AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0644050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0644050 MtrunA17_Chr4g0031671 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0644050 MtrunA17_Chr4g0031631 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0644050 MtrunA17_Chr4g0030941 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0644050 MtrunA17_Chr4g0035061 98.649 148 2 0 1 148 1 148 2.92e-101 286
Msa0644050 MtrunA17_Chr4g0035631 98.649 148 2 0 1 148 1 148 2.92e-101 286
Msa0644050 MtrunA17_Chr4g0031061 97.973 148 3 0 1 148 1 148 1.03e-100 285
Msa0644050 MtrunA17_Chr4g0032321 97.973 148 3 0 1 148 1 148 1.03e-100 285
Msa0644050 MtrunA17_Chr4g0035071 97.297 148 4 0 1 148 1 148 8.85e-100 283
Msa0644050 MtrunA17_Chr4g0030981 97.973 148 2 1 1 148 1 147 2.86e-99 281
Msa0644050 MtrunA17_Chr4g0030951 98.611 144 2 0 5 148 4 147 1.44e-98 280
Msa0644050 MtrunA17_Chr4g0046191 94.595 148 3 1 1 148 1 143 2.57e-95 271
Msa0644050 MtrunA17_Chr1g0197451 89.189 148 5 3 1 148 1 137 1.52e-78 228
Msa0644050 MtrunA17_Chr1g0198251 88.514 148 6 3 1 148 1 137 6.84e-78 227
Msa0644050 MtrunA17_Chr1g0182361 92.793 111 4 1 38 148 30 136 2.73e-64 192
Msa0644050 MtrunA17_Chr7g0263031 92.793 111 5 1 38 148 31 138 5.55e-64 192
Msa0644050 MtrunA17_Chr2g0320511 61.798 89 34 0 59 147 136 224 4.13e-37 126
Msa0644050 MtrunA17_Chr8g0368781 67.742 93 22 3 15 107 4 88 1.13e-33 114
Msa0644050 MtrunA17_Chr4g0031051 90.196 51 5 0 86 136 1 51 4.20e-27 95.9
Msa0644050 MtrunA17_Chr7g0228831 92.500 40 3 0 57 96 42 81 8.42e-23 86.3
Msa0644050 MtrunA17_Chr4g0014401 36.792 106 63 2 31 132 5 110 2.77e-13 62.8
Msa0644050 MtrunA17_Chr4g0075141 37.349 83 51 1 64 145 34 116 5.44e-12 59.3
Msa0644050 MtrunA17_Chr4g0062361 33.010 103 61 4 33 134 4 99 2.79e-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
Msa0644050 AT3G45980.1 88.742 151 13 2 1 148 1 150 2.11e-83 241
Msa0644050 AT2G28720.1 86.093 151 18 1 1 148 1 151 1.35e-80 234
Msa0644050 AT1G07790.1 86.275 153 11 3 1 148 1 148 1.25e-79 232
Msa0644050 AT5G59910.1 91.176 136 9 2 13 148 18 150 2.63e-77 226
Msa0644050 AT3G46030.1 94.444 126 6 1 23 148 21 145 1.07e-75 222
Msa0644050 AT2G37470.1 81.757 148 16 3 1 147 1 138 7.74e-71 209
Msa0644050 AT3G53650.1 81.879 149 15 3 1 148 1 138 1.02e-69 207
Msa0644050 AT5G22880.1 86.897 145 17 2 4 148 3 145 6.04e-67 200
Msa0644050 AT5G02570.1 79.730 148 14 1 1 148 1 132 1.14e-66 199
Msa0644050 AT3G09480.1 84.127 126 16 1 23 148 5 126 2.63e-62 187
Msa0644050 AT1G08170.1 56.989 93 40 0 53 145 143 235 1.79e-37 128

