AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25397

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25397.t1 MTR_8g469010 99.385 325 2 0 1 325 1 325 0.0 672
MS.gene25397.t1 MTR_0268s0080 92.121 330 21 1 1 325 1 330 0.0 634
MS.gene25397.t1 MTR_1g050472 92.424 330 20 1 1 325 1 330 0.0 634
MS.gene25397.t1 MTR_7g029110 91.818 330 22 1 1 325 1 330 0.0 611
MS.gene25397.t1 MTR_4g117370 76.543 324 72 1 6 325 18 341 0.0 531
MS.gene25397.t1 MTR_6g005270 69.767 43 13 0 265 307 25 67 4.11e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25397.t1 AT3G27060 81.024 332 56 3 1 325 1 332 0.0 537
MS.gene25397.t1 AT3G23580 76.852 324 71 1 6 325 18 341 0.0 520

Find 62 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGGATTTGATTTCGCTTC+AGG 0.266722 8.2:+40104189 MS.gene25397:CDS
TCCGAAGCGCGTGCTTTCTA+TGG 0.277078 8.2:+40103611 MS.gene25397:CDS
AACTTCTTTCATGAATCTTC+CGG 0.306172 8.2:-40103582 None:intergenic
CGCTTCCTTGTGCGTTGGTT+GGG 0.331961 8.2:+40104062 MS.gene25397:CDS
ATTTCTTTGAGAAGCGCGTT+GGG 0.337568 8.2:+40104221 MS.gene25397:CDS
GGAGCGAGAAGAGGTTCTTC+TGG 0.345478 8.2:-40103347 None:intergenic
GTTGCTTTCGCTTGTGTTGA+AGG 0.362449 8.2:+40103818 MS.gene25397:CDS
AAGCTGATTGGGCTTTGAAA+TGG 0.371966 8.2:+40103762 MS.gene25397:CDS
ATGCAGAATCGGTCTGGGTT+TGG 0.382220 8.2:-40103368 None:intergenic
ACCGTCGGAAGCGGCGAAAA+AGG 0.385604 8.2:-40103540 None:intergenic
TGCTGATTATTGCTTTACTT+TGG 0.386701 8.2:+40104276 MS.gene25397:CDS
ATGTTCAGAATCCGTTTGAT+TGG 0.390491 8.2:+40104167 MS.gene25397:CDS
GTTTGTTGCTGATAGGTTGT+TGG 0.410068 8.2:+40104117 MS.gene25397:CDS
GGGAACATGCAGAATCGGTC+TGG 0.418807 8.2:-40103374 None:intergenic
ACCATAGAAAGCACGCGCTT+CGG 0.432842 8.2:-40103612 None:intergenic
GCGCTTCCTTGTGCGTTGGT+TGG 0.437283 8.2:+40104061 MS.gene25397:CDS
GAGCGAGAAGAGGTTCTTCT+GGG 0.439709 8.2:-40103346 None:intergenic
TCAGAATCCGTTTGATTGGA+TGG 0.443597 8.2:+40104171 MS.gene25397:CDS
GATAGGTTGTTGGGTGAACT+TGG 0.452257 8.2:+40104127 MS.gene25397:CDS
GAAAATCGCACAGAAGCTTC+CGG 0.456616 8.2:-40103852 None:intergenic
TTTGTTGCTGATAGGTTGTT+GGG 0.461848 8.2:+40104118 MS.gene25397:CDS
TATTGCTAAGAAAGCTGATT+GGG 0.465189 8.2:+40103751 MS.gene25397:CDS
AATCGCTTATATACGTTTCG+AGG 0.468396 8.2:-40103682 None:intergenic
CGAAATAAGCTCGTTTGAGA+AGG 0.470666 8.2:-40103909 None:intergenic
GGCGGTCCAGAAAGAGGCTT+CGG 0.476778 8.2:-40103435 None:intergenic
ATCAAATCCATCCAATCAAA+CGG 0.489030 8.2:-40104178 None:intergenic
GGAACATGCAGAATCGGTCT+GGG 0.489835 8.2:-40103373 None:intergenic
ATGGATTTGATTTCGCTTCA+GGG 0.493555 8.2:+40104190 MS.gene25397:CDS
GGAGGAAAGATCGACTTCTT+CGG 0.499480 8.2:-40103456 None:intergenic
TTCTTCGGCGGTCCAGAAAG+AGG 0.507977 8.2:-40103441 None:intergenic
TTATTGCTTTACTTTGGATG+AGG 0.510830 8.2:+40104282 MS.gene25397:CDS
TTTCCTCCGATCTTCAACAC+TGG 0.515193 8.2:+40103471 MS.gene25397:CDS
GTATTGCTAAGAAAGCTGAT+TGG 0.515724 8.2:+40103750 MS.gene25397:CDS
CAGAAAGCTTCTGTTATGAA+TGG 0.519026 8.2:+40104250 MS.gene25397:CDS
GAATTGGGAACATGCAGAAT+CGG 0.519394 8.2:-40103379 None:intergenic
GTGATGCAGTTGAGATTGAA+AGG 0.522321 8.2:+40104023 MS.gene25397:CDS
AATTTCTTTGAGAAGCGCGT+TGG 0.523856 8.2:+40104220 MS.gene25397:CDS
ATATTGAGTTTGTTGCTGAT+AGG 0.535233 8.2:+40104110 MS.gene25397:CDS
AGAGGTTCTTCTGGGAAAGA+AGG 0.536510 8.2:-40103338 None:intergenic
GAGCTTATTTCGCGTGACGA+AGG 0.555351 8.2:+40103920 MS.gene25397:CDS
GTTGTTCCAGTGTTGAAGAT+CGG 0.557909 8.2:-40103477 None:intergenic
GACGAAGTGGCGTTCGCCGT+CGG 0.563379 8.2:-40103504 None:intergenic
GAGGACGATACCGTCGGAAG+CGG 0.563447 8.2:-40103549 None:intergenic
TGTGCGTTGGTTGGGATGAA+CGG 0.572801 8.2:+40104070 MS.gene25397:CDS
TCTGGGTTTGGAGCGAGAAG+AGG 0.577657 8.2:-40103356 None:intergenic
TGATGCAGTTGAGATTGAAA+GGG 0.582117 8.2:+40104024 MS.gene25397:CDS
ATCGTCCTCGAAAACCTCGC+CGG 0.585158 8.2:+40103563 MS.gene25397:CDS
CGACGCGCTTCCTTGTGCGT+TGG 0.585443 8.2:+40104057 MS.gene25397:CDS
TCGTTTGAGAAGGTTAATCC+CGG 0.587906 8.2:-40103899 None:intergenic
TTTCTTTGAGAAGCGCGTTG+GGG 0.598671 8.2:+40104222 MS.gene25397:CDS
CTTTCATGAATCTTCCGGCG+AGG 0.609684 8.2:-40103577 None:intergenic
GAAGCTGAGTTCAGAGCGAG+TGG 0.611132 8.2:+40103988 MS.gene25397:CDS
CACTGGAACAACCTCACCGA+CGG 0.611309 8.2:+40103488 MS.gene25397:CDS
TTCATCCCAACCAACGCACA+AGG 0.615150 8.2:-40104067 None:intergenic
AGTGGCGTTCGCCGTCGGTG+AGG 0.618653 8.2:-40103499 None:intergenic
TGGATTTGATTTCGCTTCAG+GGG 0.620413 8.2:+40104191 MS.gene25397:CDS
GTTCCAGTGTTGAAGATCGG+AGG 0.622372 8.2:-40103474 None:intergenic
CGAGGATGTGAGAGACGAAG+TGG 0.630959 8.2:-40103517 None:intergenic
TCAGCTTTCTTAGCAATACA+CGG 0.642160 8.2:-40103746 None:intergenic
AAAGCTTCTGTTATGAATGG+TGG 0.674687 8.2:+40104253 MS.gene25397:CDS
GGAAAGATCGACTTCTTCGG+CGG 0.687608 8.2:-40103453 None:intergenic
GAAGAGAATACATCTCAGAG+TGG 0.694344 8.2:-40103658 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATTCAATACCCAAAAATCT+GGG + chr8.2:40103397-40103416 MS.gene25397:CDS 25.0%
!!! AGATTTTTGGGTATTGAATT+GGG - chr8.2:40103397-40103416 None:intergenic 25.0%
AACTTCTTTCATGAATCTTC+CGG - chr8.2:40103585-40103604 None:intergenic 30.0%
ATCAAATCCATCCAATCAAA+CGG - chr8.2:40104181-40104200 None:intergenic 30.0%
CAATTCAATACCCAAAAATC+TGG + chr8.2:40103396-40103415 MS.gene25397:CDS 30.0%
TATTGCTAAGAAAGCTGATT+GGG + chr8.2:40103751-40103770 MS.gene25397:CDS 30.0%
TTATTGCTTTACTTTGGATG+AGG + chr8.2:40104282-40104301 MS.gene25397:CDS 30.0%
! TGCTGATTATTGCTTTACTT+TGG + chr8.2:40104276-40104295 MS.gene25397:CDS 30.0%
! TGTACATTTCCCAGATTTTT+GGG - chr8.2:40103409-40103428 None:intergenic 30.0%
! TTGTACATTTCCCAGATTTT+TGG - chr8.2:40103410-40103429 None:intergenic 30.0%
!! ATATTGAGTTTGTTGCTGAT+AGG + chr8.2:40104110-40104129 MS.gene25397:CDS 30.0%
!!! ATTTTCTGGTTGAAAAAACG+CGG + chr8.2:40103869-40103888 MS.gene25397:CDS 30.0%
!!! CAGATTTTTGGGTATTGAAT+TGG - chr8.2:40103398-40103417 None:intergenic 30.0%
AAAGCTTCTGTTATGAATGG+TGG + chr8.2:40104253-40104272 MS.gene25397:CDS 35.0%
AATCGCTTATATACGTTTCG+AGG - chr8.2:40103685-40103704 None:intergenic 35.0%
ATGTTCAGAATCCGTTTGAT+TGG + chr8.2:40104167-40104186 MS.gene25397:CDS 35.0%
CAGAAAGCTTCTGTTATGAA+TGG + chr8.2:40104250-40104269 MS.gene25397:CDS 35.0%
GTATTGCTAAGAAAGCTGAT+TGG + chr8.2:40103750-40103769 MS.gene25397:CDS 35.0%
TCAGCTTTCTTAGCAATACA+CGG - chr8.2:40103749-40103768 None:intergenic 35.0%
TGATGCAGTTGAGATTGAAA+GGG + chr8.2:40104024-40104043 MS.gene25397:CDS 35.0%
TTTGTTGCTGATAGGTTGTT+GGG + chr8.2:40104118-40104137 MS.gene25397:CDS 35.0%
! ATGGATTTGATTTCGCTTCA+GGG + chr8.2:40104190-40104209 MS.gene25397:CDS 35.0%
! GTTGAAGGAATTTTCTTCTC+CGG + chr8.2:40103833-40103852 MS.gene25397:CDS 35.0%
AAAAAACGCGGTTTAATGCC+GGG + chr8.2:40103881-40103900 MS.gene25397:CDS 40.0%
CGAAATAAGCTCGTTTGAGA+AGG - chr8.2:40103912-40103931 None:intergenic 40.0%
GAAAAAACGCGGTTTAATGC+CGG + chr8.2:40103880-40103899 MS.gene25397:CDS 40.0%
GAAGAGAATACATCTCAGAG+TGG - chr8.2:40103661-40103680 None:intergenic 40.0%
GAATTGGGAACATGCAGAAT+CGG - chr8.2:40103382-40103401 None:intergenic 40.0%
GTGATGCAGTTGAGATTGAA+AGG + chr8.2:40104023-40104042 MS.gene25397:CDS 40.0%
TCAGAATCCGTTTGATTGGA+TGG + chr8.2:40104171-40104190 MS.gene25397:CDS 40.0%
TCGTTTGAGAAGGTTAATCC+CGG - chr8.2:40103902-40103921 None:intergenic 40.0%
! AATTTCTTTGAGAAGCGCGT+TGG + chr8.2:40104220-40104239 MS.gene25397:CDS 40.0%
! ATTTCTTTGAGAAGCGCGTT+GGG + chr8.2:40104221-40104240 MS.gene25397:CDS 40.0%
! GATGGATTTGATTTCGCTTC+AGG + chr8.2:40104189-40104208 MS.gene25397:CDS 40.0%
! GGATGTTTTCAATAGCGATC+TGG - chr8.2:40103640-40103659 None:intergenic 40.0%
! GTTGTTCCAGTGTTGAAGAT+CGG - chr8.2:40103480-40103499 None:intergenic 40.0%
