AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27847

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27847.t1 MTR_8g087530 85.266 319 19 5 18 336 49 339 4.22e-173 484
MS.gene27847.t1 MTR_2g018030 46.875 256 106 6 98 334 112 356 6.18e-58 191
MS.gene27847.t1 MTR_5g075210 42.857 140 61 5 182 320 224 345 8.32e-25 103
MS.gene27847.t1 MTR_7g072875 59.091 66 27 0 255 320 219 284 3.18e-23 97.8
MS.gene27847.t1 MTR_7g072630 59.091 66 27 0 255 320 281 346 7.41e-23 97.8
MS.gene27847.t1 MTR_4g028930 56.716 67 29 0 256 322 315 381 1.94e-21 94.4
MS.gene27847.t1 MTR_8g103520 56.452 62 27 0 255 316 224 285 1.47e-17 82.0
MS.gene27847.t1 MTR_0907s0020 51.562 64 31 0 253 316 100 163 7.44e-15 72.4
MS.gene27847.t1 MTR_7g105790 47.458 59 31 0 258 316 113 171 2.05e-12 65.9
MS.gene27847.t1 MTR_4g052040 43.548 62 35 0 254 315 98 159 1.29e-11 62.8
MS.gene27847.t1 MTR_4g132740 44.068 59 33 0 257 315 83 141 3.83e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27847.t1 AT4G18830 53.285 137 58 3 181 315 210 342 3.41e-37 136
MS.gene27847.t1 AT1G06920 54.430 79 36 0 249 327 237 315 1.69e-24 102
MS.gene27847.t1 AT5G58360 46.296 108 54 1 217 320 182 289 5.55e-24 100
MS.gene27847.t1 AT2G30400 54.795 73 33 0 248 320 245 317 4.14e-22 95.5
MS.gene27847.t1 AT5G01840 61.017 59 23 0 259 317 202 260 1.26e-18 84.7
MS.gene27847.t1 AT5G19650 49.231 65 33 0 255 319 154 218 1.22e-16 78.2
MS.gene27847.t1 AT2G18500 45.455 66 36 0 254 319 225 290 2.34e-14 73.2
MS.gene27847.t1 AT3G52525 49.254 67 34 0 250 316 61 127 2.87e-14 70.1
MS.gene27847.t1 AT2G36026 51.923 52 25 0 265 316 96 147 4.06e-12 64.7
MS.gene27847.t1 AT4G04025 45.763 59 32 0 257 315 115 173 3.47e-11 61.6

Find 63 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGTTGTGAAGTGTTCTT+TGG 0.266311 4.1:-13162139 MS.gene27847:CDS
GAGGGAAATAATTGGGTTCT+TGG 0.266493 4.1:+13162462 None:intergenic
AACAACTCTTCCATTTCTTC+TGG 0.277466 4.1:+13162054 None:intergenic
CTACATAAGAGGGAAATAAT+TGG 0.293355 4.1:+13162454 None:intergenic
ACATCCAAACTGTACATTAC+TGG 0.306963 4.1:+13162708 None:intergenic
GGGTTCTTGGTGATTCAAAT+TGG 0.318117 4.1:+13162475 None:intergenic
TCGACTTTAGTAGCCATCTT+TGG 0.329186 4.1:+13162267 None:intergenic
TTTCAAAGTGTCGGAGAAAA+TGG 0.336592 4.1:-13162408 MS.gene27847:CDS
GAAGAAAGAAGAAGAGGAAA+TGG 0.347901 4.1:-13162193 MS.gene27847:CDS
GATAAGCCAGCCAGAAGAAA+TGG 0.364577 4.1:-13162064 MS.gene27847:CDS
TATGTAGATGCAGAAAGTTC+TGG 0.372162 4.1:-13162438 MS.gene27847:CDS
CTTACCTTGGAACTCTGCTT+TGG 0.374018 4.1:+13162300 None:intergenic
ATTTATTACACAAACTTGAA+TGG 0.396706 4.1:+13161950 None:intergenic
