AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062843

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062843.t1 MTR_2g070310 96.831 284 9 0 1 284 1 284 0.0 567
MS.gene062843.t1 MTR_1g084050 49.438 267 135 0 15 281 38 304 5.66e-93 278
MS.gene062843.t1 MTR_7g112130 47.940 267 139 0 15 281 5 271 2.45e-90 271
MS.gene062843.t1 MTR_2g034240 47.955 269 138 2 15 281 5 273 1.32e-86 260
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062843.t1 AT5G56080 52.030 271 125 3 15 281 5 274 2.19e-91 274
MS.gene062843.t1 AT5G04950 49.815 271 132 2 15 281 5 275 5.24e-91 273
MS.gene062843.t1 AT1G56430 48.881 268 132 4 18 281 9 275 3.16e-88 266
MS.gene062843.t1 AT1G09240 51.292 271 127 4 15 281 5 274 3.21e-88 266

Find 55 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCACTAAGTTCAATTATAT+TGG 0.247107 2.4:-25097562 MS.gene062843:CDS
ATTTGTGACACAAGATATTA+TGG 0.267068 2.4:-25097427 MS.gene062843:CDS
TAGCTTATCGATCAAGCTTT+AGG 0.325153 2.4:+25097144 None:intergenic
TTTCTAAGCTAGAATCTCTT+AGG 0.328740 2.4:-25097902 MS.gene062843:CDS
TCCTTCTGCTTTGCCACAAA+GGG 0.365628 2.4:+25097761 None:intergenic
CAGCTTCAAAATTGAAGGAT+TGG 0.377323 2.4:+25097976 None:intergenic
TGCTAGCAAGATTGTGGCTT+CGG 0.391793 2.4:-25097475 MS.gene062843:CDS
CATTCACAACACCATTCTCT+TGG 0.394956 2.4:+25097619 None:intergenic
TTAACATAGTTTCCATGGTA+AGG 0.396731 2.4:+25097669 None:intergenic
GCCAATATAATTGAACTTAG+TGG 0.399358 2.4:+25097561 None:intergenic
ATGGAAGCTAAGGAGAGGTT+AGG 0.399895 2.4:-25097408 MS.gene062843:CDS
AAAGTAGCATTTATAGGATC+TGG 0.401897 2.4:-25097591 MS.gene062843:CDS
ATATCATTCTCCTCAACAAT+AGG 0.407208 2.4:+25097240 None:intergenic
GAAAGCCTCATTCCCCTTTG+TGG 0.425154 2.4:-25097774 MS.gene062843:CDS
AAGAGATTCTAGCTTAGAAA+TGG 0.430571 2.4:+25097905 None:intergenic
CGCATTGTCTTAACCTCTTG+TGG 0.432545 2.4:+25097798 None:intergenic
TTGCTTGTAAGAAGTGCAAA+AGG 0.435002 2.4:-25097282 MS.gene062843:CDS
ATCTCTTAGGCCTTCAAAGC+AGG 0.436005 2.4:-25097889 MS.gene062843:CDS
AGGGTGTTAACCTGCTTTGA+AGG 0.438492 2.4:+25097879 None:intergenic
ATAATTGAACTTAGTGGCAT+TGG 0.438717 2.4:+25097567 None:intergenic
TGTCTTAACCTCTTGTGGTA+AGG 0.449698 2.4:+25097803 None:intergenic
TATTGTTGAGGAGAATGATA+TGG 0.461887 2.4:-25097238 MS.gene062843:CDS
GAGATATGAGAAGCTCTTGT+GGG 0.466406 2.4:+25097949 None:intergenic
GTTTGACTAAGTGAGTCAAA+AGG 0.470350 2.4:+25097859 None:intergenic
AACAAAATCCTCCAAGAGAA+TGG 0.470902 2.4:-25097630 MS.gene062843:CDS
GATTTCAGCTTCAAAATTGA+AGG 0.471295 2.4:+25097971 None:intergenic
CTTTGCCACAAAGGGGAATG+AGG 0.471873 2.4:+25097769 None:intergenic
CTAGTTTAACATAGTTTCCA+TGG 0.475050 2.4:+25097664 None:intergenic
TCACAACACCATTCTCTTGG+AGG 0.492086 2.4:+25097622 None:intergenic
GTCCTTCTGCTTTGCCACAA+AGG 0.493701 2.4:+25097760 None:intergenic
