AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83535

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83535.t1 MTR_2g103870 99.367 158 1 0 1 158 1 158 1.71e-115 323
MS.gene83535.t1 MTR_4g010160 86.713 143 19 0 13 155 1 143 2.81e-79 231
MS.gene83535.t1 MTR_7g114020 46.269 134 71 1 20 153 14 146 7.40e-37 124
MS.gene83535.t1 MTR_1g082290 45.161 124 67 1 20 143 18 140 8.04e-36 121
MS.gene83535.t1 MTR_1g089130 46.429 140 70 2 13 148 4 142 2.31e-35 120
MS.gene83535.t1 MTR_2g020770 46.207 145 73 3 10 154 10 149 3.58e-31 110
MS.gene83535.t1 MTR_2g100900 41.935 124 71 1 20 143 17 139 9.82e-30 106
MS.gene83535.t1 MTR_2g100880 41.935 124 71 1 20 143 17 139 1.42e-29 105
MS.gene83535.t1 MTR_2g020770 44.361 133 70 2 10 142 10 138 3.47e-27 99.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83535.t1 AT1G80100 77.273 154 35 0 1 154 1 154 1.38e-68 205
MS.gene83535.t1 AT1G80100 75.714 140 34 0 1 140 1 140 5.52e-58 178
MS.gene83535.t1 AT1G80100 66.883 154 29 1 1 154 1 132 7.78e-58 177
MS.gene83535.t1 AT5G39340 41.722 151 83 2 7 153 2 151 1.54e-36 124
MS.gene83535.t1 AT5G39340 44.030 134 74 1 20 153 52 184 8.48e-36 122
MS.gene83535.t1 AT1G03430 42.537 134 76 1 20 153 20 152 1.38e-35 121
MS.gene83535.t1 AT5G39340 44.030 134 74 1 20 153 68 200 2.15e-35 122
MS.gene83535.t1 AT5G39340 44.030 134 74 1 20 153 68 200 2.15e-35 122
MS.gene83535.t1 AT3G29350 41.221 131 77 0 20 150 19 149 8.59e-35 119
MS.gene83535.t1 AT1G03430 42.149 121 70 0 20 140 20 140 3.95e-33 115
MS.gene83535.t1 AT3G16360 41.791 134 77 1 20 153 12 144 1.37e-32 113
MS.gene83535.t1 AT3G21510 47.328 131 68 1 20 150 17 146 2.65e-32 112
MS.gene83535.t1 AT3G16360 43.333 120 67 1 23 142 9 127 9.91e-30 105
MS.gene83535.t1 AT3G29350 41.667 96 56 0 20 115 19 114 8.22e-24 90.1
MS.gene83535.t1 AT4G04402 29.012 162 98 6 4 153 6 162 1.23e-13 65.1

Find 28 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACTCTGGATGCTTGGTT+TGG 0.259246 2.2:-513464 None:intergenic
CCACTCTGGATGCTTGGTTT+GGG 0.300260 2.2:-513463 None:intergenic
ACAACTTCAGAGACAAAGTT+AGG 0.349554 2.2:+513331 None:intergenic
CAGCAACGTGCTTTGGCAGC+TGG 0.382396 2.2:-512388 MS.gene83535:CDS
GATAGAGCAGCAACGTGCTT+TGG 0.394138 2.2:-512395 MS.gene83535:CDS
ATACATTTGAATCAATTCAT+TGG 0.432634 2.2:-513009 MS.gene83535:CDS
TTTGGGTGCGGACCTCTTGT+GGG 0.440442 2.2:-513446 MS.gene83535:CDS
GGTCTTCCACTCTGGATGCT+TGG 0.445346 2.2:-513469 None:intergenic
