AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene036076

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036076.t1 MTR_1g069905 100.000 164 0 0 1 164 1 164 1.48e-120 337
MS.gene036076.t1 MTR_7g107420 99.390 164 1 0 1 164 1 164 2.29e-120 336
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036076.t1 AT1G09690 81.098 164 31 0 1 164 1 164 3.44e-101 288
MS.gene036076.t1 AT1G09590 81.098 164 31 0 1 164 1 164 3.44e-101 288
MS.gene036076.t1 AT1G57860 80.488 164 32 0 1 164 1 164 1.04e-100 286
MS.gene036076.t1 AT1G57660 80.488 164 32 0 1 164 1 164 1.04e-100 286

Find 63 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGTCGACATTAGAGTTAA+TGG 0.335175 1.1:+51986421 MS.gene036076:CDS
TCCACCATGAAACCAGGTTT+GGG 0.345744 1.1:-51987540 None:intergenic
AACTCCTCAGTGCACCTTGA+TGG 0.353770 1.1:-51987429 None:intergenic
AGATCATTAACGACATCATA+TGG 0.366035 1.1:-51987594 None:intergenic
GGGGCCCTCTGGCTTGCGCT+TGG 0.369033 1.1:-51987520 None:intergenic
TTCCACCATGAAACCAGGTT+TGG 0.392778 1.1:-51987541 None:intergenic
GGGCCCCAAACCTGGTTTCA+TGG 0.399375 1.1:+51987536 MS.gene036076:CDS
TTAACGACATCATATGGAAT+TGG 0.408404 1.1:-51987588 None:intergenic
CTTGTTGACTTCGACACCAA+TGG 0.410846 1.1:-51986518 None:intergenic
AAACCAGGTTTGGGGCCCTC+TGG 0.418683 1.1:-51987531 None:intergenic
GGAACAAGATATTGAGGAAG+AGG 0.429842 1.1:+51987379 MS.gene036076:CDS
ACGGTCGTACCGGTCGTGTC+TGG 0.430669 1.1:+51986479 MS.gene036076:CDS
AAGCCAGAGGGCCCCAAACC+TGG 0.445982 1.1:+51987528 MS.gene036076:CDS
CTCTCCCTTGGCCTTAGCCT+CGG 0.448320 1.1:-51987487 None:intergenic
CTCTCGTCCCTTCCGCAAGA+AGG 0.451916 1.1:+51986351 MS.gene036076:CDS
GGTGCTTATCACCTCTCCCT+TGG 0.453810 1.1:-51987499 None:intergenic
TTCGACACCAATGGCCCGCT+TGG 0.477602 1.1:-51986509 None:intergenic
AGTCCTGAGGTAGGTGGCTA+AGG 0.478683 1.1:-51986383 None:intergenic
CGAGGCTAAGGCCAAGGGAG+AGG 0.486454 1.1:+51987488 MS.gene036076:CDS
GGGACGAGAGAAAGAATCTC+TGG 0.497137 1.1:-51986338 None:intergenic
AGCACCAAGCGCAAGCCAGA+GGG 0.504695 1.1:+51987516 MS.gene036076:CDS
TATTGTTCCCTTCTTGCGGA+AGG 0.508429 1.1:-51986359 None:intergenic
TCAATTGAAGGCCGAGGCTA+AGG 0.510816 1.1:+51987476 MS.gene036076:CDS
AATGTCACCAAGCGGGCCAT+TGG 0.521717 1.1:+51986502 MS.gene036076:CDS
AAATTCTACCACGGTCGTAC+CGG 0.524822 1.1:+51986469 MS.gene036076:CDS
