AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31249

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31249.t1 MTR_2g095130 83.710 221 32 2 1 218 1 220 6.59e-128 360
MS.gene31249.t1 MTR_2g095080 76.126 222 49 1 1 218 1 222 8.35e-115 327
MS.gene31249.t1 MTR_2g095060 75.909 220 50 2 1 218 1 219 7.78e-111 317
MS.gene31249.t1 MTR_2g095170 93.421 152 9 1 1 152 1 151 1.07e-98 284
MS.gene31249.t1 MTR_4g036290 56.552 145 58 4 75 216 44 186 3.15e-47 154
MS.gene31249.t1 MTR_7g077050 57.047 149 58 5 71 216 39 184 3.46e-47 154
MS.gene31249.t1 MTR_7g077110 57.047 149 58 5 71 216 41 186 4.23e-47 154
MS.gene31249.t1 MTR_8g031170 59.848 132 50 3 86 216 61 190 1.19e-45 150
MS.gene31249.t1 MTR_7g077000 58.915 129 50 3 89 216 2 128 2.52e-45 147
MS.gene31249.t1 MTR_7g012350 55.705 149 60 5 71 216 41 186 8.27e-45 148
MS.gene31249.t1 MTR_7g076920 55.705 149 60 5 71 216 41 186 8.82e-45 148
MS.gene31249.t1 MTR_7g076990 55.705 149 60 5 71 216 41 186 1.18e-44 148
MS.gene31249.t1 MTR_4g036300 55.705 149 60 5 71 216 41 186 1.18e-44 148
MS.gene31249.t1 MTR_7g076770 60.465 129 48 3 89 216 61 187 1.22e-44 148
MS.gene31249.t1 MTR_7g076960 54.730 148 62 5 71 216 39 183 8.84e-44 145
MS.gene31249.t1 MTR_7g077090 52.258 155 65 5 65 216 39 187 1.45e-43 145
MS.gene31249.t1 MTR_7g077010 51.613 155 66 5 65 216 39 187 1.86e-43 145
MS.gene31249.t1 MTR_7g012340 53.691 149 63 5 71 216 41 186 2.85e-43 144
MS.gene31249.t1 MTR_4g036410 56.818 132 54 3 86 216 39 168 1.04e-42 142
MS.gene31249.t1 MTR_7g076970 56.818 132 54 3 86 216 58 187 1.33e-42 142
MS.gene31249.t1 MTR_8g031120 50.435 115 45 3 103 216 33 136 1.04e-28 105
MS.gene31249.t1 MTR_8g031150 50.435 115 45 3 103 216 41 144 9.21e-28 103
MS.gene31249.t1 MTR_8g031160 46.154 117 48 2 99 215 19 120 2.34e-24 94.0
MS.gene31249.t1 MTR_7g077040 42.735 117 39 3 86 202 36 124 4.21e-20 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 73 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTGTTTATGATGTTAAAA+AGG 0.240792 2.4:-7389065 None:intergenic
TGTCGTAACAATATTGTTGA+TGG 0.347026 2.4:+7389582 MS.gene31249:CDS
TGATTCCCCGTCGCACTCTA+AGG 0.365654 2.4:-7389265 None:intergenic
CGTTGTACCATCCGGTGGAC+AGG 0.400359 2.4:-7389434 None:intergenic
CATATGTTGGTCCCAACGTC+GGG 0.409197 2.4:-7389189 None:intergenic
CCAGTTACATGGTCTATGTC+TGG 0.410397 2.4:+7389657 MS.gene31249:CDS
GGCGACAAGTGTAAATCTTC+CGG 0.412697 2.4:+7389240 MS.gene31249:CDS
TTAGAATCACCGCGAGGAAC+GGG 0.419468 2.4:+7389481 MS.gene31249:CDS
GTAGCTGTGTGGAATGCGTT+AGG 0.427890 2.4:+7389609 MS.gene31249:CDS
TTGTCGCCACTTGGTGGTGG+AGG 0.433015 2.4:-7389225 None:intergenic
