 148 31 138 4.76e-64 192
Msa1339240 MtrunA17_Chr2g0320511 61.798 89 34 0 59 147 136 224 3.67e-37 127
Msa1339240 MtrunA17_Chr8g0368781 68.817 93 21 3 15 107 4 88 2.70e-34 115
Msa1339240 MtrunA17_Chr4g0031051 90.196 51 5 0 86 136 1 51 3.98e-27 95.9
Msa1339240 MtrunA17_Chr7g0228831 92.500 40 3 0 57 96 42 81 7.48e-23 86.7
Msa1339240 MtrunA17_Chr4g0014401 36.792 106 63 2 31 132 5 110 1.32e-13 63.5
Msa1339240 MtrunA17_Chr4g0075141 36.905 84 52 1 64 146 34 117 5.80e-12 59.3
Msa1339240 MtrunA17_Chr4g0062361 33.010 103 61 4 33 134 4 99 2.76e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1339240 AT3G45980.1 88.742 151 13 2 1 148 1 150 1.47e-83 242
Msa1339240 AT2G28720.1 86.093 151 18 1 1 148 1 151 9.70e-81 235
Msa1339240 AT1G07790.1 86.928 153 10 3 1 148 1 148 7.69e-80 233
Msa1339240 AT5G59910.1 91.176 136 9 2 13 148 18 150 2.66e-77 226
Msa1339240 AT3G46030.1 94.444 126 6 1 23 148 21 145 8.66e-76 222
Msa1339240 AT2G37470.1 82.432 148 15 3 1 147 1 138 6.01e-71 210
Msa1339240 AT3G53650.1 81.208 149 16 3 1 148 1 138 4.61e-69 205
Msa1339240 AT5G22880.1 87.586 145 16 2 4 148 3 145 4.25e-67 200
Msa1339240 AT5G02570.1 79.730 148 14 1 1 148 1 132 9.71e-67 199
Msa1339240 AT3G09480.1 84.127 126 16 1 23 148 5 126 2.13e-62 187
Msa1339240 AT1G08170.1 61.176 85 33 0 61 145 151 235 2.98e-37 127

