AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63724

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63724.t1 MTR_2g075910 97.606 376 9 0 1 376 4 379 0.0 759
MS.gene63724.t1 MTR_8g059485 57.330 382 139 9 1 376 4 367 7.70e-138 400
MS.gene63724.t1 MTR_8g059485 57.330 382 139 9 1 376 13 376 1.22e-137 400
MS.gene63724.t1 MTR_8g087400 42.895 373 204 4 9 376 14 382 1.76e-98 300
MS.gene63724.t1 MTR_4g025420 40.190 316 177 4 68 376 34 344 4.90e-74 236
MS.gene63724.t1 MTR_0178s0030 29.412 323 210 4 66 376 139 455 8.97e-39 145
MS.gene63724.t1 MTR_5g075180 31.546 317 189 5 61 376 78 367 1.54e-36 138
MS.gene63724.t1 MTR_3g462150 29.231 325 205 7 70 376 92 409 5.60e-36 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63724.t1 AT1G53380 49.476 382 180 6 1 376 4 378 1.46e-129 379
MS.gene63724.t1 AT1G53380 49.476 382 180 6 1 376 4 378 1.46e-129 379
MS.gene63724.t1 AT1G53380 49.476 382 180 6 1 376 4 378 1.46e-129 379
MS.gene63724.t1 AT1G53380 49.476 382 180 6 1 376 4 378 1.46e-129 379
MS.gene63724.t1 AT1G53380 49.476 382 180 6 1 376 4 378 1.46e-129 379
MS.gene63724.t1 AT3G14870 47.558 389 186 5 1 376 4 387 1.13e-127 375
MS.gene63724.t1 AT3G14870 47.558 389 186 5 1 376 4 387 1.13e-127 375
MS.gene63724.t1 AT3G14870 47.558 389 186 5 1 376 4 387 1.13e-127 375
MS.gene63724.t1 AT3G14870 47.558 389 186 5 1 376 8 391 1.25e-127 375
MS.gene63724.t1 AT3G14870 47.558 389 186 5 1 376 5 388 1.32e-127 375
MS.gene63724.t1 AT1G29300 39.695 393 202 6 2 376 6 381 8.32e-82 257
MS.gene63724.t1 AT2G45260 37.176 347 208 3 40 376 4 350 1.30e-75 240
MS.gene63724.t1 AT4G34080 36.786 280 170 2 59 331 2 281 7.04e-56 185
MS.gene63724.t1 AT4G33320 34.965 286 178 3 59 336 2 287 1.77e-49 168
MS.gene63724.t1 AT2G30380 30.592 304 175 2 73 376 76 343 4.87e-37 139
MS.gene63724.t1 AT3G60680 27.974 311 211 3 71 376 120 422 3.30e-36 138
MS.gene63724.t1 AT5G58960 26.866 335 206 5 70 376 86 409 1.33e-32 127
MS.gene63724.t1 AT5G58960 26.866 335 206 5 70 376 86 409 1.33e-32 127
MS.gene63724.t1 AT5G58960 27.964 329 210 6 70 376 161 484 2.20e-32 128
MS.gene63724.t1 AT2G32130 43.902 123 69 0 71 193 35 157 4.81e-26 102
MS.gene63724.t1 AT4G36100 45.098 102 53 1 59 157 2 103 8.35e-20 87.8

Find 40 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTCGCAAACGATGATTT+TGG 0.210428 2.1:+23767119 None:intergenic
TCATTTGGAAGATTGAAATT+AGG 0.213794 2.1:+23767239 None:intergenic
GCTAGCATTTCAACAGTTAA+AGG 0.231753 2.1:-23767845 MS.gene63724:CDS