! GTTTGTTGCTGATAGGTTGT+TGG + chr8.2:40104117-40104136 MS.gene25397:CDS 40.0%
! TGGATTTGATTTCGCTTCAG+GGG + chr8.2:40104191-40104210 MS.gene25397:CDS 40.0%
!! AAGCTGATTGGGCTTTGAAA+TGG + chr8.2:40103762-40103781 MS.gene25397:CDS 40.0%
AAAAAGCCGAAGCCTCTTTC+TGG + chr8.2:40103429-40103448 MS.gene25397:CDS 45.0%
GAAAATCGCACAGAAGCTTC+CGG - chr8.2:40103855-40103874 None:intergenic 45.0%
GATAGGTTGTTGGGTGAACT+TGG + chr8.2:40104127-40104146 MS.gene25397:CDS 45.0%
TTTCCTCCGATCTTCAACAC+TGG + chr8.2:40103471-40103490 MS.gene25397:CDS 45.0%
! AGAGGTTCTTCTGGGAAAGA+AGG - chr8.2:40103341-40103360 None:intergenic 45.0%
! GAAGCTTCTGTGCGATTTTC+TGG + chr8.2:40103855-40103874 MS.gene25397:CDS 45.0%
! GGAGGAAAGATCGACTTCTT+CGG - chr8.2:40103459-40103478 None:intergenic 45.0%
! GTTGCTTTCGCTTGTGTTGA+AGG + chr8.2:40103818-40103837 MS.gene25397:CDS 45.0%
! TTTCTTTGAGAAGCGCGTTG+GGG + chr8.2:40104222-40104241 MS.gene25397:CDS 45.0%
ATGCAGAATCGGTCTGGGTT+TGG - chr8.2:40103371-40103390 None:intergenic 50.0%
CTTTCATGAATCTTCCGGCG+AGG - chr8.2:40103580-40103599 None:intergenic 50.0%
GAGCGAGAAGAGGTTCTTCT+GGG - chr8.2:40103349-40103368 None:intergenic 50.0%
GAGCTTATTTCGCGTGACGA+AGG + chr8.2:40103920-40103939 MS.gene25397:CDS 50.0%
GGAACATGCAGAATCGGTCT+GGG - chr8.2:40103376-40103395 None:intergenic 50.0%
TTCATCCCAACCAACGCACA+AGG - chr8.2:40104070-40104089 None:intergenic 50.0%
! ACCATAGAAAGCACGCGCTT+CGG - chr8.2:40103615-40103634 None:intergenic 50.0%
! GGAAAGATCGACTTCTTCGG+CGG - chr8.2:40103456-40103475 None:intergenic 50.0%
! GTTCCAGTGTTGAAGATCGG+AGG - chr8.2:40103477-40103496 None:intergenic 50.0%
!! GTTTTCGAGGACGATACCGT+CGG - chr8.2:40103558-40103577 None:intergenic 50.0%
!! TGTGCGTTGGTTGGGATGAA+CGG + chr8.2:40104070-40104089 MS.gene25397:CDS 50.0%
ATCGTCCTCGAAAACCTCGC+CGG + chr8.2:40103563-40103582 MS.gene25397:CDS 55.0%
CACTGGAACAACCTCACCGA+CGG + chr8.2:40103488-40103507 MS.gene25397:CDS 55.0%
CGAGGATGTGAGAGACGAAG+TGG - chr8.2:40103520-40103539 None:intergenic 55.0%
GAAGCTGAGTTCAGAGCGAG+TGG + chr8.2:40103988-40104007 MS.gene25397:CDS 55.0%
GGAGCGAGAAGAGGTTCTTC+TGG - chr8.2:40103350-40103369 None:intergenic 55.0%
GGGAACATGCAGAATCGGTC+TGG - chr8.2:40103377-40103396 None:intergenic 55.0%
TCCGAAGCGCGTGCTTTCTA+TGG + chr8.2:40103611-40103630 MS.gene25397:CDS 55.0%
TTCTTCGGCGGTCCAGAAAG+AGG - chr8.2:40103444-40103463 None:intergenic 55.0%
! ATCTTCCGGCGAGGTTTTCG+AGG - chr8.2:40103571-40103590 None:intergenic 55.0%
! TCTGGGTTTGGAGCGAGAAG+AGG - chr8.2:40103359-40103378 None:intergenic 55.0%