GATCAAGAATGATCAATTGA+AGG 0.525684 1.1:+51987464 MS.gene036076:CDS
GAAAAGATGCCTGCAGGTCA+TGG 0.528675 1.1:+51986301 None:intergenic
GATCGTAAACCATGACCTGC+AGG 0.529368 1.1:-51986310 None:intergenic
AGGTTAGGAACAAGATATTG+AGG 0.530172 1.1:+51987373 MS.gene036076:intron
CATGGTGGAAGGTGCTACAT+TGG 0.534415 1.1:+51987554 MS.gene036076:CDS
ATTGTTCCCTTCTTGCGGAA+GGG 0.538504 1.1:-51986358 None:intergenic
GAAGAAGAAAAGATGCCTGC+AGG 0.538536 1.1:+51986295 None:intergenic
TCTCGTCCCTTCCGCAAGAA+GGG 0.539095 1.1:+51986352 MS.gene036076:CDS
AGAGAAAGAATCTCTGGTGC+GGG 0.546612 1.1:-51986332 None:intergenic
TAGCCTTAGCCACCTACCTC+AGG 0.549870 1.1:+51986380 MS.gene036076:CDS
GAATGATCAATTGAAGGCCG+AGG 0.551548 1.1:+51987470 MS.gene036076:CDS
AGGCTATTGTTCCCTTCTTG+CGG 0.554250 1.1:-51986363 None:intergenic
AAGCACCAAGCGCAAGCCAG+AGG 0.557087 1.1:+51987515 MS.gene036076:CDS
TGGAGCATGTTATGCCATCA+AGG 0.559210 1.1:+51987415 MS.gene036076:CDS
GAAGGCCGAGGCTAAGGCCA+AGG 0.560874 1.1:+51987482 MS.gene036076:CDS
TGTCTGGAATGTCACCAAGC+GGG 0.572072 1.1:+51986495 MS.gene036076:CDS
GCACCTTCCACCATGAAACC+AGG 0.576804 1.1:-51987546 None:intergenic
AAACCTGGTTTCATGGTGGA+AGG 0.589005 1.1:+51987543 MS.gene036076:CDS
GCACTGAGGAGTTCAGATTG+AGG 0.599052 1.1:+51987439 MS.gene036076:CDS
GGTGACATTCCAGACACGAC+CGG 0.600537 1.1:-51986488 None:intergenic
ATGGCATAACATGCTCCACT+CGG 0.618716 1.1:-51987410 None:intergenic
GAGAGAAAGAATCTCTGGTG+CGG 0.621626 1.1:-51986333 None:intergenic
GATGTCGTTAATGATCTCAA+AGG 0.621805 1.1:+51987600 MS.gene036076:CDS
GTCGTTAATGATCTCAAAGG+AGG 0.636972 1.1:+51987603 MS.gene036076:CDS
GTTAATGGAGCTGTTCACAA+AGG 0.639444 1.1:+51986436 MS.gene036076:CDS
AAGGCCGAGGCTAAGGCCAA+GGG 0.643263 1.1:+51987483 MS.gene036076:CDS
CCACCATGAAACCAGGTTTG+GGG 0.653619 1.1:-51987539 None:intergenic
GTGTCTGGAATGTCACCAAG+CGG 0.655012 1.1:+51986494 MS.gene036076:CDS
GTGATAAGTCCTGAGGTAGG+TGG 0.662852 1.1:-51986389 None:intergenic
CGACCGTGGTAGAATTTGTG+CGG 0.677873 1.1:-51986463 None:intergenic
CACCGATGTGATAAGTCCTG+AGG 0.683027 1.1:-51986396 None:intergenic
GATGTGATAAGTCCTGAGGT+AGG 0.683685 1.1:-51986392 None:intergenic
CCCCAAACCTGGTTTCATGG+TGG 0.684233 1.1:+51987539 MS.gene036076:CDS
AGACACGACCGGTACGACCG+TGG 0.690324 1.1:-51986477 None:intergenic
GAAGAGGATTCATGTCCGAG+TGG 0.705446 1.1:+51987395 MS.gene036076:CDS