TTTGCGAGCGTTGGAAATGC+TGG 0.454165 2.2:-512579 MS.gene83535:CDS
GTTTGGGTGCGGACCTCTTG+TGG 0.459527 2.2:-513447 MS.gene83535:CDS
ATTTATTGATGCTGCTGCAT+AGG 0.460477 2.2:+512355 None:intergenic
TTACAGCAATGATCTGAGAT+TGG 0.475206 2.2:+513273 None:intergenic
TTTATTGATGCTGCTGCATA+GGG 0.480181 2.2:+512356 None:intergenic
TCTGAGCAAGACAACCGTGC+TGG 0.483071 2.2:-512925 MS.gene83535:CDS
CTGAGCAAGACAACCGTGCT+GGG 0.507329 2.2:-512924 MS.gene83535:intron
CAACTTCAGAGACAAAGTTA+GGG 0.524139 2.2:+513332 None:intergenic
TTGTAGATGTTTGCGAGCGT+TGG 0.533372 2.2:-512588 MS.gene83535:intron
CTGGATGCTTGGTTTGGGTG+CGG 0.535283 2.2:-513458 None:intergenic
TTGCTCAGAAGCTGCACGAA+AGG 0.551654 2.2:+512939 None:intergenic
ATTGGTAGTAGCTCAAGCAT+TGG 0.586684 2.2:-512991 MS.gene83535:CDS
GATGCATGTCGGCCCACAAG+AGG 0.616168 2.2:+513434 None:intergenic
TGGTCATTGCAGAATGGAGA+GGG 0.636697 2.2:-513058 MS.gene83535:intron
AGCAAGGAGACGATGCATGT+CGG 0.637824 2.2:+513423 None:intergenic
CCTGATGGAAGAGAAAAGCA+AGG 0.647458 2.2:+513407 None:intergenic
AAAATGGAACGAACCCAGCA+CGG 0.649795 2.2:+512911 None:intergenic
TTCAGAGACAAAGTTAGGGG+AGG 0.659336 2.2:+513336 None:intergenic
GTGGTCATTGCAGAATGGAG+AGG 0.704898 2.2:-513059 MS.gene83535:intron
AACTTCAGAGACAAAGTTAG+GGG 0.715591 2.2:+513333 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATTATATTATTATTA+TGG + chr2.2:513355-513374 None:intergenic 0.0%
!! CTAAATTACGATAAATTATA+TGG - chr2.2:513384-513403 MS.gene83535:CDS 15.0%
!! ATACATTTGAATCAATTCAT+TGG - chr2.2:512802-512821 MS.gene83535:intron 20.0%
! ATTTATATTTGTGTCTGTCT+CGG - chr2.2:512676-512695 MS.gene83535:intron 25.0%
! CAATGATACAAAATGCATAA+TGG - chr2.2:513150-513169 MS.gene83535:intron 25.0%
! GATCATAGCATAGAAATATA+AGG + chr2.2:512580-512599 None:intergenic 25.0%
!!! TTTTAAGAGGGAATGAAAAA+TGG + chr2.2:512919-512938 None:intergenic 25.0%
AGATGCAATAGAACTTTACT+TGG + chr2.2:513301-513320 None:intergenic 30.0%
ATATATGTTTGTGTCATGTC+TGG + chr2.2:512649-512668 None:intergenic 30.0%
AACTTCAGAGACAAAGTTAG+GGG + chr2.2:512481-512500 None:intergenic 35.0%
ACAACTTCAGAGACAAAGTT+AGG + chr2.2:512483-512502 None:intergenic 35.0%
CAACTTCAGAGACAAAGTTA+GGG + chr2.2:512482-512501 None:intergenic 35.0%
GTGACATTAACAAATGTGTG+TGG - chr2.2:512733-512752 MS.gene83535:intron 35.0%
TACAAGTTAGAACTCATCAC+TGG + chr2.2:513190-513209 None:intergenic 35.0%
! AGTAGTGCACGAATTTTAAG+AGG + chr2.2:512932-512951 None:intergenic 35.0%
! TTACAGCAATGATCTGAGAT+TGG + chr2.2:512541-512560 None:intergenic 35.0%