TCCATGTTTGTTTCATCCTT+TGG 0.256313 2.1:+23767971 None:intergenic
GATAATGTTGTTCACATATC+AGG 0.291769 2.1:-23767479 MS.gene63724:CDS
AGCTGAATCGAAGGCGATAA+AGG 0.309655 2.1:-23767663 MS.gene63724:CDS
CATTTGGAAGATTGAAATTA+GGG 0.340570 2.1:+23767240 None:intergenic
ATGAAATGAGATCTGCAAAA+TGG 0.347278 2.1:-23767379 MS.gene63724:CDS
TTCCTAGCTAATTTCTTGCT+TGG 0.381111 2.1:+23768055 None:intergenic
TCATCAGGAAGTGCCTCATT+TGG 0.398030 2.1:+23767224 None:intergenic
GACGAAGAACAGTAGCAAAA+TGG 0.401046 2.1:+23767444 None:intergenic
CTGTGATTCCAACTTCTTTG+CGG 0.406687 2.1:+23767616 None:intergenic
TCAGAAGCTTCAATTCCATC+AGG 0.419938 2.1:+23767782 None:intergenic
TTGCTTGGTGTCACTGCTGA+AGG 0.427239 2.1:+23768070 None:intergenic
GTTTCTTAAAGAGAAATTAG+TGG 0.430754 2.1:-23767567 MS.gene63724:CDS
GAAACTCTCCACCACTCAAA+AGG 0.438973 2.1:+23767021 None:intergenic
CGAGGTTACCGCAAAGAAGT+TGG 0.473562 2.1:-23767624 MS.gene63724:CDS
CGCAAAGAAGTTGGAATCAC+AGG 0.473710 2.1:-23767615 MS.gene63724:CDS
TGCTCTAAGATGAAGAACTT+TGG 0.476082 2.1:+23768027 None:intergenic
CATCGTTTGCGAAATTCTGC+AGG 0.482019 2.1:-23767112 MS.gene63724:CDS
GCTGAATCGAAGGCGATAAA+GGG 0.482778 2.1:-23767662 MS.gene63724:CDS
TCAATTCCATCAGGGTCAAA+AGG 0.497708 2.1:+23767791 None:intergenic
GCTGCGAGTATCGCTTTCTC+TGG 0.498611 2.1:+23767683 None:intergenic
TAATTTCAATCTTCCAAATG+AGG 0.502545 2.1:-23767237 MS.gene63724:CDS
ATGAAGAGATTGAAGAACAA+AGG 0.502913 2.1:-23767901 MS.gene63724:CDS
TGAAATGAGATCTGCAAAAT+GGG 0.517744 2.1:-23767378 MS.gene63724:CDS
GAGAAGAGATTGAATCAAAG+TGG 0.546796 2.1:-23767518 MS.gene63724:CDS
TGGAAAAGACTACAATAACT+TGG 0.552801 2.1:-23767952 MS.gene63724:CDS
CTTCTTTGCGGTAACCTCGT+AGG 0.582207 2.1:+23767628 None:intergenic
TCCAAAGGATGAAACAAACA+TGG 0.604906 2.1:-23767972 MS.gene63724:CDS
CAGAAGCTTCAATTCCATCA+GGG 0.612641 2.1:+23767783 None:intergenic
AGTATCGCTTTCTCTGGTGA+AGG 0.613880 2.1:+23767689 None:intergenic
TGCTACTGTTCTTCGTCACG+CGG 0.615594 2.1:-23767438 MS.gene63724:CDS
TATATCTGATACAAATCCAA+AGG 0.615715 2.1:-23767987 MS.gene63724:CDS
GATACTCGCAGCTGAATCGA+AGG 0.617427 2.1:-23767672 MS.gene63724:CDS
GATCGATTCGAAACTTTGTG+AGG 0.621541 2.1:-23767412 MS.gene63724:CDS
CACCAAGCAAGAAATTAGCT+AGG 0.637970 2.1:-23768057 MS.gene63724:CDS
AGAACAGTAGCAAAATGGCT+AGG 0.639681 2.1:+23767449 None:intergenic
TGATGCTATTGAACACAATG+TGG 0.709156 2.1:-23767339 MS.gene63724:CDS