TACCTCAGGACTTATCACAT+CGG 0.727991 1.1:+51986394 MS.gene036076:CDS
ATGCCGCACAAATTCTACCA+CGG 0.741255 1.1:+51986460 MS.gene036076:CDS
TATGCCATCAAGGTGCACTG+AGG 0.765204 1.1:+51987425 MS.gene036076:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTTGTAGGAACATAAAAT+GGG - chr1.1:51987001-51987020 None:intergenic 20.0%
!!! ACATAAATGAAAGTATTTGT+AGG - chr1.1:51987014-51987033 None:intergenic 20.0%
!!! CAAAATTCTTCTAAGTTTTT+AGG + chr1.1:51987183-51987202 MS.gene036076:intron 20.0%
!!! GAAGAATTTTGTGTTAAATA+TGG - chr1.1:51987174-51987193 None:intergenic 20.0%
! AAGTTGGAAAACAAAAACTT+AGG - chr1.1:51986927-51986946 None:intergenic 25.0%
! AGTTGGAAAACAAAAACTTA+GGG - chr1.1:51986926-51986945 None:intergenic 25.0%
! CAATATATTTACAAGCAAAG+CGG - chr1.1:51987318-51987337 None:intergenic 25.0%
! GAACATAAAATGGGATAAAA+CGG - chr1.1:51986992-51987011 None:intergenic 25.0%
! GTATTTGTAGGAACATAAAA+TGG - chr1.1:51987002-51987021 None:intergenic 25.0%
! TCAAACAACAAAATGAATCA+AGG - chr1.1:51986783-51986802 None:intergenic 25.0%
! TTTGCTTTAGTAGTATATTC+AGG + chr1.1:51986705-51986724 MS.gene036076:intron 25.0%
!! ATTCGAGTCTTTTAATAAGT+TGG - chr1.1:51986943-51986962 None:intergenic 25.0%
!! TATATGGTTTGTCAATGAAT+TGG - chr1.1:51987099-51987118 None:intergenic 25.0%
!!! AATGTTGCTATTTATGTTTC+AGG + chr1.1:51987353-51987372 MS.gene036076:intron 25.0%
!!! CTTGACATGATGTTTTTATA+TGG + chr1.1:51987141-51987160 MS.gene036076:intron 25.0%
AATCTCTTGGATAGAATGTA+TGG + chr1.1:51987250-51987269 MS.gene036076:intron 30.0%
AGATCATTAACGACATCATA+TGG - chr1.1:51987597-51987616 None:intergenic 30.0%
CTCTTCAAAAACCTCATATA+TGG - chr1.1:51987115-51987134 None:intergenic 30.0%
GATCAAGAATGATCAATTGA+AGG + chr1.1:51987464-51987483 MS.gene036076:CDS 30.0%
GCAAATATATGTGATGTGAT+AGG + chr1.1:51986596-51986615 MS.gene036076:intron 30.0%
TATGTCGACATTAGAGTTAA+TGG + chr1.1:51986421-51986440 MS.gene036076:CDS 30.0%
TCATTGACAAACCATATATG+AGG + chr1.1:51987101-51987120 MS.gene036076:intron 30.0%
TTAACGACATCATATGGAAT+TGG - chr1.1:51987591-51987610 None:intergenic 30.0%
TTAATTTCCAGAGAATCTCT+TGG + chr1.1:51987237-51987256 MS.gene036076:intron 30.0%
!! TGCTATTTATGTTTCAGGTT+AGG + chr1.1:51987358-51987377 MS.gene036076:intron 30.0%
!!! CTTCTAAGTTTTTAGGTCTT+AGG + chr1.1:51987190-51987209 MS.gene036076:intron 30.0%