TAACATAGTTTCCATGGTAA+GGG 0.496507 2.4:+25097670 None:intergenic
TGGTAAGGCTTCAATCTCAA+TGG 0.508290 2.4:+25097818 None:intergenic
GCTTCAATCTCAATGGATGA+AGG 0.509882 2.4:+25097825 None:intergenic
ACAAGATATTATGGAAGCTA+AGG 0.511704 2.4:-25097418 MS.gene062843:CDS
CCCCTTTGTGGCAAAGCAGA+AGG 0.513729 2.4:-25097762 MS.gene062843:CDS
AAGGATTGGAAAGATGCCAT+TGG 0.518413 2.4:+25097990 None:intergenic
CGGATAAAGCACTTGAAAAG+AGG 0.520656 2.4:-25097455 MS.gene062843:CDS
TTTGACTAAGTGAGTCAAAA+GGG 0.523641 2.4:+25097860 None:intergenic
TGGAAGCTAAGGAGAGGTTA+GGG 0.528228 2.4:-25097407 MS.gene062843:CDS
GATTGAAGCCTTACCACAAG+AGG 0.528285 2.4:-25097811 MS.gene062843:CDS
TGAGATATGAGAAGCTCTTG+TGG 0.550637 2.4:+25097948 None:intergenic
ACATATAAGTAAGTATATGA+AGG 0.556331 2.4:-25097316 MS.gene062843:CDS
ATAAGTAAGTATATGAAGGA+AGG 0.558770 2.4:-25097312 MS.gene062843:CDS
TGCTTGTAAGAAGTGCAAAA+GGG 0.561089 2.4:-25097281 MS.gene062843:CDS
TGAGGTTGCTAGCAAGATTG+TGG 0.575623 2.4:-25097481 MS.gene062843:CDS
TATTGATGAGAAAGCTAATG+AGG 0.589845 2.4:-25097499 MS.gene062843:CDS
CTTCAATCTCAATGGATGAA+GGG 0.591587 2.4:+25097826 None:intergenic
AGTAAGTATATGAAGGAAGG+TGG 0.599425 2.4:-25097309 MS.gene062843:CDS
TATATTGGCAACTCATCACA+TGG 0.625569 2.4:-25097547 MS.gene062843:CDS
AACGGATGATGTTATCAACT+CGG 0.627733 2.4:-25097184 MS.gene062843:CDS
CTGCACTTGTTGGTATGCGT+AGG 0.635388 2.4:-25097362 MS.gene062843:CDS
CCTTCTGCTTTGCCACAAAG+GGG 0.652708 2.4:+25097762 None:intergenic
CAATCTCAATGGATGAAGGG+AGG 0.659476 2.4:+25097829 None:intergenic
GAGTTGATAACATCATCCGT+TGG 0.686377 2.4:+25097186 None:intergenic
ATATTATGGAAGCTAAGGAG+AGG 0.694503 2.4:-25097413 MS.gene062843:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATATAAGTAAGTATATGA+AGG - chr2.4:25097826-25097845 MS.gene062843:CDS 20.0%
!!! AAAAGTGTTAAATTTTTCAC+TGG + chr2.4:25097452-25097471 None:intergenic 20.0%
! ATAAGTAAGTATATGAAGGA+AGG - chr2.4:25097830-25097849 MS.gene062843:CDS 25.0%
! ATTTGTGACACAAGATATTA+TGG - chr2.4:25097715-25097734 MS.gene062843:CDS 25.0%
! GCAAAAAAAGTAGCATTTAT+AGG - chr2.4:25097545-25097564 MS.gene062843:CDS 25.0%
!! AGTGAAAAAGTGAAGATTTT+GGG - chr2.4:25097803-25097822 MS.gene062843:CDS 25.0%
!! GAATGATATGGTAAATTTTG+AGG - chr2.4:25097916-25097935 MS.gene062843:CDS 25.0%
!! GTTAAATTTTTCACTGGATT+TGG + chr2.4:25097446-25097465 None:intergenic 25.0%
!!! GCAATATGATTGCATTTTTT+TGG - chr2.4:25097757-25097776 MS.gene062843:CDS 25.0%
!!! TTTTTTGTATCCTATTGTTG+AGG - chr2.4:25097892-25097911 MS.gene062843:CDS 25.0%
AAAGTAGCATTTATAGGATC+TGG - chr2.4:25097551-25097570 MS.gene062843:CDS 30.0%
ACAAGATATTATGGAAGCTA+AGG - chr2.4:25097724-25097743 MS.gene062843:CDS 30.0%
ATAATTGAACTTAGTGGCAT+TGG + chr2.4:25097578-25097597 None:intergenic 30.0%