GGGTGTCATTAAAACCTACG+AGG 0.775148 2.1:-23767642 MS.gene63724:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAAAAATCAACAAAAT+TGG - chr2.1:23767651-23767670 MS.gene63724:CDS 15.0%
! CATTTGGAAGATTGAAATTA+GGG + chr2.1:23767616-23767635 None:intergenic 25.0%
! GTTTCTTAAAGAGAAATTAG+TGG - chr2.1:23767286-23767305 MS.gene63724:CDS 25.0%
! TAATTTCAATCTTCCAAATG+AGG - chr2.1:23767616-23767635 MS.gene63724:CDS 25.0%
! TATATCTGATACAAATCCAA+AGG - chr2.1:23766866-23766885 MS.gene63724:intron 25.0%
! TCATTTGGAAGATTGAAATT+AGG + chr2.1:23767617-23767636 None:intergenic 25.0%
!! AAAAATGATGACTCCATTTT+TGG + chr2.1:23767791-23767810 None:intergenic 25.0%
!!! AAAATGGAGTCATCATTTTT+TGG - chr2.1:23767791-23767810 MS.gene63724:CDS 25.0%
!!! GATGCAAAAAAATCACTTTT+TGG + chr2.1:23767857-23767876 None:intergenic 25.0%
!!! TGTTGATTTTTTCTATCATC+AGG + chr2.1:23767647-23767666 None:intergenic 25.0%
ATGAAATGAGATCTGCAAAA+TGG - chr2.1:23767474-23767493 MS.gene63724:CDS 30.0%
ATGAAGAGATTGAAGAACAA+AGG - chr2.1:23766952-23766971 MS.gene63724:intron 30.0%
GATAATGTTGTTCACATATC+AGG - chr2.1:23767374-23767393 MS.gene63724:CDS 30.0%
TGAAATGAGATCTGCAAAAT+GGG - chr2.1:23767475-23767494 MS.gene63724:CDS 30.0%
TGGAAAAGACTACAATAACT+TGG - chr2.1:23766901-23766920 MS.gene63724:intron 30.0%
! AAATCTTTCAAGTGGGAAAA+GGG - chr2.1:23767945-23767964 MS.gene63724:CDS 30.0%
! AATTTCGCAAACGATGATTT+TGG + chr2.1:23767737-23767756 None:intergenic 30.0%
! TAGATTTTCTGATGTGTACA+TGG - chr2.1:23767970-23767989 MS.gene63724:CDS 30.0%
! TTTTGCATCTTTTGCTGAAA+TGG - chr2.1:23767868-23767887 MS.gene63724:CDS 30.0%
!! TTGTTTAGCCTTTTCTTTTG+AGG - chr2.1:23767913-23767932 MS.gene63724:CDS 30.0%
ACAACAGTAAAACCAACAAC+TGG + chr2.1:23768058-23768077 None:intergenic 35.0%
AGCTTGAACCTCAAAAGAAA+AGG + chr2.1:23767924-23767943 None:intergenic 35.0%
GAGAAGAGATTGAATCAAAG+TGG - chr2.1:23767335-23767354 MS.gene63724:CDS 35.0%
GCTAGCATTTCAACAGTTAA+AGG - chr2.1:23767008-23767027 MS.gene63724:CDS 35.0%
TCAAGCTGAAATCTTTCAAG+TGG - chr2.1:23767937-23767956 MS.gene63724:CDS 35.0%
TCCAAAGGATGAAACAAACA+TGG - chr2.1:23766881-23766900 MS.gene63724:intron 35.0%
TCCATGTTTGTTTCATCCTT+TGG + chr2.1:23766885-23766904 None:intergenic 35.0%
TGATGCTATTGAACACAATG+TGG - chr2.1:23767514-23767533 MS.gene63724:CDS 35.0%
TTCCTAGCTAATTTCTTGCT+TGG + chr2.1:23766801-23766820 None:intergenic 35.0%
! ATTCACAGAAACCTTTTGAG+TGG - chr2.1:23767821-23767840 MS.gene63724:CDS 35.0%
! CAAGCTGAAATCTTTCAAGT+GGG - chr2.1:23767938-23767957 MS.gene63724:CDS 35.0%