ACAAAAACTTAGGGCATGTT+TGG - chr1.1:51986917-51986936 None:intergenic 35.0%
AGGTTAGGAACAAGATATTG+AGG + chr1.1:51987373-51987392 MS.gene036076:intron 35.0%
ATGTGATGTGATAGGTGTTA+TGG + chr1.1:51986604-51986623 MS.gene036076:intron 35.0%
ATTCTATCCAAGAGATTCTC+TGG - chr1.1:51987247-51987266 None:intergenic 35.0%
GATGTCGTTAATGATCTCAA+AGG + chr1.1:51987600-51987619 MS.gene036076:CDS 35.0%
TCCAATTCCAAGTGAGAAAT+TGG - chr1.1:51987044-51987063 None:intergenic 35.0%
TCCAATTTCTCACTTGGAAT+TGG + chr1.1:51987040-51987059 MS.gene036076:intron 35.0%
CAAGTCTCCAATTTCTCACT+TGG + chr1.1:51987034-51987053 MS.gene036076:intron 40.0%
GGAACAAGATATTGAGGAAG+AGG + chr1.1:51987379-51987398 MS.gene036076:CDS 40.0%
GTCGTTAATGATCTCAAAGG+AGG + chr1.1:51987603-51987622 MS.gene036076:CDS 40.0%
GTTAATGGAGCTGTTCACAA+AGG + chr1.1:51986436-51986455 MS.gene036076:CDS 40.0%
TACCTCAGGACTTATCACAT+CGG + chr1.1:51986394-51986413 MS.gene036076:CDS 40.0%
AAATTCTACCACGGTCGTAC+CGG + chr1.1:51986469-51986488 MS.gene036076:CDS 45.0%
AGAGAAAGAATCTCTGGTGC+GGG - chr1.1:51986335-51986354 None:intergenic 45.0%
AGGCTATTGTTCCCTTCTTG+CGG - chr1.1:51986366-51986385 None:intergenic 45.0%
ATGCCGCACAAATTCTACCA+CGG + chr1.1:51986460-51986479 MS.gene036076:CDS 45.0%
ATGGCATAACATGCTCCACT+CGG - chr1.1:51987413-51987432 None:intergenic 45.0%
ATTGTTCCCTTCTTGCGGAA+GGG - chr1.1:51986361-51986380 None:intergenic 45.0%
GAATGATCAATTGAAGGCCG+AGG + chr1.1:51987470-51987489 MS.gene036076:CDS 45.0%
GAGAGAAAGAATCTCTGGTG+CGG - chr1.1:51986336-51986355 None:intergenic 45.0%
GATGTGATAAGTCCTGAGGT+AGG - chr1.1:51986395-51986414 None:intergenic 45.0%
TATTGTTCCCTTCTTGCGGA+AGG - chr1.1:51986362-51986381 None:intergenic 45.0%
TCCACCATGAAACCAGGTTT+GGG - chr1.1:51987543-51987562 None:intergenic 45.0%
TGGAGCATGTTATGCCATCA+AGG + chr1.1:51987415-51987434 MS.gene036076:CDS 45.0%
TTCCACCATGAAACCAGGTT+TGG - chr1.1:51987544-51987563 None:intergenic 45.0%
! AAACCTGGTTTCATGGTGGA+AGG + chr1.1:51987543-51987562 MS.gene036076:CDS 45.0%
!! CTTGTTGACTTCGACACCAA+TGG - chr1.1:51986521-51986540 None:intergenic 45.0%
AACTCCTCAGTGCACCTTGA+TGG - chr1.1:51987432-51987451 None:intergenic 50.0%
CACCGATGTGATAAGTCCTG+AGG - chr1.1:51986399-51986418 None:intergenic 50.0%
CCACCATGAAACCAGGTTTG+GGG - chr1.1:51987542-51987561 None:intergenic 50.0%