CCACTTGGTGGTGGAGGGGA+CGG 0.436308 2.4:-7389219 None:intergenic
CCAGACATAGACCATGTAAC+TGG 0.445756 2.4:-7389657 None:intergenic
GCAACGATGACCCCGACGTT+GGG 0.448979 2.4:+7389178 MS.gene31249:CDS
TGGTGGTGGAGGGGACGGTT+TGG 0.450078 2.4:-7389214 None:intergenic
GTGGAGAGCACTTGAATTGA+GGG 0.454649 2.4:-7389290 None:intergenic
CCGGCACCTTAGAGTGCGAC+GGG 0.479301 2.4:+7389259 MS.gene31249:CDS
CTACTCTTTCTGAGATGCTA+TGG 0.481149 2.4:-7389407 None:intergenic
AGAGTAGTGGCCCTGTCCAC+CGG 0.488313 2.4:+7389423 MS.gene31249:CDS
CACTTGTCGCCACTTGGTGG+TGG 0.492715 2.4:-7389228 None:intergenic
GATTTCAGCGAGGGTGGCGA+TGG 0.507805 2.4:+7389354 MS.gene31249:CDS
GGTGGAGAGCACTTGAATTG+AGG 0.508261 2.4:-7389291 None:intergenic
TGTCGCCACTTGGTGGTGGA+GGG 0.508955 2.4:-7389224 None:intergenic
GGACGGTTTGGTGCATATGT+TGG 0.523330 2.4:-7389202 None:intergenic
GTCGCCACTTGGTGGTGGAG+GGG 0.524109 2.4:-7389223 None:intergenic
GACCAGTGTGATTCAGTGAA+TGG 0.526043 2.4:+7389528 MS.gene31249:CDS
GATTTACACTTGTCGCCACT+TGG 0.526065 2.4:-7389234 None:intergenic
TTCAGCGAGGGTGGCGATGG+AGG 0.531365 2.4:+7389357 MS.gene31249:CDS
AATTGCTCGTCGCACTGAGA+TGG 0.531537 2.4:-7389384 None:intergenic
ATTAGAATCACCGCGAGGAA+CGG 0.535672 2.4:+7389480 MS.gene31249:CDS
TTACACTTGTCGCCACTTGG+TGG 0.536650 2.4:-7389231 None:intergenic
TGAACCTCCGTTGTACCATC+CGG 0.538055 2.4:-7389442 None:intergenic
GGTCAACTCATTTGCATCAA+CGG 0.540764 2.4:+7389150 MS.gene31249:CDS
CCCGTCGCACTCTAAGGTGC+CGG 0.540944 2.4:-7389259 None:intergenic
GCTTGTGTGGAAGATGAAAC+TGG 0.545310 2.4:-7389312 None:intergenic
TAGCTGTGTGGAATGCGTTA+GGG 0.549174 2.4:+7389610 MS.gene31249:CDS
GCATATGTTGGTCCCAACGT+CGG 0.558869 2.4:-7389190 None:intergenic
GTTGTACCATCCGGTGGACA+GGG 0.562020 2.4:-7389433 None:intergenic
TGCAACGATGACCCCGACGT+TGG 0.562513 2.4:+7389177 MS.gene31249:CDS
TTGAATGATTTCAGCGAGGG+TGG 0.573268 2.4:+7389348 MS.gene31249:CDS
ATGGTGTGGTGCCAGTTACA+TGG 0.574649 2.4:+7389646 MS.gene31249:CDS
GACGAGTGTGATGGCGAAAG+TGG 0.577541 2.4:+7389503 MS.gene31249:CDS
AATGCTATTTCCTCATGCAA+TGG 0.584516 2.4:+7389099 MS.gene31249:CDS
AAAACTCTCAACGACTGCGC+TGG 0.587040 2.4:+7389129 MS.gene31249:CDS
GAGGAACGGGACGAGTGTGA+TGG 0.590062 2.4:+7389494 MS.gene31249:CDS
TTTACAAGGTCCATTGCATG+AGG 0.591735 2.4:-7389109 None:intergenic
ACGTTGAATGATTTCAGCGA+GGG 0.598557 2.4:+7389345 MS.gene31249:CDS
CGTGAGTAATGATGCTTGTG+TGG 0.623701 2.4:-7389325 None:intergenic
TCCGGCACCTTAGAGTGCGA+CGG 0.625179 2.4:+7389258 MS.gene31249:CDS
CTGTCCACCGGATGGTACAA+CGG 0.625342 2.4:+7389435 MS.gene31249:CDS
TTAGGGTTGGATACTGATGA+TGG 0.634958 2.4:+7389627 MS.gene31249:CDS
GAAATAGCATTTGTGAGGAA+CGG 0.636932 2.4:-7389087 None:intergenic