! GAAATCTTTCAAGTGGGAAA+AGG - chr2.1:23767944-23767963 MS.gene63724:CDS 35.0%
! GAGACTTGTTCATCCAAAAA+TGG - chr2.1:23767775-23767794 MS.gene63724:CDS 35.0%
! TTTTGCTGAAATGGCTAAGA+GGG - chr2.1:23767877-23767896 MS.gene63724:CDS 35.0%
!! TGCTCTAAGATGAAGAACTT+TGG + chr2.1:23766829-23766848 None:intergenic 35.0%
!! TTACTGTTGTTCCTGGTTTT+AGG - chr2.1:23768068-23768087 MS.gene63724:CDS 35.0%
AGAACAGTAGCAAAATGGCT+AGG + chr2.1:23767407-23767426 None:intergenic 40.0%
CACCAAGCAAGAAATTAGCT+AGG - chr2.1:23766796-23766815 MS.gene63724:intron 40.0%
CAGAAGCTTCAATTCCATCA+GGG + chr2.1:23767073-23767092 None:intergenic 40.0%
CTGTGATTCCAACTTCTTTG+CGG + chr2.1:23767240-23767259 None:intergenic 40.0%
GACGAAGAACAGTAGCAAAA+TGG + chr2.1:23767412-23767431 None:intergenic 40.0%
TCAATTCCATCAGGGTCAAA+AGG + chr2.1:23767065-23767084 None:intergenic 40.0%
TCAGAAGAAGAACCAGTTGT+TGG - chr2.1:23768043-23768062 MS.gene63724:CDS 40.0%
TCAGAAGCTTCAATTCCATC+AGG + chr2.1:23767074-23767093 None:intergenic 40.0%
! CTTTTGCTGAAATGGCTAAG+AGG - chr2.1:23767876-23767895 MS.gene63724:CDS 40.0%
!! GATCGATTCGAAACTTTGTG+AGG - chr2.1:23767441-23767460 MS.gene63724:CDS 40.0%
!!! GTTGGTTTTACTGTTGTTCC+TGG - chr2.1:23768061-23768080 MS.gene63724:CDS 40.0%
!!! GTTGTTCCTGGTTTTAGGAT+TGG - chr2.1:23768073-23768092 MS.gene63724:CDS 40.0%
AGCTGAATCGAAGGCGATAA+AGG - chr2.1:23767190-23767209 MS.gene63724:CDS 45.0%
AGTATCGCTTTCTCTGGTGA+AGG + chr2.1:23767167-23767186 None:intergenic 45.0%
CATCGTTTGCGAAATTCTGC+AGG - chr2.1:23767741-23767760 MS.gene63724:CDS 45.0%
CGCAAAGAAGTTGGAATCAC+AGG - chr2.1:23767238-23767257 MS.gene63724:CDS 45.0%
GAAACTCTCCACCACTCAAA+AGG + chr2.1:23767835-23767854 None:intergenic 45.0%
GCTGAATCGAAGGCGATAAA+GGG - chr2.1:23767191-23767210 MS.gene63724:CDS 45.0%
!! CACAGAAACCTTTTGAGTGG+TGG - chr2.1:23767824-23767843 MS.gene63724:CDS 45.0%
!! GGGTGTCATTAAAACCTACG+AGG - chr2.1:23767211-23767230 MS.gene63724:CDS 45.0%
!! TCATCAGGAAGTGCCTCATT+TGG + chr2.1:23767632-23767651 None:intergenic 45.0%
CGAGGTTACCGCAAAGAAGT+TGG - chr2.1:23767229-23767248 MS.gene63724:CDS 50.0%
CTTCTTTGCGGTAACCTCGT+AGG + chr2.1:23767228-23767247 None:intergenic 50.0%
GATACTCGCAGCTGAATCGA+AGG - chr2.1:23767181-23767200 MS.gene63724:CDS 50.0%
TGCTACTGTTCTTCGTCACG+CGG - chr2.1:23767415-23767434 MS.gene63724:CDS 50.0%
! CAGACACCTTTTGACCCTGA+TGG - chr2.1:23767056-23767075 MS.gene63724:CDS 50.0%