CGACCGTGGTAGAATTTGTG+CGG - chr1.1:51986466-51986485 None:intergenic 50.0%
GAAGAGGATTCATGTCCGAG+TGG + chr1.1:51987395-51987414 MS.gene036076:CDS 50.0%
GATCGTAAACCATGACCTGC+AGG - chr1.1:51986313-51986332 None:intergenic 50.0%
GCACTGAGGAGTTCAGATTG+AGG + chr1.1:51987439-51987458 MS.gene036076:CDS 50.0%
GGGACGAGAGAAAGAATCTC+TGG - chr1.1:51986341-51986360 None:intergenic 50.0%
GTGATAAGTCCTGAGGTAGG+TGG - chr1.1:51986392-51986411 None:intergenic 50.0%
TATGCCATCAAGGTGCACTG+AGG + chr1.1:51987425-51987444 MS.gene036076:CDS 50.0%
TCAATTGAAGGCCGAGGCTA+AGG + chr1.1:51987476-51987495 MS.gene036076:CDS 50.0%
! GTGTCTGGAATGTCACCAAG+CGG + chr1.1:51986494-51986513 MS.gene036076:CDS 50.0%
! TGTCTGGAATGTCACCAAGC+GGG + chr1.1:51986495-51986514 MS.gene036076:CDS 50.0%
!! CATGGTGGAAGGTGCTACAT+TGG + chr1.1:51987554-51987573 MS.gene036076:CDS 50.0%
AATGTCACCAAGCGGGCCAT+TGG + chr1.1:51986502-51986521 MS.gene036076:CDS 55.0%
AGTCCTGAGGTAGGTGGCTA+AGG - chr1.1:51986386-51986405 None:intergenic 55.0%
CCCCAAACCTGGTTTCATGG+TGG + chr1.1:51987539-51987558 MS.gene036076:CDS 55.0%
GCACCTTCCACCATGAAACC+AGG - chr1.1:51987549-51987568 None:intergenic 55.0%
GGTGACATTCCAGACACGAC+CGG - chr1.1:51986491-51986510 None:intergenic 55.0%
GGTGCTTATCACCTCTCCCT+TGG - chr1.1:51987502-51987521 None:intergenic 55.0%
TCTCGTCCCTTCCGCAAGAA+GGG + chr1.1:51986352-51986371 MS.gene036076:CDS 55.0%
! TAGCCTTAGCCACCTACCTC+AGG + chr1.1:51986380-51986399 MS.gene036076:CDS 55.0%
AAGCACCAAGCGCAAGCCAG+AGG + chr1.1:51987515-51987534 MS.gene036076:CDS 60.0%
AAGGCCGAGGCTAAGGCCAA+GGG + chr1.1:51987483-51987502 MS.gene036076:CDS 60.0%
AGCACCAAGCGCAAGCCAGA+GGG + chr1.1:51987516-51987535 MS.gene036076:CDS 60.0%
CTCTCGTCCCTTCCGCAAGA+AGG + chr1.1:51986351-51986370 MS.gene036076:CDS 60.0%
GGGCCCCAAACCTGGTTTCA+TGG + chr1.1:51987536-51987555 MS.gene036076:CDS 60.0%
TTCGACACCAATGGCCCGCT+TGG - chr1.1:51986512-51986531 None:intergenic 60.0%
! AAACCAGGTTTGGGGCCCTC+TGG - chr1.1:51987534-51987553 None:intergenic 60.0%
!! CTCTCCCTTGGCCTTAGCCT+CGG - chr1.1:51987490-51987509 None:intergenic 60.0%
AAGCCAGAGGGCCCCAAACC+TGG + chr1.1:51987528-51987547 MS.gene036076:CDS 65.0%
AGACACGACCGGTACGACCG+TGG - chr1.1:51986480-51986499 None:intergenic 65.0%
CGAGGCTAAGGCCAAGGGAG+AGG + chr1.1:51987488-51987507 MS.gene036076:CDS 65.0%
GAAGGCCGAGGCTAAGGCCA+AGG + chr1.1:51987482-51987501 MS.gene036076:CDS 65.0%