Find 44 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGGCTTCTTCTCTCCTTT+TGG 0.266976 tig0003042:-87395 None:intergenic
GGTAGCTTCTTTCCAGCCTT+TGG 0.299167 tig0003042:-87482 None:intergenic
GCTTGTTCTGCCCGGTGAAT+TGG 0.328727 tig0003042:+87757 Msa1339240:CDS
TTGCTTGAGATACCAATGTC+TGG 0.335174 tig0003042:-87608 None:intergenic
TCTGCGGGTTTCTTCTCTGC+TGG 0.399254 tig0003042:-87413 None:intergenic
GCCTTTGGCTTCTTCTCCGC+CGG 0.402654 tig0003042:-87467 None:intergenic
GCGGCTGAACCACCTTCCTT+TGG 0.410543 tig0003042:-87503 None:intergenic
GTGGACTTCTTCTCCTCTGC+GGG 0.437960 tig0003042:-87428 None:intergenic
TCTCTTCTTCTTCTTGTCTC+CGG 0.444808 tig0003042:-87525 None:intergenic
TGCTGTTTCTGAGGGTACTA+AGG 0.448307 tig0003042:+87787 Msa1339240:CDS
ATACAAGATCTACATCTTCA+AGG 0.451479 tig0003042:+87568 Msa1339240:CDS
CATCTTCAAGGTTCTGAAGC+AGG 0.454934 tig0003042:+87580 Msa1339240:CDS
GGGAAATTCAGACCGCGGTC+AGG 0.473209 tig0003042:+87735 Msa1339240:CDS
ATCCTTTCAATGGCGCCAAA+AGG 0.496211 tig0003042:+87380 None:intergenic
GCGGAGAAGAAGCCAAAGGC+TGG 0.504484 tig0003042:+87470 Msa1339240:CDS
AAGGAAGGTGGTTCAGCCGC+CGG 0.504946 tig0003042:+87506 Msa1339240:CDS
CGCCGGAGCTTTCTCTGCGA+CGG 0.521178 tig0003042:-87450 None:intergenic
GGCTAAGCATGCTGTTTCTG+AGG 0.531832 tig0003042:+87778 Msa1339240:CDS
TGCTTGAGATACCAATGTCT+GGG 0.532971 tig0003042:-87607 None:intergenic
TGGTATCTCAAGCAAAGCCA+TGG 0.533917 tig0003042:+87616 Msa1339240:CDS
CATCTTCGAGAAGCTTGCTC+AGG 0.534069 tig0003042:+87664 Msa1339240:CDS
AGCATGCTTAGCCAATTCAC+CGG 0.550997 tig0003042:-87768 None:intergenic
AGAAGCCGACGATCACTTCA+AGG 0.553571 tig0003042:+87714 Msa1339240:CDS
GCTAAGCATGCTGTTTCTGA+GGG 0.554009 tig0003042:+87779 Msa1339240:CDS
GCGGTCAGGCTTGTTCTGCC+CGG 0.555879 tig0003042:+87749 Msa1339240:CDS
ATTTCCCTTGAAGTGATCGT+CGG 0.564140 tig0003042:-87719 None:intergenic
CTTCTTCTTCTTGTCTCCGG+CGG 0.574610 tig0003042:-87522 None:intergenic
CACCGTCGCAGAGAAAGCTC+CGG 0.578048 tig0003042:+87448 Msa1339240:CDS
GCATGCTTAGCCAATTCACC+GGG 0.596462 tig0003042:-87767 None:intergenic
AGGAATCTTCAAGACTCGCT+AGG 0.600474 tig0003042:+87684 Msa1339240:CDS
AAGCAGGTTCACCCAGACAT+TGG 0.601452 tig0003042:+87596 Msa1339240:CDS
CGGAGCTTTCTCTGCGACGG+TGG 0.603516 tig0003042:-87447 None:intergenic
GGAAAGAAGCTACCAAAGGA+AGG 0.624050 tig0003042:+87491 Msa1339240:CDS
GAAACTGTTCATGATTCCCA+TGG 0.633384 tig0003042:-87633 None:intergenic
GGCTGGAAAGAAGCTACCAA+AGG 0.634160 tig0003042:+87487 Msa1339240:CDS
GAAGCCGACGATCACTTCAA+GGG 0.638033 tig0003042:+87715 Msa1339240:CDS
CGTCGCAGAGAAAGCTCCGG+CGG 0.643171 tig0003042:+87451 Msa1339240:CDS
GGTATCTCAAGCAAAGCCAT+GGG 0.654333 tig0003042:+87617 Msa1339240:CDS
AAGAAGCTACCAAAGGAAGG+TGG 0.666846 tig0003042:+87494 Msa1339240:CDS
GGTGGACTTCTTCTCCTCTG+CGG 0.668086 tig0003042:-87429 None:intergenic
TCCGGCGGAGAAGAAGCCAA+AGG 0.682003 tig0003042:+87466 Msa1339240:CDS
TTCAAGGGAAATTCAGACCG+CGG 0.690059 tig0003042:+87730 Msa1339240:CDS
GGGCAGAACAAGCCTGACCG+CGG 0.695125 tig0003042:-87747 None:intergenic
AGCAGAGAAGAAACCCGCAG+AGG 0.698236 tig0003042:+87415 Msa1339240:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATACAAGATCTACATCTTCA+AGG + tig0003042:87568-87587 Msa1339240:CDS 30.0%
TCTCTTCTTCTTCTTGTCTC+CGG - tig0003042:87528-87547 None:intergenic 40.0%
TGCTTGAGATACCAATGTCT+GGG - tig0003042:87610-87629 None:intergenic 40.0%
TTGCTTGAGATACCAATGTC+TGG - tig0003042:87611-87630 None:intergenic 40.0%
GAAACTGTTCATGATTCCCA+TGG - tig0003042:87636-87655 None:intergenic 40.0%
ATTTCCCTTGAAGTGATCGT+CGG - tig0003042:87722-87741 None:intergenic 40.0%
GGAAAGAAGCTACCAAAGGA+AGG + tig0003042:87491-87510 Msa1339240:CDS 45.0%
