AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051569


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051569.t1 MTR_1g015650 95.510 245 3 3 10 252 57 295 2.71e-165 459
MS.gene051569.t1 MTR_3g105210 55.758 165 58 4 10 173 2 152 8.70e-54 172
MS.gene051569.t1 MTR_4g125330 41.916 167 78 7 75 231 66 223 3.81e-23 94.7
MS.gene051569.t1 MTR_1g045430 41.860 86 44 3 50 135 48 127 5.49e-14 68.6
MS.gene051569.t1 MTR_1g009640 43.023 86 44 2 50 135 52 132 7.14e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051569.t1 AT5G21940 54.015 137 50 6 44 174 44 173 8.76e-33 120
MS.gene051569.t1 AT3G43850 49.606 127 38 5 44 170 30 130 5.31e-27 103
MS.gene051569.t1 AT3G43850 50.000 142 43 6 31 170 15 130 1.51e-26 104

Find 44 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAAGGAATGTTTACCTAAT+AGG 0.264814 1.3:-6491263 None:intergenic
TAGAAGAGGTTCTTCCTATT+AGG 0.287448 1.3:+6491249 MS.gene051569:CDS
GCCACTTCCACCGCGTCATC+CGG 0.302841 1.3:+6492637 MS.gene051569:CDS
CTTCTTGTGTATGCATTCTC+TGG 0.380516 1.3:-6492404 None:intergenic
AATTTGCTGGCTTTCAATCA+TGG 0.423862 1.3:+6492434 MS.gene051569:CDS
AAGAAGACGTAGAAATTTGC+TGG 0.426140 1.3:+6492421 MS.gene051569:CDS
GCTGGCTTTCAATCATGGTT+GGG 0.432602 1.3:+6492439 MS.gene051569:CDS
AGTATCTCAAACTTCTATAG+TGG 0.435354 1.3:+6492314 MS.gene051569:CDS
AAAGAAGACACTCTATTTCC+CGG 0.439102 1.3:-6492656 None:intergenic
CGCGGTGGAAGTGGCGAAGA+AGG 0.445270 1.3:-6492629 None:intergenic
GAAGCTGAGAGTAAATATAA+TGG 0.445348 1.3:+6491200 MS.gene051569:CDS
TGCTGGCTTTCAATCATGGT+TGG 0.445425 1.3:+6492438 MS.gene051569:CDS
TTCCCTTTGAGAAGCAATAG+TGG 0.449201 1.3:+6492476 MS.gene051569:CDS
CCCGGATGACGCGGTGGAAG+TGG 0.453467 1.3:-6492638 None:intergenic
AGCTAGGCTTGTGAAGGACT+TGG 0.454561 1.3:-6492342 None:intergenic
CACCACTATTGCTTCTCAAA+GGG 0.472099 1.3:-6492478 None:intergenic
CTGTGTTATTTGACGCGCCG+AGG 0.485567 1.3:+6491048 MS.gene051569:CDS
CCACCACTATTGCTTCTCAA+AGG 0.509782 1.3:-6492479 None:intergenic
TGTGTTATTTGACGCGCCGA+GGG 0.520967 1.3:+6491049 MS.gene051569:CDS
CCACTTCCACCGCGTCATCC+GGG 0.531769 1.3:+6492638 MS.gene051569:CDS
GACGACGACGATGATGATCA+AGG 0.535849 1.3:+6491077 MS.gene051569:CDS
AGAAGGTGCTGAAGAATATG+AGG 0.542161 1.3:-6492612 None:intergenic
GAGAGATCAATGGATGAGAA+TGG 0.545446 1.3:+6491170 MS.gene051569:CDS
GAAAAGAAATTCCTCTGCAA+AGG 0.546535 1.3:-6492686 None:intergenic