Find 47 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCTTGGGAAGCTTCTTTC+CGG 0.267514 4_3:+47587488 None:intergenic
CTTCTCCGCCGGAGCTTTCT+CGG 0.304143 4_3:+47587521 None:intergenic
CTCCTCTGCGGGTTTCTTCT+CGG 0.332683 4_3:+47587560 None:intergenic
GGCGGCGGAACCACCTTCCT+TGG 0.336629 4_3:+47587473 None:intergenic
GCTGTCAGGCTTGTTCTTCC+CGG 0.356149 4_3:-47587228 Msa0644050:CDS
GCTGGCTTCTTCTCTCCCTT+TGG 0.360478 4_3:+47587582 None:intergenic
GCTTGTTCTTCCCGGAGAAT+TGG 0.389738 4_3:-47587220 Msa0644050:CDS
CTTCTTCTTGTCTCCGGCGG+CGG 0.396932 4_3:+47587458 None:intergenic
CTTGTTGTAACGAGCAAGTC+TGG 0.399810 4_3:+47587284 None:intergenic
GGAAGCTTCTTTCCGGCCTT+CGG 0.420168 4_3:+47587495 None:intergenic
GTGGACTTCTTCTCCTCTGC+GGG 0.426139 4_3:+47587549 None:intergenic
GGGAAATTCAAACTGCTGTC+AGG 0.437048 4_3:-47587242 Msa0644050:CDS
TCTGCGGGTTTCTTCTCGGC+TGG 0.440883 4_3:+47587564 None:intergenic
TCTCTTCTTCTTCTTGTCTC+CGG 0.444808 4_3:+47587452 None:intergenic
ATACAAGATCTACATCTTCA+AGG 0.451479 4_3:-47587409 Msa0644050:CDS
GCGGCGGAACCACCTTCCTT+GGG 0.454706 4_3:+47587474 None:intergenic
TGGTATCTCAAGCAAAGCTA+TGG 0.457277 4_3:-47587361 Msa0644050:CDS
GACAGCAGTTTGAATTTCCC+TGG 0.465238 4_3:+47587245 None:intergenic
ATTTCCCTGGAAGTGATTGT+TGG 0.473734 4_3:+47587258 None:intergenic
CGCCGGAGCTTTCTCGGCAA+CGG 0.475944 4_3:+47587527 None:intergenic
AGTGAACTTAGTAACAGCTT+TGG 0.479735 4_3:+47587173 None:intergenic
AGAAGCCAACAATCACTTCC+AGG 0.480188 4_3:-47587263 Msa0644050:CDS
AGCATGCTTAGCCAATTCTC+CGG 0.485650 4_3:+47587209 None:intergenic
TTGCTTGAGATACCAATGTC+CGG 0.488923 4_3:+47587369 None:intergenic
AAGGAAGGTGGTTCCGCCGC+CGG 0.489907 4_3:-47587471 Msa0644050:CDS
GCGGAGAAGAAGCCGAAGGC+CGG 0.497699 4_3:-47587507 Msa0644050:CDS
GCCTTCGGCTTCTTCTCCGC+CGG 0.500185 4_3:+47587510 None:intergenic
ATTCGATTCAATGGCACCAA+AGG 0.504821 4_3:-47587598 None:intergenic
TGCTTGAGATACCAATGTCC+GGG 0.518516 4_3:+47587370 None:intergenic
CACCGTTGCCGAGAAAGCTC+CGG 0.523576 4_3:-47587529 Msa0644050:CDS
GGCTAAGCATGCTGTTTCTG+AGG 0.531832 4_3:-47587199 Msa0644050:CDS
TTCGATTCAATGGCACCAAA+GGG 0.536203 4_3:-47587597 None:intergenic
GCATGCTTAGCCAATTCTCC+GGG 0.551301 4_3:+47587210 None:intergenic
GCTAAGCATGCTGTTTCTGA+GGG 0.554009 4_3:-47587198 Msa0644050:CDS
AAACAAGTTCACCCGGACAT+TGG 0.567029 4_3:-47587381 Msa0644050:CDS
GGTATCTCAAGCAAAGCTAT+GGG 0.598266 4_3:-47587360 Msa0644050:CDS
GGAAAGAAGCTTCCCAAGGA+AGG 0.608356 4_3:-47587486 Msa0644050:CDS
GGTGGACTTCTTCTCCTCTG+CGG 0.628573 4_3:+47587548 None:intergenic