AAGAAGCTACCAAAGGAAGG+TGG + tig0003042:87494-87513 Msa1339240:CDS 45.0%
!! CATCTTCAAGGTTCTGAAGC+AGG + tig0003042:87580-87599 Msa1339240:CDS 45.0%
TGGTATCTCAAGCAAAGCCA+TGG + tig0003042:87616-87635 Msa1339240:CDS 45.0%
GGTATCTCAAGCAAAGCCAT+GGG + tig0003042:87617-87636 Msa1339240:CDS 45.0%
AGGAATCTTCAAGACTCGCT+AGG + tig0003042:87684-87703 Msa1339240:CDS 45.0%
TTCAAGGGAAATTCAGACCG+CGG + tig0003042:87730-87749 Msa1339240:CDS 45.0%
AGCATGCTTAGCCAATTCAC+CGG - tig0003042:87771-87790 None:intergenic 45.0%
!! GCTAAGCATGCTGTTTCTGA+GGG + tig0003042:87779-87798 Msa1339240:CDS 45.0%
!! TGCTGTTTCTGAGGGTACTA+AGG + tig0003042:87787-87806 Msa1339240:CDS 45.0%
!! GCTGGCTTCTTCTCTCCTTT+TGG - tig0003042:87398-87417 None:intergenic 50.0%
GGTAGCTTCTTTCCAGCCTT+TGG - tig0003042:87485-87504 None:intergenic 50.0%
GGCTGGAAAGAAGCTACCAA+AGG + tig0003042:87487-87506 Msa1339240:CDS 50.0%
CTTCTTCTTCTTGTCTCCGG+CGG - tig0003042:87525-87544 None:intergenic 50.0%
AAGCAGGTTCACCCAGACAT+TGG + tig0003042:87596-87615 Msa1339240:CDS 50.0%
! CATCTTCGAGAAGCTTGCTC+AGG + tig0003042:87664-87683 Msa1339240:CDS 50.0%
AGAAGCCGACGATCACTTCA+AGG + tig0003042:87714-87733 Msa1339240:CDS 50.0%
GAAGCCGACGATCACTTCAA+GGG + tig0003042:87715-87734 Msa1339240:CDS 50.0%
GCATGCTTAGCCAATTCACC+GGG - tig0003042:87770-87789 None:intergenic 50.0%
!! GGCTAAGCATGCTGTTTCTG+AGG + tig0003042:87778-87797 Msa1339240:CDS 50.0%
TCTGCGGGTTTCTTCTCTGC+TGG - tig0003042:87416-87435 None:intergenic 55.0%
AGCAGAGAAGAAACCCGCAG+AGG + tig0003042:87415-87434 Msa1339240:CDS 55.0%
GTGGACTTCTTCTCCTCTGC+GGG - tig0003042:87431-87450 None:intergenic 55.0%
! GGTGGACTTCTTCTCCTCTG+CGG - tig0003042:87432-87451 None:intergenic 55.0%
GCTTGTTCTGCCCGGTGAAT+TGG + tig0003042:87757-87776 Msa1339240:CDS 55.0%
CACCGTCGCAGAGAAAGCTC+CGG + tig0003042:87448-87467 Msa1339240:CDS 60.0%
TCCGGCGGAGAAGAAGCCAA+AGG + tig0003042:87466-87485 Msa1339240:CDS 60.0%
! GCCTTTGGCTTCTTCTCCGC+CGG - tig0003042:87470-87489 None:intergenic 60.0%
GCGGAGAAGAAGCCAAAGGC+TGG + tig0003042:87470-87489 Msa1339240:CDS 60.0%
GCGGCTGAACCACCTTCCTT+TGG - tig0003042:87506-87525 None:intergenic 60.0%
AAGGAAGGTGGTTCAGCCGC+CGG + tig0003042:87506-87525 Msa1339240:CDS 60.0%
GGGAAATTCAGACCGCGGTC+AGG + tig0003042:87735-87754 Msa1339240:CDS 60.0%
CGGAGCTTTCTCTGCGACGG+TGG - tig0003042:87450-87469 None:intergenic 65.0%
CGCCGGAGCTTTCTCTGCGA+CGG - tig0003042:87453-87472 None:intergenic 65.0%
CGTCGCAGAGAAAGCTCCGG+CGG + tig0003042:87451-87470 Msa1339240:CDS 65.0%
GGGCAGAACAAGCCTGACCG+CGG - tig0003042:87750-87769 None:intergenic 65.0%
! GCGGTCAGGCTTGTTCTGCC+CGG + tig0003042:87749-87768 Msa1339240:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0003042 gene 87389 87835 87389 ID=Msa1339240;Name=Msa1339240
tig0003042 mRNA 87389 87835 87389 ID=Msa1339240-mRNA-1;Parent=Msa1339240;Name=Msa1339240-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|148
tig0003042 exon 87389 87835 87389 ID=Msa1339240-mRNA-1:exon:1980;Parent=Msa1339240-mRNA-1
tig0003042 CDS 87389 87835 87389 ID=Msa1339240-mRNA-1:cds;Parent=Msa1339240-mRNA-1
Gene Sequence

>Msa1339240

ATGGCGCCAAAAGGAGAGAAGAAGCCAGCAGAGAAGAAACCCGCAGAGGAGAAGAAGTCCACCGTCGCAGAGAAAGCTCCGGCGGAGAAGAAGCCAAAGGCTGGAAAGAAGCTACCAAAGGAAGGTGGTTCAGCCGCCGGAGACAAGAAGAAGAAGAGAAGCAAGAAGAGCGTTGAAACATACAAGATCTACATCTTCAAGGTTCTGAAGCAGGTTCACCCAGACATTGGTATCTCAAGCAAAGCCATGGGAATCATGAACAGTTTCATCAACGACATCTTCGAGAAGCTTGCTCAGGAATCTTCAAGACTCGCTAGGTACAACAAGAAGCCGACGATCACTTCAAGGGAAATTCAGACCGCGGTCAGGCTTGTTCTGCCCGGTGAATTGGCTAAGCATGCTGTTTCTGAGGGTACTAAGGCTGTGACTAAGTTCACAAGTTCTTAG
Protein sequence

>Msa1339240

MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKKKRSKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS*