AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42222

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42222.t1 MTR_7g077620 65.952 373 117 7 1 366 1 370 1.81e-160 455
MS.gene42222.t1 MTR_7g077650 61.097 383 123 13 1 368 1 372 4.61e-144 413
MS.gene42222.t1 MTR_7g077660 60.647 371 133 9 5 368 4 368 1.10e-138 399
MS.gene42222.t1 MTR_7g076100 72.996 237 57 4 137 368 66 300 5.09e-112 329
MS.gene42222.t1 MTR_7g076100 84.615 52 8 0 1 52 1 52 1.17e-24 102
MS.gene42222.t1 MTR_7g076110 57.823 294 113 6 85 368 21 313 3.58e-103 307
MS.gene42222.t1 MTR_5g038260 43.750 400 166 16 6 368 6 383 1.79e-82 256
MS.gene42222.t1 MTR_1g108740 44.032 377 158 16 6 366 5 344 3.32e-78 244
MS.gene42222.t1 MTR_5g038230 42.278 395 149 16 6 366 4 353 2.66e-76 239
MS.gene42222.t1 MTR_1g064570 40.909 418 173 17 5 368 3 400 6.83e-72 229
MS.gene42222.t1 MTR_5g082770 44.194 310 134 11 6 301 4 288 6.91e-65 208
MS.gene42222.t1 MTR_7g076130 70.161 124 33 2 167 286 25 148 2.29e-53 174
MS.gene42222.t1 MTR_1g016150 50.562 178 81 6 6 178 5 180 3.06e-46 158
MS.gene42222.t1 MTR_1g016150 60.317 63 17 2 255 314 178 235 3.76e-12 65.9
MS.gene42222.t1 MTR_5g082780 40.265 226 103 7 112 323 1 208 1.32e-39 140
MS.gene42222.t1 MTR_1g108750 44.156 154 52 4 6 158 4 124 5.80e-24 95.9
MS.gene42222.t1 MTR_3g114970 24.165 389 228 16 5 364 3 353 8.07e-13 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 70 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGGTTGGCTTTCATTAA+TGG 0.158823 7.3:+29666860 MS.gene42222:CDS
GCAGCAACGACATAATTATT+TGG 0.166448 7.3:-29667002 None:intergenic
AAAGAGCAAGCCAACCATTT+TGG 0.203122 7.3:+29667054 MS.gene42222:CDS
AAGTCTTGATGTTTATAAAT+TGG 0.216976 7.3:+29667349 MS.gene42222:CDS
TTCTCATAGTAAGTAAAATT+AGG 0.229231 7.3:-29667206 None:intergenic
TATCCCATATGAAAATTAAA+TGG 0.274469 7.3:+29666823 MS.gene42222:CDS
TAATTATTTGGGCTTGTAAT+GGG 0.291906 7.3:-29666990 None:intergenic
TATGAAAATTAAATGGTCTA+TGG 0.323247 7.3:+29666830 MS.gene42222:CDS
GGTATAGTACTACACTTAAA+AGG 0.328753 7.3:-29666912 None:intergenic
CAGCAACGACATAATTATTT+GGG 0.330157 7.3:-29667001 None:intergenic
TATGTCGTTGCTGCCATTTA+CGG 0.330732 7.3:+29667011 MS.gene42222:CDS
AAGATGAGAAAATCCGTAAA+TGG 0.376143 7.3:-29667024 None:intergenic
AAGAACACATCGATCACATT+AGG 0.376838 7.3:+29666613 MS.gene42222:CDS
CGCATCCCCTTGAAGGAAAT+AGG 0.376883 7.3:-29667593 None:intergenic
AGAAGAACTACCTCTTAGTT+TGG 0.384813 7.3:+29666575 MS.gene42222:CDS
TCTCATAGTAAGTAAAATTA+GGG 0.387493 7.3:-29667205 None:intergenic
ATCTTTACCTATTTCCTTCA+AGG 0.391074 7.3:+29667586 MS.gene42222:CDS
AAAACCTCGCATCCCCTTGA+AGG 0.402319 7.3:-29667600 None:intergenic
TGGTCTATGGACTATTCATT+TGG 0.402663 7.3:+29666843 MS.gene42222:CDS
TTTGAGAGGTGGCAGACTAA+TGG 0.407722 7.3:-29666937 None:intergenic
GGGTTCTACCGCAATTTCAA+TGG 0.408089 7.3:+29667624 MS.gene42222:CDS
AAAAGGATTGACTAGAGTTA+TGG 0.415743 7.3:-29666895 None:intergenic
TGATGTTTATAAATTGGAAC+TGG 0.417875 7.3:+29667355 MS.gene42222:CDS
CTATGGACTATTCATTTGGT+TGG 0.424601 7.3:+29666847 MS.gene42222:CDS
TTGAGAGGTGGCAGACTAAT+GGG 0.429349 7.3:-29666936 None:intergenic
ATAATTATTTGGGCTTGTAA+TGG 0.437481 7.3:-29666991 None:intergenic
TTAGGTTTGGTGTGGTGTGC+AGG 0.455358 7.3:+29666631 MS.gene42222:CDS
CACATCGATCACATTAGGTT+TGG 0.455542 7.3:+29666618 MS.gene42222:CDS
AAAGCCTTTCATCATAGCAT+TGG 0.456480 7.3:-29667259 None:intergenic
AAGCCTTTCATCATAGCATT+GGG 0.457571 7.3:-29667258 None:intergenic
AAGAGGTAGTTCTTCTAAGT+TGG 0.460578 7.3:-29666568 None:intergenic
AATGAGGAAGGTAGTAGATT+GGG 0.475711 7.3:+29666545 None:intergenic
TAGTTTGGTTCTTGATAAGT+TGG 0.478359 7.3:+29666590 MS.gene42222:CDS
GGTTCTACCGCAATTTCAAT+GGG 0.481590 7.3:+29667625 MS.gene42222:CDS
CTATATGAATCCAAAATGGT+TGG 0.483203 7.3:-29667064 None:intergenic
CAATGAGGAAGGTAGTAGAT+TGG 0.484957 7.3:+29666544 None:intergenic
AATCTTTGAATGGAAACATA+TGG 0.491516 7.3:+29667291 MS.gene42222:CDS
AGGAGGATTGTTGATCTTGA+AGG 0.506138 7.3:-29667165 None:intergenic
ATACAAGGATCTCTTCTCGT+TGG 0.507143 7.3:-29666763 None:intergenic
GAGATCTATAATGTGAAGGA+TGG 0.509549 7.3:+29667548 MS.gene42222:CDS
CTGCTAATTGCTGATGGCAG+CGG 0.512572 7.3:+29667128 MS.gene42222:CDS
ACCTCTCAAATCTGTTTACA+AGG 0.516115 7.3:+29666950 MS.gene42222:CDS
TTATCAAGAACCAAACTAAG+AGG 0.520565 7.3:-29666585 None:intergenic
TCTTTACCTATTTCCTTCAA+GGG 0.520742 7.3:+29667587 MS.gene42222:CDS
TTGGTGTGGTGTGCAGGAGT+TGG 0.525759 7.3:+29666637 MS.gene42222:CDS
CATCCCAATGCTATGATGAA+AGG 0.550966 7.3:+29667255 MS.gene42222:CDS
TTCTAACTTGGAGAAACAAG+AGG 0.552906 7.3:-29667474 None:intergenic
ATAAATTGGAACTGGATGCC+CGG 0.559787 7.3:+29667363 MS.gene42222:CDS
GTTGATCTTGAAGGATACAA+TGG 0.562836 7.3:-29667156 None:intergenic
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.3:-29666976 None:intergenic
CTTTACCTATTTCCTTCAAG+GGG 0.577911 7.3:+29667588 MS.gene42222:CDS
AATTATTTGGGCTTGTAATG+GGG 0.583882 7.3:-29666989 None:intergenic
AAAGGTCTGCTAATTGCTGA+TGG 0.586662 7.3:+29667122 MS.gene42222:CDS
GTGACTTAGAATGCTATACA+AGG 0.596070 7.3:-29666778 None:intergenic
GTGAGGATCATGAGCATAGG+TGG 0.597353 7.3:-29666711 None:intergenic
TATCAATCCCATTGAAATTG+CGG 0.597459 7.3:-29667632 None:intergenic
CTTAGGCTTAGCAATGAGGA+AGG 0.598112 7.3:+29666533 None:intergenic
CTTTCATCATAGCATTGGGA+TGG 0.603237 7.3:-29667254 None:intergenic
TTGTAAACAGATTTGAGAGG+TGG 0.604090 7.3:-29666948 None:intergenic
CGATCACATTAGGTTTGGTG+TGG 0.607424 7.3:+29666623 MS.gene42222:CDS
TTCGAGACAGTTTGTCTGTG+AGG 0.609415 7.3:-29666728 None:intergenic
ATTTCCTTCAAGGGGATGCG+AGG 0.609973 7.3:+29667596 MS.gene42222:CDS
GTTAGAGATCTATAATGTGA+AGG 0.621618 7.3:+29667544 MS.gene42222:CDS
TTGGAACTGGATGCCCGGAG+TGG 0.634177 7.3:+29667368 MS.gene42222:CDS
TTTGAATGGAAACATATGGA+TGG 0.653937 7.3:+29667295 MS.gene42222:CDS
GGGTCATATGAGTCAGCACA+AGG 0.657673 7.3:-29667185 None:intergenic
TCTGTGAGGATCATGAGCAT+AGG 0.687755 7.3:-29666714 None:intergenic
GCCTTGTAAACAGATTTGAG+AGG 0.700590 7.3:-29666951 None:intergenic
AGAGGTGGCAGACTAATGGG+AGG 0.724272 7.3:-29666933 None:intergenic
TCATATGAGTCAGCACAAGG+AGG 0.731539 7.3:-29667182 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGATGTTGTATTTTATAA+AGG + chr7.3:29667104-29667123 MS.gene42222:CDS 15.0%
!! AAGTCTTGATGTTTATAAAT+TGG + chr7.3:29667349-29667368 MS.gene42222:CDS 20.0%
!! ACCATAAAAATCATCAATTT+AGG + chr7.3:29666679-29666698 MS.gene42222:CDS 20.0%
!! TATCCCATATGAAAATTAAA+TGG + chr7.3:29666823-29666842 MS.gene42222:CDS 20.0%
!! TATGAAAATTAAATGGTCTA+TGG + chr7.3:29666830-29666849 MS.gene42222:CDS 20.0%
!! TCTCATAGTAAGTAAAATTA+GGG - chr7.3:29667208-29667227 None:intergenic 20.0%
!! TTCTCATAGTAAGTAAAATT+AGG - chr7.3:29667209-29667228 None:intergenic 20.0%
!!! AATTGAATCTTTTTCTAACT+TGG - chr7.3:29667489-29667508 None:intergenic 20.0%
!!! AGACCATTTAATTTTCATAT+GGG - chr7.3:29666829-29666848 None:intergenic 20.0%
!!! TAGACCATTTAATTTTCATA+TGG - chr7.3:29666830-29666849 None:intergenic 20.0%
!!! TATTTTGTGAAATCTTTGAA+TGG + chr7.3:29667281-29667300 MS.gene42222:CDS 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG - chr7.3:29666683-29666702 None:intergenic 20.0%
!!! TTTTCTATATGAATCCAAAA+TGG - chr7.3:29667071-29667090 None:intergenic 20.0%
! AATCTTTGAATGGAAACATA+TGG + chr7.3:29667291-29667310 MS.gene42222:CDS 25.0%
! ATAATTATTTGGGCTTGTAA+TGG - chr7.3:29666994-29667013 None:intergenic 25.0%
! ATATGGGATAAAAATGCAAT+GGG - chr7.3:29666813-29666832 None:intergenic 25.0%
! TAATTATTTGGGCTTGTAAT+GGG - chr7.3:29666993-29667012 None:intergenic 25.0%
! TGATGTTTATAAATTGGAAC+TGG + chr7.3:29667355-29667374 MS.gene42222:CDS 25.0%
!!! AAGACAACATTTTATTTGTC+GGG + chr7.3:29667426-29667445 MS.gene42222:CDS 25.0%
!!! GAAGACAACATTTTATTTGT+CGG + chr7.3:29667425-29667444 MS.gene42222:CDS 25.0%
AAAAGGATTGACTAGAGTTA+TGG - chr7.3:29666898-29666917 None:intergenic 30.0%
AAGATGAGAAAATCCGTAAA+TGG - chr7.3:29667027-29667046 None:intergenic 30.0%
AATGAAAAAGCTTGAGAGTT+TGG + chr7.3:29667403-29667422 MS.gene42222:CDS 30.0%
AATTATTTGGGCTTGTAATG+GGG - chr7.3:29666992-29667011 None:intergenic 30.0%
ATCTTTACCTATTTCCTTCA+AGG + chr7.3:29667586-29667605 MS.gene42222:CDS 30.0%
CAGCAACGACATAATTATTT+GGG - chr7.3:29667004-29667023 None:intergenic 30.0%
CATATGGGATAAAAATGCAA+TGG - chr7.3:29666814-29666833 None:intergenic 30.0%
CTATATGAATCCAAAATGGT+TGG - chr7.3:29667067-29667086 None:intergenic 30.0%
GGTATAGTACTACACTTAAA+AGG - chr7.3:29666915-29666934 None:intergenic 30.0%
GTTAGAGATCTATAATGTGA+AGG + chr7.3:29667544-29667563 MS.gene42222:CDS 30.0%
TATGGGATAAAAATGCAATG+GGG - chr7.3:29666812-29666831 None:intergenic 30.0%
TCTTTACCTATTTCCTTCAA+GGG + chr7.3:29667587-29667606 MS.gene42222:CDS 30.0%
TTATCAAGAACCAAACTAAG+AGG - chr7.3:29666588-29666607 None:intergenic 30.0%
TTTGAATGGAAACATATGGA+TGG + chr7.3:29667295-29667314 MS.gene42222:CDS 30.0%
!! AACATTTTATTTGTCGGGAT+TGG + chr7.3:29667431-29667450 MS.gene42222:CDS 30.0%
!! ATTTGGTTGGCTTTCATTAA+TGG + chr7.3:29666860-29666879 MS.gene42222:CDS 30.0%
!! TAGTTTGGTTCTTGATAAGT+TGG + chr7.3:29666590-29666609 MS.gene42222:CDS 30.0%
AAAGCCTTTCATCATAGCAT+TGG - chr7.3:29667262-29667281 None:intergenic 35.0%
AAGAACACATCGATCACATT+AGG + chr7.3:29666613-29666632 MS.gene42222:CDS 35.0%
AAGAGGTAGTTCTTCTAAGT+TGG - chr7.3:29666571-29666590 None:intergenic 35.0%
AAGCCTTTCATCATAGCATT+GGG - chr7.3:29667261-29667280 None:intergenic 35.0%
ACCTCTCAAATCTGTTTACA+AGG + chr7.3:29666950-29666969 MS.gene42222:CDS 35.0%
AGAAGAACTACCTCTTAGTT+TGG + chr7.3:29666575-29666594 MS.gene42222:CDS 35.0%
CTTTACCTATTTCCTTCAAG+GGG + chr7.3:29667588-29667607 MS.gene42222:CDS 35.0%
GAGATCTATAATGTGAAGGA+TGG + chr7.3:29667548-29667567 MS.gene42222:CDS 35.0%
GCAGCAACGACATAATTATT+TGG - chr7.3:29667005-29667024 None:intergenic 35.0%
GTGACTTAGAATGCTATACA+AGG - chr7.3:29666781-29666800 None:intergenic 35.0%
GTTGATCTTGAAGGATACAA+TGG - chr7.3:29667159-29667178 None:intergenic 35.0%
TTCTAACTTGGAGAAACAAG+AGG - chr7.3:29667477-29667496 None:intergenic 35.0%
TTGTAAACAGATTTGAGAGG+TGG - chr7.3:29666951-29666970 None:intergenic 35.0%
! CTATGGACTATTCATTTGGT+TGG + chr7.3:29666847-29666866 MS.gene42222:CDS 35.0%
! TGGTCTATGGACTATTCATT+TGG + chr7.3:29666843-29666862 MS.gene42222:CDS 35.0%
!! TTTGTTCAAGTTTTCCACTC+CGG - chr7.3:29667385-29667404 None:intergenic 35.0%
AAAGGTCTGCTAATTGCTGA+TGG + chr7.3:29667122-29667141 MS.gene42222:CDS 40.0%
AGGAGGATTGTTGATCTTGA+AGG - chr7.3:29667168-29667187 None:intergenic 40.0%
ATAAATTGGAACTGGATGCC+CGG + chr7.3:29667363-29667382 MS.gene42222:CDS 40.0%
ATACAAGGATCTCTTCTCGT+TGG - chr7.3:29666766-29666785 None:intergenic 40.0%
CACATCGATCACATTAGGTT+TGG + chr7.3:29666618-29666637 MS.gene42222:CDS 40.0%
CATCCCAATGCTATGATGAA+AGG + chr7.3:29667255-29667274 MS.gene42222:CDS 40.0%
GCCTTGTAAACAGATTTGAG+AGG - chr7.3:29666954-29666973 None:intergenic 40.0%
GGTTCTACCGCAATTTCAAT+GGG + chr7.3:29667625-29667644 MS.gene42222:CDS 40.0%
! AAAGAGCAAGCCAACCATTT+TGG + chr7.3:29667054-29667073 MS.gene42222:CDS 40.0%
! CTTTCATCATAGCATTGGGA+TGG - chr7.3:29667257-29667276 None:intergenic 40.0%
! TATGTCGTTGCTGCCATTTA+CGG + chr7.3:29667011-29667030 MS.gene42222:CDS 40.0%
!! TTGTTCAAGTTTTCCACTCC+GGG - chr7.3:29667384-29667403 None:intergenic 40.0%
GGGTTCTACCGCAATTTCAA+TGG + chr7.3:29667624-29667643 MS.gene42222:CDS 45.0%
TCATATGAGTCAGCACAAGG+AGG - chr7.3:29667185-29667204 None:intergenic 45.0%
TCTGTGAGGATCATGAGCAT+AGG - chr7.3:29666717-29666736 None:intergenic 45.0%
TTCGAGACAGTTTGTCTGTG+AGG - chr7.3:29666731-29666750 None:intergenic 45.0%
TTGAGAGGTGGCAGACTAAT+GGG - chr7.3:29666939-29666958 None:intergenic 45.0%
TTTGAGAGGTGGCAGACTAA+TGG - chr7.3:29666940-29666959 None:intergenic 45.0%
!! CGATCACATTAGGTTTGGTG+TGG + chr7.3:29666623-29666642 MS.gene42222:CDS 45.0%
AAAACCTCGCATCCCCTTGA+AGG - chr7.3:29667603-29667622 None:intergenic 50.0%
ATTTCCTTCAAGGGGATGCG+AGG + chr7.3:29667596-29667615 MS.gene42222:CDS 50.0%
CGCATCCCCTTGAAGGAAAT+AGG - chr7.3:29667596-29667615 None:intergenic 50.0%
CTGCTAATTGCTGATGGCAG+CGG + chr7.3:29667128-29667147 MS.gene42222:CDS 50.0%
GGGTCATATGAGTCAGCACA+AGG - chr7.3:29667188-29667207 None:intergenic 50.0%
GTGAGGATCATGAGCATAGG+TGG - chr7.3:29666714-29666733 None:intergenic 50.0%
! CAAGGGGATGCGAGGTTTTT+GGG + chr7.3:29667604-29667623 MS.gene42222:CDS 50.0%
