AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49470

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49470.t1 MTR_5g006470 93.085 188 13 0 1 188 1 188 5.86e-131 365
MS.gene49470.t1 MTR_5g006450 78.421 190 39 1 1 188 1 190 5.65e-104 297
MS.gene49470.t1 MTR_5g006460 77.436 195 35 6 1 188 1 193 2.27e-99 285
MS.gene49470.t1 MTR_5g006520 76.316 190 43 1 1 188 1719 1908 4.24e-96 305
MS.gene49470.t1 MTR_5g006510 72.778 180 44 3 12 188 14 191 5.60e-90 261
MS.gene49470.t1 MTR_1g103110 64.737 190 65 1 1 188 1 190 4.44e-86 251
MS.gene49470.t1 MTR_1g103150 63.158 190 68 1 1 188 1 190 1.38e-84 248
MS.gene49470.t1 MTR_7g114410 44.970 169 92 1 17 185 4 171 1.00e-46 151
MS.gene49470.t1 MTR_7g024780 42.941 170 95 2 16 185 3 170 6.21e-42 139
MS.gene49470.t1 MTR_7g114410 44.156 154 85 1 17 170 4 156 2.74e-41 137
MS.gene49470.t1 MTR_3g463610 42.442 172 95 2 17 185 3 173 5.60e-41 138
MS.gene49470.t1 MTR_7g024760 41.566 166 94 2 20 185 7 169 2.33e-39 132
MS.gene49470.t1 MTR_7g024765 41.566 166 94 2 20 185 7 169 2.28e-38 130
MS.gene49470.t1 MTR_1g103320 49.367 79 40 0 51 129 11 89 5.45e-20 81.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49470.t1 AT2G32020 54.491 167 71 3 20 185 18 180 3.78e-57 178
MS.gene49470.t1 AT2G32030 51.381 181 75 4 6 185 17 185 1.79e-56 176
MS.gene49470.t1 AT3G22560 39.535 172 101 2 16 185 2 172 7.81e-37 126