ATATCATTCTCCTCAACAAT+AGG + chr2.4:25097905-25097924 None:intergenic 30.0%
CTAGTTTAACATAGTTTCCA+TGG + chr2.4:25097481-25097500 None:intergenic 30.0%
GATTTCAGCTTCAAAATTGA+AGG + chr2.4:25097174-25097193 None:intergenic 30.0%
GCCAATATAATTGAACTTAG+TGG + chr2.4:25097584-25097603 None:intergenic 30.0%
GCCACTAAGTTCAATTATAT+TGG - chr2.4:25097580-25097599 MS.gene062843:CDS 30.0%
TAACATAGTTTCCATGGTAA+GGG + chr2.4:25097475-25097494 None:intergenic 30.0%
TATTGATGAGAAAGCTAATG+AGG - chr2.4:25097643-25097662 MS.gene062843:CDS 30.0%
TATTGTTGAGGAGAATGATA+TGG - chr2.4:25097904-25097923 MS.gene062843:CDS 30.0%
TTAACATAGTTTCCATGGTA+AGG + chr2.4:25097476-25097495 None:intergenic 30.0%
TTTCTAAGCTAGAATCTCTT+AGG - chr2.4:25097240-25097259 MS.gene062843:CDS 30.0%
TTTGACTAAGTGAGTCAAAA+GGG + chr2.4:25097285-25097304 None:intergenic 30.0%
! GAGTGAAAAAGTGAAGATTT+TGG - chr2.4:25097802-25097821 MS.gene062843:CDS 30.0%
! GCTTACAATTTTTCATCCAA+CGG - chr2.4:25097940-25097959 MS.gene062843:CDS 30.0%
!! AAGAGATTCTAGCTTAGAAA+TGG + chr2.4:25097240-25097259 None:intergenic 30.0%
AACAAAATCCTCCAAGAGAA+TGG - chr2.4:25097512-25097531 MS.gene062843:CDS 35.0%
AACGGATGATGTTATCAACT+CGG - chr2.4:25097958-25097977 MS.gene062843:CDS 35.0%
AGTAAGTATATGAAGGAAGG+TGG - chr2.4:25097833-25097852 MS.gene062843:CDS 35.0%
ATATTATGGAAGCTAAGGAG+AGG - chr2.4:25097729-25097748 MS.gene062843:CDS 35.0%
CAGCTTCAAAATTGAAGGAT+TGG + chr2.4:25097169-25097188 None:intergenic 35.0%
CTTCAATCTCAATGGATGAA+GGG + chr2.4:25097319-25097338 None:intergenic 35.0%
GTTTGACTAAGTGAGTCAAA+AGG + chr2.4:25097286-25097305 None:intergenic 35.0%
TATATTGGCAACTCATCACA+TGG - chr2.4:25097595-25097614 MS.gene062843:CDS 35.0%
! TGCTTGTAAGAAGTGCAAAA+GGG - chr2.4:25097861-25097880 MS.gene062843:CDS 35.0%
! TTAACACTTTTCCCTTACCA+TGG - chr2.4:25097461-25097480 MS.gene062843:CDS 35.0%
! TTGCTTGTAAGAAGTGCAAA+AGG - chr2.4:25097860-25097879 MS.gene062843:CDS 35.0%
!!! ATTTTTTTGGCTGCACTTGT+TGG - chr2.4:25097770-25097789 MS.gene062843:CDS 35.0%
!!! TTTTCACTGGATTTGGTGTT+TGG + chr2.4:25097439-25097458 None:intergenic 35.0%
CATTCACAACACCATTCTCT+TGG + chr2.4:25097526-25097545 None:intergenic 40.0%
GAGATATGAGAAGCTCTTGT+GGG + chr2.4:25097196-25097215 None:intergenic 40.0%
GCTTCAATCTCAATGGATGA+AGG + chr2.4:25097320-25097339 None:intergenic 40.0%
TGAGATATGAGAAGCTCTTG+TGG + chr2.4:25097197-25097216 None:intergenic 40.0%
TGGTAAGGCTTCAATCTCAA+TGG + chr2.4:25097327-25097346 None:intergenic 40.0%
TGTCTTAACCTCTTGTGGTA+AGG + chr2.4:25097342-25097361 None:intergenic 40.0%
! CGGATAAAGCACTTGAAAAG+AGG - chr2.4:25097687-25097706 MS.gene062843:CDS 40.0%
!! GAGTTGATAACATCATCCGT+TGG + chr2.4:25097959-25097978 None:intergenic 40.0%
ATCTCTTAGGCCTTCAAAGC+AGG - chr2.4:25097253-25097272 MS.gene062843:CDS 45.0%