!! AAAGTGCGTGCATTTTTAAG+TGG + chr2.2:513056-513075 None:intergenic 35.0%
!! GTAGTGCACGAATTTTAAGA+GGG + chr2.2:512931-512950 None:intergenic 35.0%
!!! AAGTGCGTGCATTTTTAAGT+GGG + chr2.2:513055-513074 None:intergenic 35.0%
!!! GTGCATTTTTAAGTGGGAAA+AGG + chr2.2:513049-513068 None:intergenic 35.0%
! ATTGGTAGTAGCTCAAGCAT+TGG - chr2.2:512820-512839 MS.gene83535:intron 40.0%
!! CTTGCTTTTCTCTTCCATCA+GGG - chr2.2:512405-512424 MS.gene83535:intron 40.0%
!! TTGCTTTTCTCTTCCATCAG+GGG - chr2.2:512406-512425 MS.gene83535:intron 40.0%
AAAATGGAACGAACCCAGCA+CGG + chr2.2:512903-512922 None:intergenic 45.0%
CCTGATGGAAGAGAAAAGCA+AGG + chr2.2:512407-512426 None:intergenic 45.0%
GCTCGCAAACATCTACAATC+AGG + chr2.2:513221-513240 None:intergenic 45.0%
TGGTCATTGCAGAATGGAGA+GGG - chr2.2:512753-512772 MS.gene83535:intron 45.0%
TGTGTGTGGTCATTGCAGAA+TGG - chr2.2:512747-512766 MS.gene83535:intron 45.0%
TTCAGAGACAAAGTTAGGGG+AGG + chr2.2:512478-512497 None:intergenic 45.0%
TTGTAGATGTTTGCGAGCGT+TGG - chr2.2:513223-513242 MS.gene83535:intron 45.0%
! AAAGGAAAGTGTGACAGTGG+AGG + chr2.2:513031-513050 None:intergenic 45.0%
! AAGGAAAGTGTGACAGTGGA+GGG + chr2.2:513030-513049 None:intergenic 45.0%
! ACGTCTTGCATCAGAAGTGT+CGG + chr2.2:512620-512639 None:intergenic 45.0%
! GGAAAAGGAAAGTGTGACAG+TGG + chr2.2:513034-513053 None:intergenic 45.0%
! TGCTTTTCTCTTCCATCAGG+GGG - chr2.2:512407-512426 MS.gene83535:intron 45.0%
!! CCTTGCTTTTCTCTTCCATC+AGG - chr2.2:512404-512423 MS.gene83535:intron 45.0%
!!! AATTTTTTATCAATAAAATA+AGG - chr2.2:512971-512990 MS.gene83535:CDS 5.0%
AGCAAGGAGACGATGCATGT+CGG + chr2.2:512391-512410 None:intergenic 50.0%
CACTTCTGATGCAAGACGTC+TGG - chr2.2:512621-512640 MS.gene83535:intron 50.0%
GATAGAGCAGCAACGTGCTT+TGG - chr2.2:513416-513435 MS.gene83535:CDS 50.0%
GTGGTCATTGCAGAATGGAG+AGG - chr2.2:512752-512771 MS.gene83535:intron 50.0%
TTGCTCAGAAGCTGCACGAA+AGG + chr2.2:512875-512894 None:intergenic 50.0%
!! TTTGCGAGCGTTGGAAATGC+TGG - chr2.2:513232-513251 MS.gene83535:intron 50.0%
AGTGTGACAGTGGAGGGTTG+CGG + chr2.2:513024-513043 None:intergenic 55.0%
CTGAGCAAGACAACCGTGCT+GGG - chr2.2:512887-512906 MS.gene83535:intron 55.0%
TCTGAGCAAGACAACCGTGC+TGG - chr2.2:512886-512905 MS.gene83535:intron 55.0%
TTTGGGTGCGGACCTCTTGT+GGG - chr2.2:512365-512384 MS.gene83535:CDS 55.0%
! TCTCTTCCATCAGGGGGTGT+TGG - chr2.2:512413-512432 MS.gene83535:intron 55.0%