Find 39 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCAATGATCTCTTCTT+TGG 0.196407 5.1:+1247734 None:intergenic
GGGAGTTCTTAGGAAGTATT+TGG 0.241791 5.1:-1247289 MS.gene49470:CDS
CTCTTCTTTGGCACATGGTT+TGG 0.246122 5.1:+1247746 None:intergenic
ATAATCTAAGCTCTATATAT+TGG 0.258828 5.1:-1247458 MS.gene49470:CDS
TCCTAAGAACTCCCTCCTTT+TGG 0.260104 5.1:+1247298 None:intergenic
ATCAAGGTCAGAAAGATTAA+AGG 0.290557 5.1:+1247692 None:intergenic
TAATCTAAGCTCTATATATT+GGG 0.291812 5.1:-1247457 MS.gene49470:CDS
GTTGATGCCATCTTCTTTGC+TGG 0.294680 5.1:+1247608 None:intergenic
AGGTTCCCATGAGCAGAATT+TGG 0.303996 5.1:+1247635 None:intergenic
TGCTGTGAAACAAATTATTA+AGG 0.312252 5.1:-1247415 MS.gene49470:CDS
CCATCTTCTTTGCTGGTGTA+AGG 0.323803 5.1:+1247615 None:intergenic
AAAATGAAACTTATTAAAGT+TGG 0.351635 5.1:+1247211 None:intergenic
TCTCCAAGTATGAAAATTCA+TGG 0.373432 5.1:+1247385 None:intergenic
TCCAAAAGGAGGGAGTTCTT+AGG 0.394554 5.1:-1247299 MS.gene49470:CDS
TAAAGGGTCGGAGTGTGATT+TGG 0.396804 5.1:+1247709 None:intergenic
TGCATTGATGATCGTGCTAT+TGG 0.407515 5.1:-1247540 MS.gene49470:CDS
AGGAAACAATCTGCAGAACT+TGG 0.436712 5.1:-1247483 MS.gene49470:CDS
TTCTGACCTTGATGATGTAA+TGG 0.440976 5.1:-1247682 MS.gene49470:CDS
TCAAGGTCAGAAAGATTAAA+GGG 0.477441 5.1:+1247693 None:intergenic
CTTGTCGATGTTGAAAATGT+TGG 0.484592 5.1:-1247351 MS.gene49470:CDS
GCTCTATATATTGGGGCAAA+GGG 0.493310 5.1:-1247449 MS.gene49470:CDS
CAAAGAGTGTTGGAGAAAGC+TGG 0.499760 5.1:-1247324 MS.gene49470:CDS
AGCTCTATATATTGGGGCAA+AGG 0.501996 5.1:-1247450 MS.gene49470:CDS
TTGTCGATGTTGAAAATGTT+GGG 0.503194 5.1:-1247350 MS.gene49470:CDS
AAGTGGCCAAATTCTGCTCA+TGG 0.511724 5.1:-1247641 MS.gene49470:CDS
AGGAAGTATTTGGTCATGAA+AGG 0.520639 5.1:-1247279 MS.gene49470:CDS
ATGATCTCTTCTTTGGCACA+TGG 0.535452 5.1:+1247741 None:intergenic
GGAGAAAGCTGGTTTCCAAA+AGG 0.547990 5.1:-1247313 MS.gene49470:CDS
CCTTACACCAGCAAAGAAGA+TGG 0.560893 5.1:-1247615 MS.gene49470:CDS
GAAAGCTGGTTTCCAAAAGG+AGG 0.562242 5.1:-1247310 MS.gene49470:CDS
TGTTGGGTCACAAAGAGTGT+TGG 0.566749 5.1:-1247334 MS.gene49470:CDS
AGTGGCCAAATTCTGCTCAT+GGG 0.587986 5.1:-1247640 MS.gene49470:CDS
AATCTAAGCTCTATATATTG+GGG 0.593409 5.1:-1247456 MS.gene49470:CDS
GCCACACCATTACATCATCA+AGG 0.594693 5.1:+1247676 None:intergenic
GGTCAGAAAGATTAAAGGGT+CGG 0.596865 5.1:+1247697 None:intergenic
TCACACCTGAAGATAAAAGC+AGG 0.598275 5.1:-1247503 MS.gene49470:CDS
GTGGCATACTGATGATAAAG+TGG 0.623600 5.1:-1247658 MS.gene49470:CDS
AAAGCTGGTTTCCAAAAGGA+GGG 0.657724 5.1:-1247309 MS.gene49470:CDS
ACCTTGATGATGTAATGGTG+TGG 0.686805 5.1:-1247677 MS.gene49470:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTAAGCTCTATATAT+TGG - chr5.1:1247534-1247553 MS.gene49470:CDS 20.0%
!! TAATCTAAGCTCTATATATT+GGG - chr5.1:1247535-1247554 MS.gene49470:CDS 20.0%
! AATCTAAGCTCTATATATTG+GGG - chr5.1:1247536-1247555 MS.gene49470:CDS 25.0%
! TGCTGTGAAACAAATTATTA+AGG - chr5.1:1247577-1247596 MS.gene49470:CDS 25.0%
!! ATTCCATGAATTTTCATACT+TGG - chr5.1:1247604-1247623 MS.gene49470:CDS 25.0%
ATCAAGGTCAGAAAGATTAA+AGG + chr5.1:1247303-1247322 None:intergenic 30.0%
CAAATCAATGATCTCTTCTT+TGG + chr5.1:1247261-1247280 None:intergenic 30.0%
TCAAGGTCAGAAAGATTAAA+GGG + chr5.1:1247302-1247321 None:intergenic 30.0%
TCTCCAAGTATGAAAATTCA+TGG + chr5.1:1247610-1247629 None:intergenic 30.0%
TTGTCGATGTTGAAAATGTT+GGG - chr5.1:1247642-1247661 MS.gene49470:CDS 30.0%
! ATGAATTTTCATACTTGGAG+AGG - chr5.1:1247609-1247628 MS.gene49470:CDS 30.0%
CTTGTCGATGTTGAAAATGT+TGG - chr5.1:1247641-1247660 MS.gene49470:CDS 35.0%
!! AGGAAGTATTTGGTCATGAA+AGG - chr5.1:1247713-1247732 MS.gene49470:CDS 35.0%
!! TGTTTCCTGCTTTTATCTTC+AGG + chr5.1:1247497-1247516 None:intergenic 35.0%
!! TTCTGACCTTGATGATGTAA+TGG - chr5.1:1247310-1247329 MS.gene49470:CDS 35.0%
AGCTCTATATATTGGGGCAA+AGG - chr5.1:1247542-1247561 MS.gene49470:CDS 40.0%
AGGAAACAATCTGCAGAACT+TGG - chr5.1:1247509-1247528 MS.gene49470:CDS 40.0%
ATGATCTCTTCTTTGGCACA+TGG + chr5.1:1247254-1247273 None:intergenic 40.0%
GCTCTATATATTGGGGCAAA+GGG - chr5.1:1247543-1247562 MS.gene49470:CDS 40.0%
GGTCAGAAAGATTAAAGGGT+CGG + chr5.1:1247298-1247317 None:intergenic 40.0%
GTGGCATACTGATGATAAAG+TGG - chr5.1:1247334-1247353 MS.gene49470:CDS 40.0%
TCACACCTGAAGATAAAAGC+AGG - chr5.1:1247489-1247508 MS.gene49470:CDS 40.0%
! AAAGCTGGTTTCCAAAAGGA+GGG - chr5.1:1247683-1247702 MS.gene49470:CDS 40.0%
! TGCATTGATGATCGTGCTAT+TGG - chr5.1:1247452-1247471 MS.gene49470:CDS 40.0%
!! ACCTTGATGATGTAATGGTG+TGG - chr5.1:1247315-1247334 MS.gene49470:CDS 40.0%
!! GGGAGTTCTTAGGAAGTATT+TGG - chr5.1:1247703-1247722 MS.gene49470:CDS 40.0%
AAGTGGCCAAATTCTGCTCA+TGG - chr5.1:1247351-1247370 MS.gene49470:CDS 45.0%
AGGTTCCCATGAGCAGAATT+TGG + chr5.1:1247360-1247379 None:intergenic 45.0%
AGTGGCCAAATTCTGCTCAT+GGG - chr5.1:1247352-1247371 MS.gene49470:CDS 45.0%
CCATCTTCTTTGCTGGTGTA+AGG + chr5.1:1247380-1247399 None:intergenic 45.0%
CCTTACACCAGCAAAGAAGA+TGG - chr5.1:1247377-1247396 MS.gene49470:CDS 45.0%
CTCTTCTTTGGCACATGGTT+TGG + chr5.1:1247249-1247268 None:intergenic 45.0%
GCCACACCATTACATCATCA+AGG + chr5.1:1247319-1247338 None:intergenic 45.0%
GTTGATGCCATCTTCTTTGC+TGG + chr5.1:1247387-1247406 None:intergenic 45.0%
TAAAGGGTCGGAGTGTGATT+TGG + chr5.1:1247286-1247305 None:intergenic 45.0%
TCCAAAAGGAGGGAGTTCTT+AGG - chr5.1:1247693-1247712 MS.gene49470:CDS 45.0%
! GAAAGCTGGTTTCCAAAAGG+AGG - chr5.1:1247682-1247701 MS.gene49470:CDS 45.0%
! GGAGAAAGCTGGTTTCCAAA+AGG - chr5.1:1247679-1247698 MS.gene49470:CDS 45.0%
! TCCTAAGAACTCCCTCCTTT+TGG + chr5.1:1247697-1247716 None:intergenic 45.0%
! TGTTGGGTCACAAAGAGTGT+TGG - chr5.1:1247658-1247677 MS.gene49470:CDS 45.0%
!! CAAAGAGTGTTGGAGAAAGC+TGG - chr5.1:1247668-1247687 MS.gene49470:CDS 45.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 1247224 1247790 1247224 ID=MS.gene49470
chr5.1 mRNA 1247224 1247790 1247224 ID=MS.gene49470.t1;Parent=MS.gene49470
chr5.1 exon 1247224 1247790 1247224 ID=MS.gene49470.t1.exon1;Parent=MS.gene49470.t1
chr5.1 CDS 1247224 1247790 1247224 ID=cds.MS.gene49470.t1;Parent=MS.gene49470.t1
Gene Sequence