!! CGCTTCCTTGTGCGTTGGTT+GGG + chr8.2:40104062-40104081 MS.gene25397:CDS 55.0%
ACCGTCGGAAGCGGCGAAAA+AGG - chr8.2:40103543-40103562 None:intergenic 60.0%
GAGGACGATACCGTCGGAAG+CGG - chr8.2:40103552-40103571 None:intergenic 60.0%
GGCGGTCCAGAAAGAGGCTT+CGG - chr8.2:40103438-40103457 None:intergenic 60.0%
! GCGCTTCCTTGTGCGTTGGT+TGG + chr8.2:40104061-40104080 MS.gene25397:CDS 60.0%
!! GCCTTTTTCGCCGCTTCCGA+CGG + chr8.2:40103539-40103558 MS.gene25397:CDS 60.0%
CGACGCGCTTCCTTGTGCGT+TGG + chr8.2:40104057-40104076 MS.gene25397:CDS 65.0%
CGGAAGCGGCGAAAAAGGCG+AGG - chr8.2:40103538-40103557 None:intergenic 65.0%
GACGAAGTGGCGTTCGCCGT+CGG - chr8.2:40103507-40103526 None:intergenic 65.0%
AGTGGCGTTCGCCGTCGGTG+AGG - chr8.2:40103502-40103521 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 40103335 40104312 40103335 ID=MS.gene25397
chr8.2 mRNA 40103335 40104312 40103335 ID=MS.gene25397.t1;Parent=MS.gene25397
chr8.2 exon 40103335 40104312 40103335 ID=MS.gene25397.t1.exon1;Parent=MS.gene25397.t1
chr8.2 CDS 40103335 40104312 40103335 ID=cds.MS.gene25397.t1;Parent=MS.gene25397.t1
Gene Sequence

>MS.gene25397

ATGCCTTCTTTCCCAGAAGAACCTCTTCTCGCTCCAAACCCAGACCGATTCTGCATGTTCCCAATTCAATACCCAAAAATCTGGGAAATGTACAAAAAAGCCGAAGCCTCTTTCTGGACCGCCGAAGAAGTCGATCTTTCCTCCGATCTTCAACACTGGAACAACCTCACCGACGGCGAACGCCACTTCGTCTCTCACATCCTCGCCTTTTTCGCCGCTTCCGACGGTATCGTCCTCGAAAACCTCGCCGGAAGATTCATGAAAGAAGTTCAAATCTCCGAAGCGCGTGCTTTCTATGGTTTCCAGATCGCTATTGAAAACATCCACTCTGAGATGTATTCTCTTCTCCTCGAAACGTATATAAGCGATTCTGCTGAAAAGAATCGATTATTTCACGCAATTGACACAATTCCGTGTATTGCTAAGAAAGCTGATTGGGCTTTGAAATGGATCGATTCAAGCGATTCTTTTGCAGAAAGAATCGTTGCTTTCGCTTGTGTTGAAGGAATTTTCTTCTCCGGAAGCTTCTGTGCGATTTTCTGGTTGAAAAAACGCGGTTTAATGCCGGGATTAACCTTCTCAAACGAGCTTATTTCGCGTGACGAAGGTTTACACTGCGATTTCGCTTGTTTGTTATACTCGCTATTGCGTCAGAAGCTGAGTTCAGAGCGAGTGGTGAAGATTGTTCGTGATGCAGTTGAGATTGAAAGGGAGTTTGTATGCGACGCGCTTCCTTGTGCGTTGGTTGGGATGAACGGTGAATTGATGAGTCAGTATATTGAGTTTGTTGCTGATAGGTTGTTGGGTGAACTTGGTTGTGAGAAAGTTTATAATGTTCAGAATCCGTTTGATTGGATGGATTTGATTTCGCTTCAGGGGAAGACGAATTTCTTTGAGAAGCGCGTTGGGGAGTATCAGAAAGCTTCTGTTATGAATGGTGGTGCTGATTATTGCTTTACTTTGGATGAGGATTTTTAG
Protein sequence

>MS.gene25397.t1

MPSFPEEPLLAPNPDRFCMFPIQYPKIWEMYKKAEASFWTAEEVDLSSDLQHWNNLTDGERHFVSHILAFFAASDGIVLENLAGRFMKEVQISEARAFYGFQIAIENIHSEMYSLLLETYISDSAEKNRLFHAIDTIPCIAKKADWALKWIDSSDSFAERIVAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRQKLSSERVVKIVRDAVEIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGELGCEKVYNVQNPFDWMDLISLQGKTNFFEKRVGEYQKASVMNGGADYCFTLDEDF