AAGAAGCTTCCCAAGGAAGG+TGG 0.629895 4_3:-47587483 Msa0644050:CDS
GGTTCTTAAACAAGTTCACC+CGG 0.632369 4_3:-47587388 Msa0644050:CDS
TCCGGCGGAGAAGAAGCCGA+AGG 0.636700 4_3:-47587511 Msa0644050:CDS
GAAGCCAACAATCACTTCCA+GGG 0.639164 4_3:-47587262 Msa0644050:CDS
GGCCGGAAAGAAGCTTCCCA+AGG 0.642326 4_3:-47587490 Msa0644050:CDS
CGTTGCCGAGAAAGCTCCGG+CGG 0.643171 4_3:-47587526 Msa0644050:CDS
CGGAGCTTTCTCGGCAACGG+TGG 0.653690 4_3:+47587530 None:intergenic
CTTCTTCTTCTTGTCTCCGG+CGG 0.655854 4_3:+47587455 None:intergenic
AGCCGAGAAGAAACCCGCAG+AGG 0.676003 4_3:-47587562 Msa0644050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATACAAGATCTACATCTTCA+AGG - chr4_3:47587343-47587362 Msa0644050:CDS 30.0%
AGTGAACTTAGTAACAGCTT+TGG + chr4_3:47587582-47587601 None:intergenic 35.0%
TCTCTTCTTCTTCTTGTCTC+CGG + chr4_3:47587303-47587322 None:intergenic 40.0%
GGTTCTTAAACAAGTTCACC+CGG - chr4_3:47587364-47587383 Msa0644050:CDS 40.0%
TTGCTTGAGATACCAATGTC+CGG + chr4_3:47587386-47587405 None:intergenic 40.0%
TGGTATCTCAAGCAAAGCTA+TGG - chr4_3:47587391-47587410 Msa0644050:CDS 40.0%
GGTATCTCAAGCAAAGCTAT+GGG - chr4_3:47587392-47587411 Msa0644050:CDS 40.0%
ATTTCCCTGGAAGTGATTGT+TGG + chr4_3:47587497-47587516 None:intergenic 40.0%
TTCCTTGGGAAGCTTCTTTC+CGG + chr4_3:47587267-47587286 None:intergenic 45.0%
AAACAAGTTCACCCGGACAT+TGG - chr4_3:47587371-47587390 Msa0644050:CDS 45.0%
TGCTTGAGATACCAATGTCC+GGG + chr4_3:47587385-47587404 None:intergenic 45.0%
! CTTGTTGTAACGAGCAAGTC+TGG + chr4_3:47587471-47587490 None:intergenic 45.0%
AGAAGCCAACAATCACTTCC+AGG - chr4_3:47587489-47587508 Msa0644050:CDS 45.0%
GAAGCCAACAATCACTTCCA+GGG - chr4_3:47587490-47587509 Msa0644050:CDS 45.0%
GACAGCAGTTTGAATTTCCC+TGG + chr4_3:47587510-47587529 None:intergenic 45.0%
GGGAAATTCAAACTGCTGTC+AGG - chr4_3:47587510-47587529 Msa0644050:CDS 45.0%
AGCATGCTTAGCCAATTCTC+CGG + chr4_3:47587546-47587565 None:intergenic 45.0%
!! GCTAAGCATGCTGTTTCTGA+GGG - chr4_3:47587554-47587573 Msa0644050:CDS 45.0%
GGAAAGAAGCTTCCCAAGGA+AGG - chr4_3:47587266-47587285 Msa0644050:CDS 50.0%
AAGAAGCTTCCCAAGGAAGG+TGG - chr4_3:47587269-47587288 Msa0644050:CDS 50.0%
CTTCTTCTTCTTGTCTCCGG+CGG + chr4_3:47587300-47587319 None:intergenic 50.0%
GCTTGTTCTTCCCGGAGAAT+TGG - chr4_3:47587532-47587551 Msa0644050:CDS 50.0%
GCATGCTTAGCCAATTCTCC+GGG + chr4_3:47587545-47587564 None:intergenic 50.0%
!! GGCTAAGCATGCTGTTTCTG+AGG - chr4_3:47587553-47587572 Msa0644050:CDS 50.0%
! GCTGGCTTCTTCTCTCCCTT+TGG + chr4_3:47587173-47587192 None:intergenic 55.0%