AATGATATCATGGTATTCAT+TGG 0.398859 4.1:+13162008 None:intergenic
GTGGTGAGGATGATGCATTC+TGG 0.406825 4.1:-13162794 MS.gene27847:CDS
GAAGCCAGTAATGTACAGTT+TGG 0.411136 4.1:-13162712 MS.gene27847:CDS
GATGCAGAAAGTTCTGGTCT+TGG 0.420949 4.1:-13162432 MS.gene27847:CDS
CAATTTCCTTGTGGGAATAG+AGG 0.421459 4.1:-13162831 MS.gene27847:CDS
ACTTTCTGCATCTACATAAG+AGG 0.429055 4.1:+13162443 None:intergenic
GTTCATCACAATTTCCTTGT+GGG 0.429553 4.1:-13162839 MS.gene27847:CDS
TGGAGAATGTACTCTTACCT+TGG 0.430524 4.1:+13162287 None:intergenic
ACTCTTCCATTTCTTCTGGC+TGG 0.432481 4.1:+13162058 None:intergenic
TACATAAGAGGGAAATAATT+GGG 0.446625 4.1:+13162455 None:intergenic
GAAAGAAGAAGAGGAAATGG+TGG 0.463652 4.1:-13162190 MS.gene27847:CDS
GCATTCTGGAGATTGTCATT+TGG 0.470215 4.1:-13162780 MS.gene27847:CDS
TTCCTTGTGGGAATAGAGGC+AGG 0.471947 4.1:-13162827 MS.gene27847:CDS
AAAGATGAAGAAAGAAGAAG+AGG 0.484787 4.1:-13162199 MS.gene27847:CDS
TCAAAGCATTTCGACAGGTA+TGG 0.486694 4.1:-13161984 MS.gene27847:CDS
ATTGTTGTCGTTGCATCAGA+CGG 0.491811 4.1:+13162897 None:intergenic
TTGTTGTCGTTGCATCAGAC+GGG 0.493988 4.1:+13162898 None:intergenic
AGAAGAAGAGGAAATGGTGG+AGG 0.494303 4.1:-13162187 MS.gene27847:CDS
TTAAAGCAAAGGTTAACAAA+AGG 0.494673 4.1:-13162365 MS.gene27847:CDS
TAAATGTAAATCCTTAGAAA+AGG 0.497808 4.1:-13162505 MS.gene27847:CDS
ATGCTTTGATAATGATATCA+TGG 0.506592 4.1:+13161998 None:intergenic
AAGAGTACATTCTCCAAAGA+TGG 0.518216 4.1:-13162280 MS.gene27847:CDS
AAGCAAAGGTTAACAAAAGG+AGG 0.522101 4.1:-13162362 MS.gene27847:CDS
GGTCTTGGATTTCAAAGTGT+CGG 0.531784 4.1:-13162417 MS.gene27847:CDS
ACTCAGAACTCCCCGTCTGA+TGG 0.532872 4.1:-13162861 MS.gene27847:CDS
AGTCGAAATACGCAAAATGA+AGG 0.533126 4.1:-13162250 MS.gene27847:CDS
ATGGTGGAGGAAACAGAAGA+AGG 0.542284 4.1:-13162174 MS.gene27847:CDS
CATTATCAAAGCATTTCGAC+AGG 0.549940 4.1:-13161989 MS.gene27847:CDS
TGGTGGAGGAAACAGAAGAA+GGG 0.553251 4.1:-13162173 MS.gene27847:CDS
ATGTGAGGAGTTTAAAGCAA+AGG 0.562245 4.1:-13162376 MS.gene27847:CDS
CTTTCTGCATCTACATAAGA+GGG 0.562393 4.1:+13162444 None:intergenic
GAATCTCTAAAATCTTGTTG+TGG 0.573719 4.1:+13162114 None:intergenic
AGGAAGTTGAGTGCTTAAAG+AGG 0.596150 4.1:-13162617 MS.gene27847:CDS
GCTTAAAGAGGAGATATGAG+AGG 0.596446 4.1:-13162605 MS.gene27847:CDS
GGTTCATCACAATTTCCTTG+TGG 0.598854 4.1:-13162840 MS.gene27847:CDS
AGCAAAGGTTAACAAAAGGA+GGG 0.601137 4.1:-13162361 MS.gene27847:CDS
AATTGTGATGAACCATCAGA+CGG 0.617022 4.1:+13162849 None:intergenic
ATTGTGATGAACCATCAGAC+GGG 0.626786 4.1:+13162850 None:intergenic
GAAACCAAAGCAGAGTTCCA+AGG 0.627313 4.1:-13162304 MS.gene27847:CDS