CAGCAACGTGCTTTGGCAGC+TGG - chr2.2:513423-513442 MS.gene83535:CDS 60.0%
GATGCATGTCGGCCCACAAG+AGG + chr2.2:512380-512399 None:intergenic 60.0%
GCTCATCCAACACCCCCTGA+TGG + chr2.2:512422-512441 None:intergenic 60.0%
GTTTGGGTGCGGACCTCTTG+TGG - chr2.2:512364-512383 MS.gene83535:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 512357 513476 512357 ID=MS.gene83535
chr2.2 mRNA 512357 513476 512357 ID=MS.gene83535.t1;Parent=MS.gene83535
chr2.2 exon 513277 513476 513277 ID=MS.gene83535.t1.exon1;Parent=MS.gene83535.t1
chr2.2 CDS 513277 513476 513277 ID=cds.MS.gene83535.t1;Parent=MS.gene83535.t1
chr2.2 exon 512925 513068 512925 ID=MS.gene83535.t1.exon2;Parent=MS.gene83535.t1
chr2.2 CDS 512925 513068 512925 ID=cds.MS.gene83535.t1;Parent=MS.gene83535.t1
chr2.2 exon 512532 512604 512532 ID=MS.gene83535.t1.exon3;Parent=MS.gene83535.t1
chr2.2 CDS 512532 512604 512532 ID=cds.MS.gene83535.t1;Parent=MS.gene83535.t1
chr2.2 exon 512357 512416 512357 ID=MS.gene83535.t1.exon4;Parent=MS.gene83535.t1
chr2.2 CDS 512357 512416 512357 ID=cds.MS.gene83535.t1;Parent=MS.gene83535.t1
Gene Sequence

>MS.gene83535

ATGCTTGGTTTGGGTGCGGACCTCTTGTGGGCCGACATGCATCGTCTCCTTGCTTTTCTCTTCCATCAGGGGGTGTTGGATGAGCAATTTTTGCAGCTTCAACAGCTTCAAGATCATACCTCCCCTAACTTTGTCTCTGAAGTTGTCAACATTTATTTTCATGAGTCTGAAAAACTACTCACCAATCTCAGATCATTGCTGTAATAACTCATTAATCTCTCCTTATATTTCTATGCTATGATCATAAATATTATGTAACACCGACACTTCTGATGCAAGACGTCTGGTGCCAGACATGACACAAACATATATAGTTACTATTTATATTTGTGTCTGTCTCGGTGCATCATAGCAGAAATATATTAGTGTTATTATTGTGACATTAACAAATGTGTGTGGTCATTGCAGAATGGAGAGGGAGTTTTCAGACTACAAGAAAATTGAAATACATTTGAATCAATTCATTGGTAGTAGCTCAAGCATTGGTGCTAAAAGAGTGACAAGCATTTGCATTGCCTTTCGTGCAGCTTCTGAGCAAGACAACCGTGCTGGGTTCGTTCCATTTTTCATTCCCTCTTAAAATTCGTGCACTACTCTTTTTGTTAAATTTAGCTAATTTTTTATCAATAAAATAAGGATAATAGTTGCACTTGCTTTTAGTACTCCGCAACCCTCCACTGTCACACTTTCCTTTTCCCACTTAAAAATGCACGCACTTTATAGTTTAATACATTAATTAATTTATCATTATAGTTAATTATGATACTCTCAAATTCATTCATTCATAATACAACAATGATACAAAATGCATAATGGCTATATCATATTATCCAGTGATGAGTTCTAACTTGTAAGTATGTGCCTGATTGTAGATGTTTGCGAGCGTTGGAAATGCTGGAGCATGAATATTGCTATCTTAAAAACAAATTGCACGAACTCTTCCAAGTAAAGTTCTATTGCATCTAATTTAATCATGTTAATTTTATCATACATTACCATAATAATAATATAATATATTAGTAGTGTACTAAATTACGATAAATTATATGGTTTTGTTCAGATAGAGCAGCAACGTGCTTTGGCAGCTGGAGTGAGATACCCTATGCAGCAGCATCAATAA
Protein sequence

>MS.gene83535.t1

MLGLGADLLWADMHRLLAFLFHQGVLDEQFLQLQQLQDHTSPNFVSEVVNIYFHESEKLLTNLRSLLMEREFSDYKKIEIHLNQFIGSSSSIGAKRVTSICIAFRAASEQDNRAGCLRALEMLEHEYCYLKNKLHELFQIEQQRALAAGVRYPMQQHQ