CTCCTCTGCGGGTTTCTTCT+CGG + chr4_3:47587195-47587214 None:intergenic 55.0%
GTGGACTTCTTCTCCTCTGC+GGG + chr4_3:47587206-47587225 None:intergenic 55.0%
! GGTGGACTTCTTCTCCTCTG+CGG + chr4_3:47587207-47587226 None:intergenic 55.0%
GGAAGCTTCTTTCCGGCCTT+CGG + chr4_3:47587260-47587279 None:intergenic 55.0%
! GCTGTCAGGCTTGTTCTTCC+CGG - chr4_3:47587524-47587543 Msa0644050:CDS 55.0%
TCTGCGGGTTTCTTCTCGGC+TGG + chr4_3:47587191-47587210 None:intergenic 60.0%
AGCCGAGAAGAAACCCGCAG+AGG - chr4_3:47587190-47587209 Msa0644050:CDS 60.0%
CACCGTTGCCGAGAAAGCTC+CGG - chr4_3:47587223-47587242 Msa0644050:CDS 60.0%
CTTCTCCGCCGGAGCTTTCT+CGG + chr4_3:47587234-47587253 None:intergenic 60.0%
GGCCGGAAAGAAGCTTCCCA+AGG - chr4_3:47587262-47587281 Msa0644050:CDS 60.0%
CTTCTTCTTGTCTCCGGCGG+CGG + chr4_3:47587297-47587316 None:intergenic 60.0%
CGGAGCTTTCTCGGCAACGG+TGG + chr4_3:47587225-47587244 None:intergenic 65.0%
CGCCGGAGCTTTCTCGGCAA+CGG + chr4_3:47587228-47587247 None:intergenic 65.0%
CGTTGCCGAGAAAGCTCCGG+CGG - chr4_3:47587226-47587245 Msa0644050:CDS 65.0%
TCCGGCGGAGAAGAAGCCGA+AGG - chr4_3:47587241-47587260 Msa0644050:CDS 65.0%
GCCTTCGGCTTCTTCTCCGC+CGG + chr4_3:47587245-47587264 None:intergenic 65.0%
GCGGAGAAGAAGCCGAAGGC+CGG - chr4_3:47587245-47587264 Msa0644050:CDS 65.0%
GCGGCGGAACCACCTTCCTT+GGG + chr4_3:47587281-47587300 None:intergenic 65.0%
AAGGAAGGTGGTTCCGCCGC+CGG - chr4_3:47587281-47587300 Msa0644050:CDS 65.0%
GGCGGCGGAACCACCTTCCT+TGG + chr4_3:47587282-47587301 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 47587164 47587610 47587164 ID=Msa0644050;Name=Msa0644050
chr4_3 mRNA 47587164 47587610 47587164 ID=Msa0644050-mRNA-1;Parent=Msa0644050;Name=Msa0644050-mRNA-1;_AED=0.32;_eAED=0.32;_QI=0|-1|0|1|-1|1|1|0|148
chr4_3 exon 47587164 47587610 47587164 ID=Msa0644050-mRNA-1:exon:11277;Parent=Msa0644050-mRNA-1
chr4_3 CDS 47587164 47587610 47587164 ID=Msa0644050-mRNA-1:cds;Parent=Msa0644050-mRNA-1
Gene Sequence

>Msa0644050

ATGGCACCAAAGGGAGAGAAGAAGCCAGCCGAGAAGAAACCCGCAGAGGAGAAGAAGTCCACCGTTGCCGAGAAAGCTCCGGCGGAGAAGAAGCCGAAGGCCGGAAAGAAGCTTCCCAAGGAAGGTGGTTCCGCCGCCGGAGACAAGAAGAAGAAGAGAAACAAGAAGAGTGTTGAAACATACAAGATCTACATCTTCAAGGTTCTTAAACAAGTTCACCCGGACATTGGTATCTCAAGCAAAGCTATGGGTATCATGAACAGTTTCATCAATGACATCTTCGAGAAGCTCGCTCAAGAATCATCCAGACTTGCTCGTTACAACAAGAAGCCAACAATCACTTCCAGGGAAATTCAAACTGCTGTCAGGCTTGTTCTTCCCGGAGAATTGGCTAAGCATGCTGTTTCTGAGGGTACCAAAGCTGTTACTAAGTTCACTAGTTCTTAG
Protein sequence

>Msa0644050

MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKKKRNKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS*