AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene68365

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68365.t1 MTR_5g023880 57.609 184 35 5 1 158 1 167 4.89e-58 179
MS.gene68365.t1 MTR_5g023900 54.237 177 59 3 1 157 1 175 1.47e-56 176
MS.gene68365.t1 MTR_5g023870 67.910 134 24 4 1 130 1 119 3.62e-54 167
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.1:-14521338 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.1:-14521337 None:intergenic
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.1:-14521369 None:intergenic
GGGCTTCTTGATCGTCCTCT+TGG 0.324765 5.1:-14522270 None:intergenic
TGCTTATCAGTTGTATCGGC+TGG 0.335441 5.1:-14522291 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.1:-14521372 None:intergenic
AGTTGGGTTGGTTTCTTTGA+GGG 0.364234 5.1:-14521414 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.1:-14521344 None:intergenic
GGCTTCTTGATCGTCCTCTT+GGG 0.380085 5.1:-14522269 None:intergenic
TAGTTGGGTTGGTTTCTTTG+AGG 0.387471 5.1:-14521415 None:intergenic
AAAGAACTCTGAAGGGTAGT+TGG 0.402173 5.1:-14521431 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.1:-14521368 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.1:-14521366 None:intergenic
TCAGAGTCCTCTATCTCTAT+TGG 0.410192 5.1:-14522176 None:intergenic
CTCTTGGGCCTTCCTTCCTC+TGG 0.410975 5.1:-14522254 None:intergenic
AAGAACTCTGAAGGGTAGTT+GGG 0.428150 5.1:-14521430 None:intergenic
CATGGTTATTCAGCACCTCC+TGG 0.431962 5.1:+14521623 MS.gene68365:CDS
TACAATGTCAAGTCAGGAAG+AGG 0.434728 5.1:+14522199 MS.gene68365:CDS
TCTTTAAGAGCTCGTGAGAA+TGG 0.434908 5.1:+14521449 MS.gene68365:CDS
CAGTGTTGTTGTTTGCGCCT+TGG 0.435389 5.1:-14522229 None:intergenic
ACCTCAACCTGATCAATATG+AGG 0.437745 5.1:+14521682 MS.gene68365:CDS
AGGTGGGGTGGCTGTTGATG+TGG 0.445640 5.1:-14521663 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.1:-14521385 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.1:-14521683 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.463748 5.1:+14521552 MS.gene68365:CDS
CTTTAAGAGCTCGTGAGAAT+GGG 0.465502 5.1:+14521450 MS.gene68365:CDS
AAGTGATGGTCAAGCTATGA+AGG 0.473835 5.1:+14521499 MS.gene68365:CDS
AAGCCAGCCAATAGAGATAG+AGG 0.474391 5.1:+14522169 MS.gene68365:CDS
GCTGTTGATGTGGAAGGAAG+TGG 0.478632 5.1:-14521653 None:intergenic
CTCTGATACAATGTCAAGTC+AGG 0.478904 5.1:+14522193 MS.gene68365:CDS
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.1:-14521679 None:intergenic
AGTCCTCTATCTCTATTGGC+TGG 0.503791 5.1:-14522172 None:intergenic
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.1:-14521386 None:intergenic
ACTCTGAAGGGTAGTTGGGT+TGG 0.513668 5.1:-14521426 None:intergenic
AGCTCGTGAGAATGGGAAGC+TGG 0.517710 5.1:+14521457 MS.gene68365:CDS
CAAACATGTGTTTCCCACTT+GGG 0.531651 5.1:+14521553 MS.gene68365:CDS
GCTTATCAGTTGTATCGGCT+GGG 0.531837 5.1:-14522290 None:intergenic
TATATTTGTTGTCATCCTCA+TGG 0.532111 5.1:+14521605 MS.gene68365:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.544768 5.1:-14521675 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.1:-14521367 None:intergenic
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.1:-14521680 None:intergenic
ACACTGGACCAGAGGAAGGA+AGG 0.561168 5.1:+14522246 MS.gene68365:CDS
TTTGAGGGATTCATCATCAG+AGG 0.561409 5.1:-14521399 None:intergenic
GAGCTGCTTATCAGTTGTAT+CGG 0.563493 5.1:-14522295 None:intergenic
GAGCTCTTAAAGAACTCTGA+AGG 0.564348 5.1:-14521439 None:intergenic
TTGAGGGATTCATCATCAGA+GGG 0.579951 5.1:-14521398 None:intergenic
CAAGGCGCAAACAACAACAC+TGG 0.583137 5.1:+14522230 MS.gene68365:CDS
AAACAACAACACTGGACCAG+AGG 0.583233 5.1:+14522238 MS.gene68365:CDS
CAGGAAGAGGGAAGGAACCA+AGG 0.586582 5.1:+14522212 MS.gene68365:CDS
GGGGTGGCTGTTGATGTGGA+AGG 0.586960 5.1:-14521659 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.1:-14521678 None:intergenic
AACAACACTGGACCAGAGGA+AGG 0.595528 5.1:+14522242 MS.gene68365:CDS
CAGAGGAAGGAAGGCCCAAG+AGG 0.596615 5.1:+14522255 MS.gene68365:CDS
AGTGATGGTCAAGCTATGAA+GGG 0.603559 5.1:+14521500 MS.gene68365:CDS
AATGGGAAGCTGGCAGCTGA+TGG 0.610197 5.1:+14521467 MS.gene68365:CDS
AAGCTGGCAGCTGATGGCGA+AGG 0.613924 5.1:+14521473 MS.gene68365:CDS
AGCTCTTAAAGAACTCTGAA+GGG 0.626255 5.1:-14521438 None:intergenic
AGGGATTCATCATCAGAGGG+AGG 0.627786 5.1:-14521395 None:intergenic
CTTCATCAAAGTAGCCCAAG+TGG 0.635469 5.1:-14521567 None:intergenic
ATGGTCAAGCTATGAAGGGG+AGG 0.636182 5.1:+14521504 MS.gene68365:CDS
ACAATGTCAAGTCAGGAAGA+GGG 0.642713 5.1:+14522200 MS.gene68365:CDS
GGGATTCATCATCAGAGGGA+GGG 0.650027 5.1:-14521394 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.1:+14521683 MS.gene68365:CDS
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.1:-14521384 None:intergenic
TTCATCAAAGTAGCCCAAGT+GGG 0.657037 5.1:-14521566 None:intergenic
TGTCAAGTCAGGAAGAGGGA+AGG 0.657401 5.1:+14522204 MS.gene68365:CDS
GATGGCGAAGGAGTAAGTGA+TGG 0.658846 5.1:+14521485 MS.gene68365:CDS
GTGATGGTCAAGCTATGAAG+GGG 0.659294 5.1:+14521501 MS.gene68365:CDS
GGAGGTGCTGAATAACCATG+AGG 0.763451 5.1:-14521620 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTAAATAATTGAATCT+TGG - chr5.1:14521829-14521848 None:intergenic 15.0%
!!! TTTTTCACACTATAATTTTT+AGG + chr5.1:14521759-14521778 MS.gene68365:intron 15.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.1:14522137-14522156 MS.gene68365:intron 20.0%
!!! ACAATAAATAGTTTTGAGAT+AGG - chr5.1:14521728-14521747 None:intergenic 20.0%
! CATATATATGTTTGTGTCTA+TGG - chr5.1:14521954-14521973 None:intergenic 25.0%
! TTATGAGATCTAATTCATGT+AGG + chr5.1:14521997-14522016 MS.gene68365:intron 25.0%
!!! TAGTTTTGAGATAGGAAATT+AGG - chr5.1:14521720-14521739 None:intergenic 25.0%
GAATCTTGGACATGATATAT+AGG - chr5.1:14521815-14521834 None:intergenic 30.0%
TATATAGGCAATAAAACCCT+AGG - chr5.1:14521800-14521819 None:intergenic 30.0%
!! TATATTTGTTGTCATCCTCA+TGG + chr5.1:14521605-14521624 MS.gene68365:CDS 30.0%
AGCTCTTAAAGAACTCTGAA+GGG - chr5.1:14521441-14521460 None:intergenic 35.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.1:14521692-14521711 None:intergenic 35.0%
AAGTGATGGTCAAGCTATGA+AGG + chr5.1:14521499-14521518 MS.gene68365:CDS 40.0%
ACAATGTCAAGTCAGGAAGA+GGG + chr5.1:14522200-14522219 MS.gene68365:CDS 40.0%
ACCTCAACCTGATCAATATG+AGG + chr5.1:14521682-14521701 MS.gene68365:CDS 40.0%
AGTGATGGTCAAGCTATGAA+GGG + chr5.1:14521500-14521519 MS.gene68365:CDS 40.0%
CAAACATGTGTTTCCCACTT+GGG + chr5.1:14521553-14521572 MS.gene68365:CDS 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.1:14521683-14521702 MS.gene68365:CDS 40.0%
CTCTGATACAATGTCAAGTC+AGG + chr5.1:14522193-14522212 MS.gene68365:CDS 40.0%
GAGCTCTTAAAGAACTCTGA+AGG - chr5.1:14521442-14521461 None:intergenic 40.0%
TACAATGTCAAGTCAGGAAG+AGG + chr5.1:14522199-14522218 MS.gene68365:CDS 40.0%
TCAGAGTCCTCTATCTCTAT+TGG - chr5.1:14522179-14522198 None:intergenic 40.0%
TTCATCAAAGTAGCCCAAGT+GGG - chr5.1:14521569-14521588 None:intergenic 40.0%
TTGAGGGATTCATCATCAGA+GGG - chr5.1:14521401-14521420 None:intergenic 40.0%
TTTGAGGGATTCATCATCAG+AGG - chr5.1:14521402-14521421 None:intergenic 40.0%
! AAAGAACTCTGAAGGGTAGT+TGG - chr5.1:14521434-14521453 None:intergenic 40.0%
! AAGAACTCTGAAGGGTAGTT+GGG - chr5.1:14521433-14521452 None:intergenic 40.0%
! CTTTAAGAGCTCGTGAGAAT+GGG + chr5.1:14521450-14521469 MS.gene68365:CDS 40.0%
! TCTTTAAGAGCTCGTGAGAA+TGG + chr5.1:14521449-14521468 MS.gene68365:CDS 40.0%
!! AGTTGGGTTGGTTTCTTTGA+GGG - chr5.1:14521417-14521436 None:intergenic 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.1:14521681-14521700 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.1:14521682-14521701 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+AGG - chr5.1:14521418-14521437 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.1:14521683-14521702 None:intergenic 40.0%
AAACAACAACACTGGACCAG+AGG + chr5.1:14522238-14522257 MS.gene68365:CDS 45.0%
AAGCCAGCCAATAGAGATAG+AGG + chr5.1:14522169-14522188 MS.gene68365:CDS 45.0%
AGTCCTCTATCTCTATTGGC+TGG - chr5.1:14522175-14522194 None:intergenic 45.0%
CTTCATCAAAGTAGCCCAAG+TGG - chr5.1:14521570-14521589 None:intergenic 45.0%
GAAGGAAGTGGAGAAAAACC+AGG - chr5.1:14521644-14521663 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.1:14521552-14521571 MS.gene68365:CDS 45.0%
GCAATAAAACCCTAGGTCAC+TGG - chr5.1:14521793-14521812 None:intergenic 45.0%
GTGATGGTCAAGCTATGAAG+GGG + chr5.1:14521501-14521520 MS.gene68365:CDS 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.1:14521347-14521366 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.1:14521340-14521359 None:intergenic 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.1:14521341-14521360 None:intergenic 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.1:14521686-14521705 None:intergenic 45.0%
!!! TAATTTTTTTTATAACTTAT+TGG + chr5.1:14522038-14522057 MS.gene68365:intron 5.0%
AACAACACTGGACCAGAGGA+AGG + chr5.1:14522242-14522261 MS.gene68365:CDS 50.0%
AGGGATTCATCATCAGAGGG+AGG - chr5.1:14521398-14521417 None:intergenic 50.0%
ATGGTCAAGCTATGAAGGGG+AGG + chr5.1:14521504-14521523 MS.gene68365:CDS 50.0%
CAAGGCGCAAACAACAACAC+TGG + chr5.1:14522230-14522249 MS.gene68365:CDS 50.0%
CATGGTTATTCAGCACCTCC+TGG + chr5.1:14521623-14521642 MS.gene68365:CDS 50.0%
GATGGCGAAGGAGTAAGTGA+TGG + chr5.1:14521485-14521504 MS.gene68365:CDS 50.0%
GCTGTTGATGTGGAAGGAAG+TGG - chr5.1:14521656-14521675 None:intergenic 50.0%
GGAAGTGGAGAAAAACCAGG+AGG - chr5.1:14521641-14521660 None:intergenic 50.0%
GGCTTCTTGATCGTCCTCTT+GGG - chr5.1:14522272-14522291 None:intergenic 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.1:14521397-14521416 None:intergenic 50.0%
GTCAACACTCCAGTGACCTA+GGG + chr5.1:14521781-14521800 MS.gene68365:intron 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.1:14521352-14521371 None:intergenic 50.0%
TGTCAAGTCAGGAAGAGGGA+AGG + chr5.1:14522204-14522223 MS.gene68365:CDS 50.0%
! ACTCTGAAGGGTAGTTGGGT+TGG - chr5.1:14521429-14521448 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.1:14521357-14521376 None:intergenic 50.0%
!! CAGTGTTGTTGTTTGCGCCT+TGG - chr5.1:14522232-14522251 None:intergenic 50.0%
!! GGAGGTGCTGAATAACCATG+AGG - chr5.1:14521623-14521642 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.1:14521375-14521394 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.1:14521371-14521390 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.1:14521372-14521391 None:intergenic 50.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.1:14521467-14521486 MS.gene68365:CDS 55.0%
ACACTGGACCAGAGGAAGGA+AGG + chr5.1:14522246-14522265 MS.gene68365:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.1:14521457-14521476 MS.gene68365:CDS 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.1:14521387-14521406 None:intergenic 55.0%
CAGGAAGAGGGAAGGAACCA+AGG + chr5.1:14522212-14522231 MS.gene68365:CDS 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.1:14521388-14521407 None:intergenic 55.0%
GGGCTTCTTGATCGTCCTCT+TGG - chr5.1:14522273-14522292 None:intergenic 55.0%
GGTCAACACTCCAGTGACCT+AGG + chr5.1:14521780-14521799 MS.gene68365:intron 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.1:14521353-14521372 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.1:14521389-14521408 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.1:14521369-14521388 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.1:14521370-14521389 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.1:14521678-14521697 None:intergenic 55.0%
AGGTGGGGTGGCTGTTGATG+TGG - chr5.1:14521666-14521685 None:intergenic 60.0%
CAGAGGAAGGAAGGCCCAAG+AGG + chr5.1:14522255-14522274 MS.gene68365:CDS 60.0%
CTCTTGGGCCTTCCTTCCTC+TGG - chr5.1:14522257-14522276 None:intergenic 60.0%
GGGGTGGCTGTTGATGTGGA+AGG - chr5.1:14521662-14521681 None:intergenic 60.0%
! AAGCTGGCAGCTGATGGCGA+AGG + chr5.1:14521473-14521492 MS.gene68365:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14521329 14522307 14521329 ID=MS.gene68365
chr5.1 mRNA 14521329 14522307 14521329 ID=MS.gene68365.t1;Parent=MS.gene68365
chr5.1 exon 14521329 14521704 14521329 ID=MS.gene68365.t1.exon1;Parent=MS.gene68365.t1
chr5.1 CDS 14521329 14521704 14521329 ID=cds.MS.gene68365.t1;Parent=MS.gene68365.t1
chr5.1 exon 14522159 14522307 14522159 ID=MS.gene68365.t1.exon2;Parent=MS.gene68365.t1
chr5.1 CDS 14522159 14522307 14522159 ID=cds.MS.gene68365.t1;Parent=MS.gene68365.t1
Gene Sequence

>MS.gene68365

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCTCAAAGAAACCAACCCAACTACCCTTCAGAGTTCTTTAAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGCGAAGGAGTAAGTGATGGTCAAGCTATGAAGGGGAGGAAGAGTAATATTTGTTGTCATAGATGCAAACATGTGTTTCCCACTTGGGCTACTTTGATGAAGCATTATCAAGAACACTATATTTGTTGTCATCCTCATGGTTATTCAGCACCTCCTGGTTTTTCTCCACTTCCTTCCACATCAACAGCCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTCCTATCTCAAAACTATTTATTGTCATGTCTTTTTTTTTTCACACTATAATTTTTAGGTCAACACTCCAGTGACCTAGGGTTTTATTGCCTATATATCATGTCCAAGATTCAATTATTTAATGTTATATAATTATTATTTTTTTCATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGATCATTCATAAAATACTTGTGTATAGATCATTCATAAAAGATTGCACCATAGACACAAACATATATATGTTCACTTTGAGTGTTGCTTAATTTTATGAGATCTAATTCATGTAGGCATCTATATATATATCTTTAATTTTTTTTATAACTTATTGGTTTTTAATTTAACAATTTGTTTTTTTTTTCTTTCAAACTAATGATTTTACAATGAAGCAATTATAATTATAATTTGAATGTTTTTCTTTTGTTACTAGGTGATGATCAAAGCCAGCCAATAGAGATAGAGGACTCTGATACAATGTCAAGTCAGGAAGAGGGAAGGAACCAAGGCGCAAACAACAACACTGGACCAGAGGAAGGAAGGCCCAAGAGGACGATCAAGAAGCCCAGCCGATACAACTGA
Protein sequence

>MS.gene68365.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESLKETNPTTLQSSLRARENGKLAADGEGVSDGQAMKGRKSNICCHRCKHVFPTWATLMKHYQEHYICCHPHGYSAPPGFSPLPSTSTATPPQPDQYEGDDQSQPIEIEDSDTMSSQEEGRNQGANNNTGPEEGRPKRTIKKPSRYN