AGTTTGGATGTGAAAAGACA+TGG 0.628614 4.1:-13162696 MS.gene27847:CDS
GAAATTACAGAATGCAGCAG+AGG 0.634808 4.1:-13162550 MS.gene27847:CDS
TAATGAAACAAAGAGTGCAA+AGG 0.636359 4.1:-13162637 MS.gene27847:CDS
TGTTGTCGTTGCATCAGACG+GGG 0.638223 4.1:+13162899 None:intergenic
ATCAGACGGGGAGTTCTGAG+TGG 0.651626 4.1:+13162863 None:intergenic
TGAGCAGAGAATTACAGAGG+AGG 0.661098 4.1:-13162326 MS.gene27847:CDS
TCAGACGGGGAGTTCTGAGT+GGG 0.663234 4.1:+13162864 None:intergenic
AACCTGCCTCTATTCCCACA+AGG 0.669707 4.1:+13162825 None:intergenic
ATGTGAGCAGAGAATTACAG+AGG 0.684434 4.1:-13162329 MS.gene27847:CDS
AAATGGTGTGAATCAATGTG+AGG 0.711307 4.1:-13162391 MS.gene27847:CDS
TTGTGATGAACCATCAGACG+GGG 0.714122 4.1:+13162851 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATTACACAAACTTGAA+TGG + chr4.1:13162883-13162902 None:intergenic 20.0%
!! TAAATGTAAATCCTTAGAAA+AGG - chr4.1:13162325-13162344 MS.gene27847:CDS 20.0%
!!! TATCTTTACTTTTCTTCTTT+TGG + chr4.1:13162094-13162113 None:intergenic 20.0%
! AATGATATCATGGTATTCAT+TGG + chr4.1:13162825-13162844 None:intergenic 25.0%
! TACATAAGAGGGAAATAATT+GGG + chr4.1:13162378-13162397 None:intergenic 25.0%
! TTAAAGCAAAGGTTAACAAA+AGG - chr4.1:13162465-13162484 MS.gene27847:CDS 25.0%
!!! ATGCTTTGATAATGATATCA+TGG + chr4.1:13162835-13162854 None:intergenic 25.0%
AAAGATGAAGAAAGAAGAAG+AGG - chr4.1:13162631-13162650 MS.gene27847:CDS 30.0%
CTACATAAGAGGGAAATAAT+TGG + chr4.1:13162379-13162398 None:intergenic 30.0%
! TAATGAAACAAAGAGTGCAA+AGG - chr4.1:13162193-13162212 MS.gene27847:CDS 30.0%
!! GAATCTCTAAAATCTTGTTG+TGG + chr4.1:13162719-13162738 None:intergenic 30.0%
AAATGGTGTGAATCAATGTG+AGG - chr4.1:13162439-13162458 MS.gene27847:CDS 35.0%
AACAACTCTTCCATTTCTTC+TGG + chr4.1:13162779-13162798 None:intergenic 35.0%
AAGCAAAGGTTAACAAAAGG+AGG - chr4.1:13162468-13162487 MS.gene27847:CDS 35.0%
AATTGTGATGAACCATCAGA+CGG + chr4.1:13161984-13162003 None:intergenic 35.0%
ACATCCAAACTGTACATTAC+TGG + chr4.1:13162125-13162144 None:intergenic 35.0%
ACTTTCTGCATCTACATAAG+AGG + chr4.1:13162390-13162409 None:intergenic 35.0%
AGCAAAGGTTAACAAAAGGA+GGG - chr4.1:13162469-13162488 MS.gene27847:CDS 35.0%
AGTCGAAATACGCAAAATGA+AGG - chr4.1:13162580-13162599 MS.gene27847:CDS 35.0%
AGTTTGGATGTGAAAAGACA+TGG - chr4.1:13162134-13162153 MS.gene27847:CDS 35.0%
CTTTCTGCATCTACATAAGA+GGG + chr4.1:13162389-13162408 None:intergenic 35.0%
GAAGAAAGAAGAAGAGGAAA+TGG - chr4.1:13162637-13162656 MS.gene27847:CDS 35.0%
GTTCATCACAATTTCCTTGT+GGG - chr4.1:13161991-13162010 MS.gene27847:CDS 35.0%
TATGTAGATGCAGAAAGTTC+TGG - chr4.1:13162392-13162411 MS.gene27847:CDS 35.0%