! TCAAGGGGATGCGAGGTTTT+TGG + chr7.3:29667603-29667622 MS.gene42222:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG - chr7.3:29666979-29666998 None:intergenic 50.0%
!! TTAGGTTTGGTGTGGTGTGC+AGG + chr7.3:29666631-29666650 MS.gene42222:CDS 50.0%
AGAGGTGGCAGACTAATGGG+AGG - chr7.3:29666936-29666955 None:intergenic 55.0%
TTGGTGTGGTGTGCAGGAGT+TGG + chr7.3:29666637-29666656 MS.gene42222:CDS 55.0%
TTGGAACTGGATGCCCGGAG+TGG + chr7.3:29667368-29667387 MS.gene42222:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 29666546 29667652 29666546 ID=MS.gene42222
chr7.3 mRNA 29666546 29667652 29666546 ID=MS.gene42222.t1;Parent=MS.gene42222
chr7.3 exon 29666546 29667652 29666546 ID=MS.gene42222.t1.exon1;Parent=MS.gene42222.t1
chr7.3 CDS 29666546 29667652 29666546 ID=cds.MS.gene42222.t1;Parent=MS.gene42222.t1
Gene Sequence

>MS.gene42222

ATGAGGAAGGTAGTAGATTGGGCCAACTTAGAAGAACTACCTCTTAGTTTGGTTCTTGATAAGTTGGAAGAACACATCGATCACATTAGGTTTGGTGTGGTGTGCAGGAGTTGGCTATCTGTTGCAAAGCTTAACCATAAAAATCATCAATTTAGGATTAGTATACCACCTATGCTCATGATCCTCACAGACAAACTGTCTCGAAGACGTAAAAAAACCAACGAGAAGAGATCCTTGTATAGCATTCTAAGTCACAAAGAGTACCCCATTGCATTTTTATCCCATATGAAAATTAAATGGTCTATGGACTATTCATTTGGTTGGCTTTCATTAATGGAATATAACGATGCCATAACTCTAGTCAATCCTTTTAAGTGTAGTACTATACCTCCCATTAGTCTGCCACCTCTCAAATCTGTTTACAAGGCTACCTTGTCTGCTGACCCCATTACAAGCCCAAATAATTATGTCGTTGCTGCCATTTACGGATTTTCTCATCTTGCATTCAAAAGAGCAAGCCAACCATTTTGGATTCATATAGAAAATGAATGTGCTATCATTGATGTTGTATTTTATAAAGGTCTGCTAATTGCTGATGGCAGCGGAAAAACCATTGTATCCTTCAAGATCAACAATCCTCCTTGTGCTGACTCATATGACCCTAATTTTACTTACTATGAGAAGATAGCTAGCACTAGATATAGTGTTCCATCCCAATGCTATGATGAAAGGCTTTATTTTGTGAAATCTTTGAATGGAAACATATGGATGGTGAGAAGATATTTAAATATCGTTTTAGATGAAAGTCTTGATGTTTATAAATTGGAACTGGATGCCCGGAGTGGAAAACTTGAACAAATGAAAAAGCTTGAGAGTTTGGAAGACAACATTTTATTTGTCGGGATTGGTGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCCAAGTTAGAAAAAGATTCAATTTATTTTATTTATGACAATGATATGCATGATTTAGCGTTAGAGATCTATAATGTGAAGGATGGAAGCTGTCAGAGACAATCTTTACCTATTTCCTTCAAGGGGATGCGAGGTTTTTGGGTTCTACCGCAATTTCAATGGGATTGA
Protein sequence

>MS.gene42222.t1

MRKVVDWANLEELPLSLVLDKLEEHIDHIRFGVVCRSWLSVAKLNHKNHQFRISIPPMLMILTDKLSRRRKKTNEKRSLYSILSHKEYPIAFLSHMKIKWSMDYSFGWLSLMEYNDAITLVNPFKCSTIPPISLPPLKSVYKATLSADPITSPNNYVVAAIYGFSHLAFKRASQPFWIHIENECAIIDVVFYKGLLIADGSGKTIVSFKINNPPCADSYDPNFTYYEKIASTRYSVPSQCYDERLYFVKSLNGNIWMVRRYLNIVLDESLDVYKLELDARSGKLEQMKKLESLEDNILFVGIGDSISVSASCFSKLEKDSIYFIYDNDMHDLALEIYNVKDGSCQRQSLPISFKGMRGFWVLPQFQWD