! ACGGTCGTACCGGTCGTGTC+TGG + chr1.1:51986479-51986498 MS.gene036076:CDS 65.0%
! GGGGCCCTCTGGCTTGCGCT+TGG - chr1.1:51987523-51987542 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 51986307 51987632 51986307 ID=MS.gene036076
chr1.1 mRNA 51986307 51987632 51986307 ID=MS.gene036076.t1;Parent=MS.gene036076
chr1.1 exon 51986307 51986543 51986307 ID=MS.gene036076.t1.exon1;Parent=MS.gene036076.t1
chr1.1 CDS 51986307 51986543 51986307 ID=cds.MS.gene036076.t1;Parent=MS.gene036076.t1
chr1.1 exon 51987375 51987632 51987375 ID=MS.gene036076.t1.exon2;Parent=MS.gene036076.t1
chr1.1 CDS 51987375 51987632 51987375 ID=cds.MS.gene036076.t1;Parent=MS.gene036076.t1
Gene Sequence

>MS.gene036076

ATGCCTGCAGGTCATGGTTTACGATCCCGCACCAGAGATTCTTTCTCTCGTCCCTTCCGCAAGAAGGGAACAATAGCCTTAGCCACCTACCTCAGGACTTATCACATCGGTGACTATGTCGACATTAGAGTTAATGGAGCTGTTCACAAAGGTATGCCGCACAAATTCTACCACGGTCGTACCGGTCGTGTCTGGAATGTCACCAAGCGGGCCATTGGTGTCGAAGTCAACAAGCAAGTATGTCAAATCTTCTTCTTATATGACTCATTTTCATTTTAGTGTTATATCTGCAAATATATGTGATGTGATAGGTGTTATGGTTTGTTCGATTGATATTTATTTTTGTTTCATTTCGAGCTTTCTTTTGAATTGTTATGTATTTGTTGCAAGTATGTTTCTTTGCTTTAGTAGTATATTCAGGATCTAGTTTAAGTTGTTCATGTTACAAATGAATTGTTTATTGTTGTTTCATTCCTTGATTCATTTTGTTGTTTGAGATAGCTTACTGCTTATAGCATATACAGAAACAATTCAATTTTATTTTATCATTTGCAGCAAAAATAAGCTCTTATCATGACAATAAGCACTTGTGCTATAAGCTGTCTATCCAAACATGCCCTAAGTTTTTGTTTTCCAACTTATTAAAAGACTCGAATTTTGACTCATATATGATATAGTAGTACCGTTTTATCCCATTTTATGTTCCTACAAATACTTTCATTTATGTCAAGTCTCCAATTTCTCACTTGGAATTGGAACAATTATTTATAAAAATTTTCATCAAAATCACCAATTCATTGACAAACCATATATGAGGTTTTTGAAGAGACTGAACTTGACATGATGTTTTTATATGGACTCGAACCATATTTAACACAAAATTCTTCTAAGTTTTTAGGTCTTAGGTAAATGAGATTGAGACTAACATTTTTAATTTCCAGAGAATCTCTTGGATAGAATGTATGGTTGTTGCATAAGTATCTCAATTTTTTATATTCTCTGCAAGTGCCGCTTTGCTTGTAAATATATTGTTTACTCAATTTTAAAATGTTGCTATTTATGTTTCAGGTTAGGAACAAGATATTGAGGAAGAGGATTCATGTCCGAGTGGAGCATGTTATGCCATCAAGGTGCACTGAGGAGTTCAGATTGAGGAAGATCAAGAATGATCAATTGAAGGCCGAGGCTAAGGCCAAGGGAGAGGTGATAAGCACCAAGCGCAAGCCAGAGGGCCCCAAACCTGGTTTCATGGTGGAAGGTGCTACATTGGAGACTGTTACTCCAATTCCATATGATGTCGTTAATGATCTCAAAGGAGGATACTAG
Protein sequence

>MS.gene036076.t1

MPAGHGLRSRTRDSFSRPFRKKGTIALATYLRTYHIGDYVDIRVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEVNKQVRNKILRKRIHVRVEHVMPSRCTEEFRLRKIKNDQLKAEAKAKGEVISTKRKPEGPKPGFMVEGATLETVTPIPYDVVNDLKGGY