! AAGAGTACATTCTCCAAAGA+TGG - chr4.1:13162550-13162569 MS.gene27847:CDS 35.0%
! ATGTGAGGAGTTTAAAGCAA+AGG - chr4.1:13162454-13162473 MS.gene27847:CDS 35.0%
! CATTATCAAAGCATTTCGAC+AGG - chr4.1:13162841-13162860 MS.gene27847:CDS 35.0%
!! TTTCAAAGTGTCGGAGAAAA+TGG - chr4.1:13162422-13162441 MS.gene27847:CDS 35.0%
AGGAAGTTGAGTGCTTAAAG+AGG - chr4.1:13162213-13162232 MS.gene27847:CDS 40.0%
ATGTGAGCAGAGAATTACAG+AGG - chr4.1:13162501-13162520 MS.gene27847:CDS 40.0%
ATTGTGATGAACCATCAGAC+GGG + chr4.1:13161983-13162002 None:intergenic 40.0%
ATTGTTGTCGTTGCATCAGA+CGG + chr4.1:13161936-13161955 None:intergenic 40.0%
CAATTTCCTTGTGGGAATAG+AGG - chr4.1:13161999-13162018 MS.gene27847:CDS 40.0%
GAAAGAAGAAGAGGAAATGG+TGG - chr4.1:13162640-13162659 MS.gene27847:CDS 40.0%
GAAATTACAGAATGCAGCAG+AGG - chr4.1:13162280-13162299 MS.gene27847:CDS 40.0%
GAAGCCAGTAATGTACAGTT+TGG - chr4.1:13162118-13162137 MS.gene27847:CDS 40.0%
GAGGGAAATAATTGGGTTCT+TGG + chr4.1:13162371-13162390 None:intergenic 40.0%
GCTTAAAGAGGAGATATGAG+AGG - chr4.1:13162225-13162244 MS.gene27847:CDS 40.0%
GGTCTTGGATTTCAAAGTGT+CGG - chr4.1:13162413-13162432 MS.gene27847:CDS 40.0%
GGTTCATCACAATTTCCTTG+TGG - chr4.1:13161990-13162009 MS.gene27847:CDS 40.0%
TCGACTTTAGTAGCCATCTT+TGG + chr4.1:13162566-13162585 None:intergenic 40.0%
TGGAGAATGTACTCTTACCT+TGG + chr4.1:13162546-13162565 None:intergenic 40.0%
! GCATTCTGGAGATTGTCATT+TGG - chr4.1:13162050-13162069 MS.gene27847:CDS 40.0%
! GGGTTCTTGGTGATTCAAAT+TGG + chr4.1:13162358-13162377 None:intergenic 40.0%
! TCAAAGCATTTCGACAGGTA+TGG - chr4.1:13162846-13162865 MS.gene27847:CDS 40.0%
! TGCAGTTGTGAAGTGTTCTT+TGG - chr4.1:13162691-13162710 MS.gene27847:CDS 40.0%
! TTGGAGCTCATCCTTTTCTA+AGG + chr4.1:13162339-13162358 None:intergenic 40.0%
!! AATAGAGGCAGGTTTTATGG+AGG - chr4.1:13162014-13162033 MS.gene27847:CDS 40.0%
ACTCTTCCATTTCTTCTGGC+TGG + chr4.1:13162775-13162794 None:intergenic 45.0%
AGAAGAAGAGGAAATGGTGG+AGG - chr4.1:13162643-13162662 MS.gene27847:CDS 45.0%
CTTACCTTGGAACTCTGCTT+TGG + chr4.1:13162533-13162552 None:intergenic 45.0%
GAAACCAAAGCAGAGTTCCA+AGG - chr4.1:13162526-13162545 MS.gene27847:CDS 45.0%
GATAAGCCAGCCAGAAGAAA+TGG - chr4.1:13162766-13162785 MS.gene27847:CDS 45.0%
TGAGCAGAGAATTACAGAGG+AGG - chr4.1:13162504-13162523 MS.gene27847:CDS 45.0%
TGGTGGAGGAAACAGAAGAA+GGG - chr4.1:13162657-13162676 MS.gene27847:CDS 45.0%
TTGTGATGAACCATCAGACG+GGG + chr4.1:13161982-13162001 None:intergenic 45.0%
TTGTTGTCGTTGCATCAGAC+GGG + chr4.1:13161935-13161954 None:intergenic 45.0%
! ATGGTGGAGGAAACAGAAGA+AGG - chr4.1:13162656-13162675 MS.gene27847:CDS 45.0%