>MS.gene49470

ATGGAAGAAACTTTTATTTCTTCCAAACCATGTGCCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGACCCTTTAATCTTTCTGACCTTGATGATGTAATGGTGTGGCATACTGATGATAAAGTGGCCAAATTCTGCTCATGGGAACCTTACACCAGCAAAGAAGATGGCATCAACTTCATTGAAAATATAGAAAGCAAGTTTCTATGTTGCAAAGCAATATGCATTGATGATCGTGCTATTGGTTGTATTCTTTTGTTCACACCTGAAGATAAAAGCAGGAAACAATCTGCAGAACTTGGCTATAATCTAAGCTCTATATATTGGGGCAAAGGGATTGTCACGTGTGCTGTGAAACAAATTATTAAGGTTGCATTCCATGAATTTTCATACTTGGAGAGGCTTGAAGCACTTGTCGATGTTGAAAATGTTGGGTCACAAAGAGTGTTGGAGAAAGCTGGTTTCCAAAAGGAGGGAGTTCTTAGGAAGTATTTGGTCATGAAAGGAAAAAGCAGAGATATGATCATGTTTAGTGTTCTTTCTACTGATCTCCAACTTTAA
Protein sequence

>MS.gene49470.t1

MEETFISSKPCAKEEIIDLNQITLRPFNLSDLDDVMVWHTDDKVAKFCSWEPYTSKEDGINFIENIESKFLCCKAICIDDRAIGCILLFTPEDKSRKQSAELGYNLSSIYWGKGIVTCAVKQIIKVAFHEFSYLERLEALVDVENVGSQRVLEKAGFQKEGVLRKYLVMKGKSRDMIMFSVLSTDLQL