TGGTGGTGCTTTAGATTGCA+TGG 0.548478 1.3:+6491220 MS.gene051569:CDS
GATGATTATGGAGCTTGAAA+CGG 0.556496 1.3:+6490995 None:intergenic
AACGGTGGCGATTAAGCGCG+TGG 0.559763 1.3:+6491013 MS.gene051569:CDS
CTTTAGCATCTCCTTTGCAG+AGG 0.570257 1.3:+6492675 MS.gene051569:CDS
TCGTCGTCGTCATGATCCCT+CGG 0.586543 1.3:-6491065 None:intergenic
GGTTTCATCAGAGAGATCAA+TGG 0.590893 1.3:+6491160 MS.gene051569:CDS
CCTTTGAGAAGCAATAGTGG+TGG 0.600401 1.3:+6492479 MS.gene051569:CDS
TTGCATGGAAGCTTTAGAAG+AGG 0.606872 1.3:+6491235 MS.gene051569:CDS
CTATTTCCCGGATGACGCGG+TGG 0.613883 1.3:-6492644 None:intergenic
ACAATGATGCAGATCAGCCA+AGG 0.617708 1.3:-6492708 None:intergenic
AACATCAGCTAGGCTTGTGA+AGG 0.619105 1.3:-6492348 None:intergenic
ACGACGTCGTCTTCATCGAT+CGG 0.620053 1.3:+6491113 MS.gene051569:CDS
ACGACGACGATGATGATCAA+GGG 0.626067 1.3:+6491078 MS.gene051569:CDS
GTGTTGTGACAACATCAGCT+AGG 0.640480 1.3:-6492358 None:intergenic
CGACGATGATGATCAAGGGA+AGG 0.650149 1.3:+6491082 MS.gene051569:CDS
AAATAGTGATGATGATGATG+AGG 0.659114 1.3:+6491139 MS.gene051569:CDS
ACTCTATTTCCCGGATGACG+CGG 0.665825 1.3:-6492647 None:intergenic
GCTGAGAGTAAATATAATGG+TGG 0.695812 1.3:+6491203 MS.gene051569:CDS
GATTATGGAGCTTGAAACGG+TGG 0.699571 1.3:+6490998 None:intergenic
ACGGTGGCGATTAAGCGCGT+GGG 0.700701 1.3:+6491014 MS.gene051569:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATATATATATATATAA+TGG - chr1.3:6491300-6491319 None:intergenic 0.0%
!! ATTTATATCAAAATTTACTA+TGG + chr1.3:6492186-6492205 MS.gene051569:intron 10.0%
!!! AAAGATTGTATATTTTTTTT+TGG + chr1.3:6491512-6491531 MS.gene051569:intron 10.0%
!!! AAGATTGTATATTTTTTTTT+GGG + chr1.3:6491513-6491532 MS.gene051569:intron 10.0%
!!! AATATTGCCTTTTTTATTTT+TGG + chr1.3:6491979-6491998 MS.gene051569:intron 15.0%
!!! AATTTTGCTAAAAATAGTAA+GGG + chr1.3:6491786-6491805 MS.gene051569:intron 15.0%
!!! TTTTTTAAATGTTTTAAGCA+GGG + chr1.3:6491477-6491496 MS.gene051569:intron 15.0%
!!! TTTTTTTAAATGTTTTAAGC+AGG + chr1.3:6491476-6491495 MS.gene051569:intron 15.0%
!! AAAAGTTTGTGAATGAAATT+TGG + chr1.3:6491636-6491655 MS.gene051569:intron 20.0%
!! GGCATTAGTTAAATTAATTA+GGG + chr1.3:6491584-6491603 MS.gene051569:intron 20.0%
!! TAATGGAAAAACTGTTAATA+AGG - chr1.3:6491283-6491302 None:intergenic 20.0%
!! TGATATAAATCTACACAATT+TGG - chr1.3:6492176-6492195 None:intergenic 20.0%
!!! ATTAGTGTTCTAAATAATGA+AGG + chr1.3:6492260-6492279 MS.gene051569:intron 20.0%
!!! GAATTTTGCTAAAAATAGTA+AGG + chr1.3:6491785-6491804 MS.gene051569:intron 20.0%
!!! TCATTTTCAATTGAAGAATT+TGG - chr1.3:6492758-6492777 None:intergenic 20.0%
! AACAAAACATTCAAAAGTGA+AGG - chr1.3:6491362-6491381 None:intergenic 25.0%
! ATAAGGAATGTTTACCTAAT+AGG - chr1.3:6491266-6491285 None:intergenic 25.0%
! ATCCAATTCAAAAGTTTATC+CGG - chr1.3:6491944-6491963 None:intergenic 25.0%
! GGGCATTAGTTAAATTAATT+AGG + chr1.3:6491583-6491602 MS.gene051569:intron 25.0%
! TCCTCAACCAAAAATAAAAA+AGG - chr1.3:6491989-6492008 None:intergenic 25.0%
! TGTTTCAGTTTCACAAAATT+AGG + chr1.3:6491744-6491763 MS.gene051569:intron 25.0%
!! AATTGTTGGATCAATTTTTG+TGG + chr1.3:6491561-6491580 MS.gene051569:intron 25.0%
!! AATTTGGTGATTGTATTGTA+AGG + chr1.3:6491652-6491671 MS.gene051569:intron 25.0%
!! ATTAATTAGGGTACTATTGT+TGG + chr1.3:6491596-6491615 MS.gene051569:intron 25.0%
!! ATTGTTGGATCAATTTTTGT+GGG + chr1.3:6491562-6491581 MS.gene051569:intron 25.0%
!! ATTTTGTGAAACTGAAACAA+AGG - chr1.3:6491743-6491762 None:intergenic 25.0%
!! CTTTTGATAGAAGAAAACTT+GGG + chr1.3:6491885-6491904 MS.gene051569:intron 25.0%
!! GGTATTAGTTAAATTAGCTT+GGG + chr1.3:6491534-6491553 MS.gene051569:intron 25.0%
!! TTTACAATGTCTTTTACAGA+TGG - chr1.3:6492383-6492402 None:intergenic 25.0%
!! TTTTGTGAAACTGAAACAAA+GGG - chr1.3:6491742-6491761 None:intergenic 25.0%
!!! ATTTTTAGCAAAATTCCACA+TGG - chr1.3:6491781-6491800 None:intergenic 25.0%
AGTATCTCAAACTTCTATAG+TGG + chr1.3:6492314-6492333 MS.gene051569:CDS 30.0%
CTAAAGAACATGTTTGCAAT+TGG + chr1.3:6491914-6491933 MS.gene051569:intron 30.0%
GAAGCTGAGAGTAAATATAA+TGG + chr1.3:6491200-6491219 MS.gene051569:CDS 30.0%
GGGTATTAGTTAAATTAGCT+TGG + chr1.3:6491533-6491552 MS.gene051569:intron 30.0%
GTTTGAATCAACTTTCATTC+TGG - chr1.3:6492147-6492166 None:intergenic 30.0%
GTTTGGTACTTGTTTGTAAA+TGG + chr1.3:6492034-6492053 MS.gene051569:intron 30.0%
TTACAAACAAGTACCAAACA+AGG - chr1.3:6492033-6492052 None:intergenic 30.0%
! AAATAGTGATGATGATGATG+AGG + chr1.3:6491139-6491158 MS.gene051569:CDS 30.0%
! AAGGCTAATCCAATCTTTTA+TGG + chr1.3:6492279-6492298 MS.gene051569:intron 30.0%
! GCTTTTGATAGAAGAAAACT+TGG + chr1.3:6491884-6491903 MS.gene051569:intron 30.0%
! TAATTCATGTTTGCCTTGTT+TGG + chr1.3:6492017-6492036 MS.gene051569:intron 30.0%
! TACCGGATAAACTTTTGAAT+TGG + chr1.3:6491939-6491958 MS.gene051569:intron 30.0%
! TTGTTGGATCAATTTTTGTG+GGG + chr1.3:6491563-6491582 MS.gene051569:intron 30.0%
!!! GCCTTTTTTATTTTTGGTTG+AGG + chr1.3:6491985-6492004 MS.gene051569:intron 30.0%
!!! TAGGTTTATTTTGTACCATG+TGG + chr1.3:6491763-6491782 MS.gene051569:intron 30.0%
AAAGAAGACACTCTATTTCC+CGG - chr1.3:6492659-6492678 None:intergenic 35.0%
AAGAAGACGTAGAAATTTGC+TGG + chr1.3:6492421-6492440 MS.gene051569:CDS 35.0%
CAACGTGATTGTATAGTTTC+GGG + chr1.3:6492083-6492102 MS.gene051569:intron 35.0%
CCAAAACATGACGAATTCAT+TGG - chr1.3:6491838-6491857 None:intergenic 35.0%
CCTGCATAACCATAAAAGAT+TGG - chr1.3:6492291-6492310 None:intergenic 35.0%
GAAAAGAAATTCCTCTGCAA+AGG - chr1.3:6492689-6492708 None:intergenic 35.0%
GCAACGTGATTGTATAGTTT+CGG + chr1.3:6492082-6492101 MS.gene051569:intron 35.0%
GCATGATTGAAGCTTACAAA+AGG - chr1.3:6491866-6491885 None:intergenic 35.0%
GCTGAGAGTAAATATAATGG+TGG + chr1.3:6491203-6491222 MS.gene051569:CDS 35.0%
TAGAAGAGGTTCTTCCTATT+AGG + chr1.3:6491249-6491268 MS.gene051569:CDS 35.0%
! CATTTTCATTGTTGCAGCAA+TGG - chr1.3:6492735-6492754 None:intergenic 35.0%
! CCAATCTTTTATGGTTATGC+AGG + chr1.3:6492288-6492307 MS.gene051569:intron 35.0%
! CCAATGAATTCGTCATGTTT+TGG + chr1.3:6491835-6491854 MS.gene051569:intron 35.0%
! TGTGTGATGATGTGATCTAT+AGG + chr1.3:6491696-6491715 MS.gene051569:intron 35.0%
! TTAGCTTGGGTACTAATTGT+TGG + chr1.3:6491547-6491566 MS.gene051569:intron 35.0%
!! AATTTGCTGGCTTTCAATCA+TGG + chr1.3:6492434-6492453 MS.gene051569:CDS 35.0%
ATCACATCATCACACACTAC+TGG - chr1.3:6491692-6491711 None:intergenic 40.0%
CACCACTATTGCTTCTCAAA+GGG - chr1.3:6492481-6492500 None:intergenic 40.0%
CATGTTTGCAATTGGTGTAC+CGG + chr1.3:6491922-6491941 MS.gene051569:intron 40.0%
CTGTGAGTTTGACGATATCA+CGG + chr1.3:6492057-6492076 MS.gene051569:intron 40.0%
CTTCTTGTGTATGCATTCTC+TGG - chr1.3:6492407-6492426 None:intergenic 40.0%
GAGAGATCAATGGATGAGAA+TGG + chr1.3:6491170-6491189 MS.gene051569:CDS 40.0%
GGTTTCATCAGAGAGATCAA+TGG + chr1.3:6491160-6491179 MS.gene051569:CDS 40.0%
! GCAGAGGAATTTCTTTTCCT+TGG + chr1.3:6492691-6492710 MS.gene051569:CDS 40.0%
! TTCCCTTTGAGAAGCAATAG+TGG + chr1.3:6492476-6492495 MS.gene051569:CDS 40.0%
!! AGAAGGTGCTGAAGAATATG+AGG - chr1.3:6492615-6492634 None:intergenic 40.0%
!! TTGCATGGAAGCTTTAGAAG+AGG + chr1.3:6491235-6491254 MS.gene051569:CDS 40.0%
AACATCAGCTAGGCTTGTGA+AGG - chr1.3:6492351-6492370 None:intergenic 45.0%
ACAATGATGCAGATCAGCCA+AGG - chr1.3:6492711-6492730 None:intergenic 45.0%
ACGACGACGATGATGATCAA+GGG + chr1.3:6491078-6491097 MS.gene051569:CDS 45.0%
CCACCACTATTGCTTCTCAA+AGG - chr1.3:6492482-6492501 None:intergenic 45.0%
CTTTAGCATCTCCTTTGCAG+AGG + chr1.3:6492675-6492694 MS.gene051569:CDS 45.0%
GTGTTGTGACAACATCAGCT+AGG - chr1.3:6492361-6492380 None:intergenic 45.0%
TGAGTTTGACGATATCACGG+TGG + chr1.3:6492060-6492079 MS.gene051569:intron 45.0%
! CCTTTGAGAAGCAATAGTGG+TGG + chr1.3:6492479-6492498 MS.gene051569:CDS 45.0%
! TGGTGGTGCTTTAGATTGCA+TGG + chr1.3:6491220-6491239 MS.gene051569:CDS 45.0%
!! GCTGGCTTTCAATCATGGTT+GGG + chr1.3:6492439-6492458 MS.gene051569:CDS 45.0%
!! TGCTGGCTTTCAATCATGGT+TGG + chr1.3:6492438-6492457 MS.gene051569:CDS 45.0%
ACGACGTCGTCTTCATCGAT+CGG + chr1.3:6491113-6491132 MS.gene051569:CDS 50.0%
ACTCTATTTCCCGGATGACG+CGG - chr1.3:6492650-6492669 None:intergenic 50.0%
AGCTAGGCTTGTGAAGGACT+TGG - chr1.3:6492345-6492364 None:intergenic 50.0%
CGACGATGATGATCAAGGGA+AGG + chr1.3:6491082-6491101 MS.gene051569:CDS 50.0%
GACGACGACGATGATGATCA+AGG + chr1.3:6491077-6491096 MS.gene051569:CDS 50.0%
!! TGTGTTATTTGACGCGCCGA+GGG + chr1.3:6491049-6491068 MS.gene051569:CDS 50.0%
TCGTCGTCGTCATGATCCCT+CGG - chr1.3:6491068-6491087 None:intergenic 55.0%
!! CTGTGTTATTTGACGCGCCG+AGG + chr1.3:6491048-6491067 MS.gene051569:CDS 55.0%
AACGGTGGCGATTAAGCGCG+TGG + chr1.3:6491013-6491032 MS.gene051569:CDS 60.0%
ACGGTGGCGATTAAGCGCGT+GGG + chr1.3:6491014-6491033 MS.gene051569:CDS 60.0%
CTATTTCCCGGATGACGCGG+TGG - chr1.3:6492647-6492666 None:intergenic 60.0%
CCACTTCCACCGCGTCATCC+GGG + chr1.3:6492638-6492657 MS.gene051569:CDS 65.0%
CGCGGTGGAAGTGGCGAAGA+AGG - chr1.3:6492632-6492651 None:intergenic 65.0%
GCCACTTCCACCGCGTCATC+CGG + chr1.3:6492637-6492656 MS.gene051569:CDS 65.0%
CCCGGATGACGCGGTGGAAG+TGG - chr1.3:6492641-6492660 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 6491002 6492799 6491002 ID=MS.gene051569
chr1.3 mRNA 6491002 6492799 6491002 ID=MS.gene051569.t1;Parent=MS.gene051569
chr1.3 exon 6491002 6491270 6491002 ID=MS.gene051569.t1.exon1;Parent=MS.gene051569.t1
chr1.3 CDS 6491002 6491270 6491002 ID=cds.MS.gene051569.t1;Parent=MS.gene051569.t1