! GATGCAGAAAGTTCTGGTCT+TGG - chr4.1:13162398-13162417 MS.gene27847:CDS 45.0%
! GGGAATAGAGGCAGGTTTTA+TGG - chr4.1:13162011-13162030 MS.gene27847:CDS 45.0%
AACCTGCCTCTATTCCCACA+AGG + chr4.1:13162008-13162027 None:intergenic 50.0%
GTGGTGAGGATGATGCATTC+TGG - chr4.1:13162036-13162055 MS.gene27847:CDS 50.0%
TGTTGTCGTTGCATCAGACG+GGG + chr4.1:13161934-13161953 None:intergenic 50.0%
TTCCTTGTGGGAATAGAGGC+AGG - chr4.1:13162003-13162022 MS.gene27847:CDS 50.0%
!! AGAGGCAGGTTTTATGGAGG+TGG - chr4.1:13162017-13162036 MS.gene27847:CDS 50.0%
!! CAGGTTTTATGGAGGTGGTG+AGG - chr4.1:13162022-13162041 MS.gene27847:CDS 50.0%
ACTCAGAACTCCCCGTCTGA+TGG - chr4.1:13161969-13161988 MS.gene27847:CDS 55.0%
!! ATCAGACGGGGAGTTCTGAG+TGG + chr4.1:13161970-13161989 None:intergenic 55.0%
!! TCAGACGGGGAGTTCTGAGT+GGG + chr4.1:13161969-13161988 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 13161921 13162931 13161921 ID=MS.gene27847
chr4.1 mRNA 13161921 13162931 13161921 ID=MS.gene27847.t1;Parent=MS.gene27847
chr4.1 exon 13161921 13162931 13161921 ID=MS.gene27847.t1.exon1;Parent=MS.gene27847.t1
chr4.1 CDS 13161921 13162931 13161921 ID=cds.MS.gene27847.t1;Parent=MS.gene27847.t1
Gene Sequence

>MS.gene27847

ATGCAGAACTCCCCGTCTGATGCAACGACAACAATCAAGCATTATCCCACTCAGAACTCCCCGTCTGATGGTTCATCACAATTTCCTTGTGGGAATAGAGGCAGGTTTTATGGAGGTGGTGAGGATGATGCATTCTGGAGATTGTCATTTGGTGAAGAGTTTACTAATGACCAAAAGAAGAAAAGTAAAGATATTCTGAAGCCAGTAATGTACAGTTTGGATGTGAAAAGACATGGAAGAAGAAGAAGAAGAAGAGAAGATAGAAAATTGCTTAATGAAACAAAGAGTGCAAAGGAAGTTGAGTGCTTAAAGAGGAGATATGAGAGGAAAGCACAAAGAGCTTTACAAGAGCAGCTCTTGAAATTACAGAATGCAGCAGAGGAAGCTGAATTTGTTGCATCAAGTAAATGTAAATCCTTAGAAAAGGATGAGCTCCAATTTGAATCACCAAGAACCCAATTATTTCCCTCTTATGTAGATGCAGAAAGTTCTGGTCTTGGATTTCAAAGTGTCGGAGAAAATGGTGTGAATCAATGTGAGGAGTTTAAAGCAAAGGTTAACAAAAGGAGGGAATCAGTTCATGTGAGCAGAGAATTACAGAGGAGGAAACCAAAGCAGAGTTCCAAGGTAAGAGTACATTCTCCAAAGATGGCTACTAAAGTCGAAATACGCAAAATGAAGGCGATAGAAGACAAAAAGAAAGCAAAACTAAAGATGAAGAAAGAAGAAGAGGAAATGGTGGAGGAAACAGAAGAAGGGTTAGATAGTTTTGCAGTTGTGAAGTGTTCTTTGGATCCACAACAAGATTTTAGAGATTCAATGATTGAGATGATCAAAGAGAAAGAGATAAGCCAGCCAGAAGAAATGGAAGAGTTGTTAGCATGCTATTTGAGTTTGAATTCCAATGAATACCATGATATCATTATCAAAGCATTTCGACAGGTATGGTTATGCATGAGCCATTCAAGTTTGTGTAATAAATCAGAGAAACAATGTTGTTACTATGATTAG
Protein sequence

>MS.gene27847.t1

MQNSPSDATTTIKHYPTQNSPSDGSSQFPCGNRGRFYGGGEDDAFWRLSFGEEFTNDQKKKSKDILKPVMYSLDVKRHGRRRRRREDRKLLNETKSAKEVECLKRRYERKAQRALQEQLLKLQNAAEEAEFVASSKCKSLEKDELQFESPRTQLFPSYVDAESSGLGFQSVGENGVNQCEEFKAKVNKRRESVHVSRELQRRKPKQSSKVRVHSPKMATKVEIRKMKAIEDKKKAKLKMKKEEEEMVEETEEGLDSFAVVKCSLDPQQDFRDSMIEMIKEKEISQPEEMEELLACYLSLNSNEYHDIIIKAFRQVWLCMSHSSLCNKSEKQCCYYD