!! TTGCTTGGTGTCACTGCTGA+AGG + chr2.1:23766786-23766805 None:intergenic 50.0%
! GCTGCGAGTATCGCTTTCTC+TGG + chr2.1:23767173-23767192 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 23766777 23768098 23766777 ID=MS.gene63724
chr2.1 mRNA 23766777 23768098 23766777 ID=MS.gene63724.t1;Parent=MS.gene63724
chr2.1 exon 23766977 23768098 23766977 ID=MS.gene63724.t1.exon1;Parent=MS.gene63724.t1
chr2.1 CDS 23766977 23768098 23766977 ID=cds.MS.gene63724.t1;Parent=MS.gene63724.t1
chr2.1 exon 23766777 23766785 23766777 ID=MS.gene63724.t1.exon2;Parent=MS.gene63724.t1
chr2.1 CDS 23766777 23766785 23766777 ID=cds.MS.gene63724.t1;Parent=MS.gene63724.t1
Gene Sequence

>MS.gene63724

ATGAAACCTTCAGCAGTGACACCAAGCAAGAAATTAGCTAGGAATTTCGCCAAAGTTCTTCATCTTAGAGCATTTTTGAAGAATGTTACTATATCTGATACAAATCCAAAGGATGAAACAAACATGGAAAAGACTACAATAACTTGGTCTGAATCATTCAAAAAAGTTGATGAAGATGAAGAGATTGAAGAACAAAGGATTGCAACAGAAGCACTTCTTTCAAAGATTTTTGCTAGCATTTCAACAGTTAAAGGTGCATATGCTGAACTGCAACATTTTCAGACACCTTTTGACCCTGATGGAATTGAAGCTTCTGATAAACTACTAGTTTCTGAGTTGAAGCATTTATCTGAGCTAAAACAATGTTACTTGAAGAAACAATTTGATCCTTCACCAGAGAAAGCGATACTCGCAGCTGAATCGAAGGCGATAAAGGGTGTCATTAAAACCTACGAGGTTACCGCAAAGAAGTTGGAATCACAGGTAAGACTCAAAGATTCTGAGATTATGTTTCTTAAAGAGAAATTAGTGGAAGCTAATAGTCATAACAAGTTGATTGAGAAGAGATTGAATCAAAGTGGAACATTATCAGTACTTGATAATGTTGTTCACATATCAGGATTAAGTCCTAGCCATTTTGCTACTGTTCTTCGTCACGCGGTTAGATCGATTCGAAACTTTGTGAGGATTATTGTTGATGAAATGAGATCTGCAAAATGGGATATTGATGCTGCTGTTGATGCTATTGAACACAATGTGGTTTATATGATAGAAGATCACAAGTGTTTCACAATTGAATCTTTTGTTTGCAAAGAAATGTTTGATGCATTTCACTTCCCTAATTTCAATCTTCCAAATGAGGCACTTCCTGATGATAGAAAAAATCAACAAAATTGGTTCTTTGAAAAGTTCAATGAGTTGAAATCGACGAAAGCTAAAGACTTTCTTGCTGAGAAACCAAAATCATCGTTTGCGAAATTCTGCAGGAACAAGTATTTGAGACTTGTTCATCCAAAAATGGAGTCATCATTTTTTGGCAACATGATTCACAGAAACCTTTTGAGTGGTGGAGAGTTTCCAAAAAGTGATTTTTTTGCATCTTTTGCTGAAATGGCTAAGAGGGTTTATCTCTTACATTGTTTAGCCTTTTCTTTTGAGGTTCAAGCTGAAATCTTTCAAGTGGGAAAAGGGTGTAGATTTTCTGATGTGTACATGGAAAGTGTGAATGATGAAATGTTTGTGTTTTCAGACAAGACAGTTGTTGAATCAGAAGAAGAACCAGTTGTTGGTTTTACTGTTGTTCCTGGTTTTAGGATTGGTAA
Protein sequence

>MS.gene63724.t1

MKPSAVTPSKKLARNFAKVLHLRAFLKNVTISDTNPKDETNMEKTTITWSESFKKVDEDEEIEEQRIATEALLSKIFASISTVKGAYAELQHFQTPFDPDGIEASDKLLVSELKHLSELKQCYLKKQFDPSPEKAILAAESKAIKGVIKTYEVTAKKLESQVRLKDSEIMFLKEKLVEANSHNKLIEKRLNQSGTLSVLDNVVHISGLSPSHFATVLRHAVRSIRNFVRIIVDEMRSAKWDIDAAVDAIEHNVVYMIEDHKCFTIESFVCKEMFDAFHFPNFNLPNEALPDDRKNQQNWFFEKFNELKSTKAKDFLAEKPKSSFAKFCRNKYLRLVHPKMESSFFGNMIHRNLLSGGEFPKSDFFASFAEMAKRDW