chr1.3 exon 6492310 6492799 6492310 ID=MS.gene051569.t1.exon2;Parent=MS.gene051569.t1
chr1.3 CDS 6492310 6492799 6492310 ID=cds.MS.gene051569.t1;Parent=MS.gene051569.t1
Gene Sequence

>MS.gene051569

ATGGAGCTTGAAACGGTGGCGATTAAGCGCGTGGGTTCACGTACTTCTGTGTTATTTGACGCGCCGAGGGATCATGACGACGACGATGATGATCAAGGGAAGGTGTGTAGTACGACGTCGTCTTCATCGATCGGAAGAAATAGTGATGATGATGATGAGGTTTCATCAGAGAGATCAATGGATGAGAATGGTGATAATGAAGCTGAGAGTAAATATAATGGTGGTGCTTTAGATTGCATGGAAGCTTTAGAAGAGGTTCTTCCTATTAGGTAAACATTCCTTATTAACAGTTTTTCCATTATATATATATATATTTATTGTTTTGTTAGATTATATCATGTGAATTTGATGTTAGATCCTTCACTTTTGAATGTTTTGTTTTACTAAAATGATTCAATTTTTTATCTTTTTTGTTTGATCTTAGTTTCAATTAATATTATTTGTTTGCTTGTTGATTGTGTTATGATATTTAGTTTTTTTTAAATGTTTTAAGCAGGGTTGTTAAATTGTAAAGATTGTATATTTTTTTTTGGGTATTAGTTAAATTAGCTTGGGTACTAATTGTTGGATCAATTTTTGTGGGGCATTAGTTAAATTAATTAGGGTACTATTGTTGGATCAATTTGATGAAATGAAAAGTTTGTGAATGAAATTTGGTGATTGTATTGTAAGGCATGTGATGTCTATCCAGTAGTGTGTGATGATGTGATCTATAGGTTTTGTCTGTATCTGTGTTTCCCTTTGTTTCAGTTTCACAAAATTAGGTTTATTTTGTACCATGTGGAATTTTGCTAAAAATAGTAAGGGTTTGTGTTGATTTGATATAGTTTGAACCAATGAATTCGTCATGTTTTGGATTAACCTTTTGTAAGCTTCAATCATGCTTTTGATAGAAGAAAACTTGGGTTTGTACTAAAGAACATGTTTGCAATTGGTGTACCGGATAAACTTTTGAATTGGATTGAATACTAAAACTGAATATTGCCTTTTTTATTTTTGGTTGAGGATATTTTGCTAATTCATGTTTGCCTTGTTTGGTACTTGTTTGTAAATGGCTGTGAGTTTGACGATATCACGGTGGCAACGTGATTGTATAGTTTCGGGTAATTCACTATGATTCTGCTAAACTCAGCGTTAATCTGCCAGAATGAAAGTTGATTCAAACTTCATTCCAAATTGTGTAGATTTATATCAAAATTTACTATGGAAATTTTTTTTTCAAACATTGTACACTTCATTTCATATTCAGTTTTGACAAATTAGTGTTCTAAATAATGAAGGCTAATCCAATCTTTTATGGTTATGCAGGAGAAGTATCTCAAACTTCTATAGTGGAAAATCCAAGTCCTTCACAAGCCTAGCTGATGTTGTCACAACACCATCTGTAAAAGACATTGTAAAACCAGAGAATGCATACACAAGAAGACGTAGAAATTTGCTGGCTTTCAATCATGGTTGGGACAAGAACAAAAATTTCCCTTTGAGAAGCAATAGTGGTGGAATTTCAAAGAGAACAATGAGCTTAAGTAGAAGTGCTTTAGCTCTTGCAGTTGCATTAAGCAATTCTGATAGTAGCTCTAGTTTTACAAGTGATGATTCAGCTGCTTCAACCTCATATTCTTCAGCACCTTCTTCGCCACTTCCACCGCGTCATCCGGGAAATAGAGTGTCTTCTTTAGCATCTCCTTTGCAGAGGAATTTCTTTTCCTTGGCTGATCTGCATCATTGTGCCATTGCTGCAACAATGAAAATGCCAAATTCTTCAATTGAAAATGAAACAACTAATCATCCATCATAG

Protein sequence

>MS.gene051569.t1

MELETVAIKRVGSRTSVLFDAPRDHDDDDDDQGKVCSTTSSSSIGRNSDDDDEVSSERSMDENGDNEAESKYNGGALDCMEALEEVLPIRRSISNFYSGKSKSFTSLADVVTTPSVKDIVKPENAYTRRRRNLLAFNHGWDKNKNFPLRSNSGGISKRTMSLSRSALALAVALSNSDSSSSFTSDDSAASTSYSSAPSSPLPPRHPGNRVSSLASPLQRNFFSLADLHHCAIAATMKMPNSSIENETTNHPS