ATGGAAGCTAAGGAGAGGTT+AGG - chr2.4:25097734-25097753 MS.gene062843:CDS 45.0%
CAATCTCAATGGATGAAGGG+AGG + chr2.4:25097316-25097335 None:intergenic 45.0%
CGCATTGTCTTAACCTCTTG+TGG + chr2.4:25097347-25097366 None:intergenic 45.0%
GATTGAAGCCTTACCACAAG+AGG - chr2.4:25097331-25097350 MS.gene062843:CDS 45.0%
TCACAACACCATTCTCTTGG+AGG + chr2.4:25097523-25097542 None:intergenic 45.0%
TCCTTCTGCTTTGCCACAAA+GGG + chr2.4:25097384-25097403 None:intergenic 45.0%
TGAGGTTGCTAGCAAGATTG+TGG - chr2.4:25097661-25097680 MS.gene062843:CDS 45.0%
TGCTAGCAAGATTGTGGCTT+CGG - chr2.4:25097667-25097686 MS.gene062843:CDS 45.0%
TGGAAGCTAAGGAGAGGTTA+GGG - chr2.4:25097735-25097754 MS.gene062843:CDS 45.0%
! AGGGTGTTAACCTGCTTTGA+AGG + chr2.4:25097266-25097285 None:intergenic 45.0%
CCTTCTGCTTTGCCACAAAG+GGG + chr2.4:25097383-25097402 None:intergenic 50.0%
CTTTGCCACAAAGGGGAATG+AGG + chr2.4:25097376-25097395 None:intergenic 50.0%
GAAAGCCTCATTCCCCTTTG+TGG - chr2.4:25097368-25097387 MS.gene062843:CDS 50.0%
GTCCTTCTGCTTTGCCACAA+AGG + chr2.4:25097385-25097404 None:intergenic 50.0%
! CTGCACTTGTTGGTATGCGT+AGG - chr2.4:25097780-25097799 MS.gene062843:CDS 50.0%
CCCCTTTGTGGCAAAGCAGA+AGG - chr2.4:25097380-25097399 MS.gene062843:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 25097155 25098009 25097155 ID=MS.gene062843
chr2.4 mRNA 25097155 25098009 25097155 ID=MS.gene062843.t1;Parent=MS.gene062843
chr2.4 exon 25097155 25098009 25097155 ID=MS.gene062843.t1.exon1;Parent=MS.gene062843.t1
chr2.4 CDS 25097155 25098009 25097155 ID=cds.MS.gene062843.t1;Parent=MS.gene062843.t1
Gene Sequence

>MS.gene062843

ATGGCATCTTTCCAATCCTTCAATTTTGAAGCTGAAATCCCACAAGAGCTTCTCATATCTCAAATCATGCAAATTCATGCAACCATTTCTAAGCTAGAATCTCTTAGGCCTTCAAAGCAGGTTAACACCCTTTTGACTCACTTAGTCAAACTTTGCATCCTCCCTTCATCCATTGAGATTGAAGCCTTACCACAAGAGGTTAAGACAATGCGTGAAAGCCTCATTCCCCTTTGTGGCAAAGCAGAAGGACTTTTAGAGCTTGAATTCTCAACTTTCATTAGCCAAACACCAAATCCAGTGAAAAATTTAACACTTTTCCCTTACCATGGAAACTATGTTAAACTAGCAAACTATGAGAACAAAATCCTCCAAGAGAATGGTGTTGTGAATGCAAAAAAAGTAGCATTTATAGGATCTGGTCCAATGCCACTAAGTTCAATTATATTGGCAACTCATCACATGGAATCAACTCACTTTGATAATTTTGATATTGATGAGAAAGCTAATGAGGTTGCTAGCAAGATTGTGGCTTCGGATAAAGCACTTGAAAAGAGGATGAAATTTGTGACACAAGATATTATGGAAGCTAAGGAGAGGTTAGGGCAATATGATTGCATTTTTTTGGCTGCACTTGTTGGTATGCGTAGGAGTGAAAAAGTGAAGATTTTGGGACATATAAGTAAGTATATGAAGGAAGGTGGTGTTTTGCTTGTAAGAAGTGCAAAAGGGAGTAGAGCTTTTTTGTATCCTATTGTTGAGGAGAATGATATGGTAAATTTTGAGGTGCTTACAATTTTTCATCCAACGGATGATGTTATCAACTCGGTTGTTCTTCTTCGCAAGCCTAAAGCTTGA
Protein sequence

>MS.gene062843.t1

MASFQSFNFEAEIPQELLISQIMQIHATISKLESLRPSKQVNTLLTHLVKLCILPSSIEIEALPQEVKTMRESLIPLCGKAEGLLELEFSTFISQTPNPVKNLTLFPYHGNYVKLANYENKILQENGVVNAKKVAFIGSGPMPLSSIILATHHMESTHFDNFDIDEKANEVASKIVASDKALEKRMKFVTQDIMEAKERLGQYDCIFLAALVGMRRSEKVKILGHISKYMKEGGVLLVRSAKGSRAFLYPIVEENDMVNFEVLTIFHPTDDVINSVVLLRKPKA