GTTGGATACTGATGATGGTG+TGG 0.638034 2.4:+7389632 MS.gene31249:CDS
TACAACGGAGGTTCAAGATG+TGG 0.638491 2.4:+7389450 MS.gene31249:CDS
TAGTGGCCCTGTCCACCGGA+TGG 0.641578 2.4:+7389427 MS.gene31249:CDS
ATGAGGAAATAGCATTTGTG+AGG 0.643440 2.4:-7389092 None:intergenic
GGATGTGATGAGGAACATGC+AGG 0.645551 2.4:+7389549 MS.gene31249:CDS
CCGTCCCCTCCACCACCAAG+TGG 0.646637 2.4:+7389219 MS.gene31249:CDS
GAGTGTGATGGCGAAAGTGG+TGG 0.650984 2.4:+7389506 MS.gene31249:CDS
CACACTCGTCCCGTTCCTCG+CGG 0.654913 2.4:-7389490 None:intergenic
ATCCATTCACTGAATCACAC+TGG 0.661311 2.4:-7389530 None:intergenic
ACCTCCGTTGTACCATCCGG+TGG 0.666402 2.4:-7389439 None:intergenic
TAGCATCTCAGAAAGAGTAG+TGG 0.673721 2.4:+7389410 MS.gene31249:CDS
CACGTTGAATGATTTCAGCG+AGG 0.674472 2.4:+7389344 MS.gene31249:CDS
TTCAGTGAATGGATGTGATG+AGG 0.675998 2.4:+7389539 MS.gene31249:CDS
TGTGTGGAATGCGTTAGGGT+TGG 0.682131 2.4:+7389614 MS.gene31249:CDS
ATATGTTGGTCCCAACGTCG+GGG 0.692316 2.4:-7389188 None:intergenic
ACAATATTGTTACGACAAGG+TGG 0.698524 2.4:-7389576 None:intergenic
TCAACAATATTGTTACGACA+AGG 0.725534 2.4:-7389579 None:intergenic
TTGATGGATCTGTAGCTGTG+TGG 0.729799 2.4:+7389598 MS.gene31249:CDS
CGGCACCTTAGAGTGCGACG+GGG 0.757349 2.4:+7389260 MS.gene31249:CDS
TCCACCGGATGGTACAACGG+AGG 0.763995 2.4:+7389438 MS.gene31249:CDS
TGTGTGGAAGATGAAACTGG+TGG 0.770461 2.4:-7389309 None:intergenic
AAATGATTAGAATCACCGCG+AGG 0.806861 2.4:+7389475 MS.gene31249:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGATGTTAAAAAGGAAAA+TGG - chr2.4:7389061-7389080 None:intergenic 20.0%
! GACTGTTTATGATGTTAAAA+AGG - chr2.4:7389068-7389087 None:intergenic 25.0%
TCAACAATATTGTTACGACA+AGG - chr2.4:7389582-7389601 None:intergenic 30.0%
TGTCGTAACAATATTGTTGA+TGG + chr2.4:7389582-7389601 MS.gene31249:CDS 30.0%
ACAATATTGTTACGACAAGG+TGG - chr2.4:7389579-7389598 None:intergenic 35.0%
ATGAGGAAATAGCATTTGTG+AGG - chr2.4:7389095-7389114 None:intergenic 35.0%
GAAATAGCATTTGTGAGGAA+CGG - chr2.4:7389090-7389109 None:intergenic 35.0%
!! AATGCTATTTCCTCATGCAA+TGG + chr2.4:7389099-7389118 MS.gene31249:CDS 35.0%
AAATGATTAGAATCACCGCG+AGG + chr2.4:7389475-7389494 MS.gene31249:CDS 40.0%
ACGTTGAATGATTTCAGCGA+GGG + chr2.4:7389345-7389364 MS.gene31249:CDS 40.0%
ATCCATTCACTGAATCACAC+TGG - chr2.4:7389533-7389552 None:intergenic 40.0%
GGTCAACTCATTTGCATCAA+CGG + chr2.4:7389150-7389169 MS.gene31249:CDS 40.0%
TAGCATCTCAGAAAGAGTAG+TGG + chr2.4:7389410-7389429 MS.gene31249:CDS 40.0%
TTAGGGTTGGATACTGATGA+TGG + chr2.4:7389627-7389646 MS.gene31249:CDS 40.0%
TTCAGTGAATGGATGTGATG+AGG + chr2.4:7389539-7389558 MS.gene31249:CDS 40.0%
TTTACAAGGTCCATTGCATG+AGG - chr2.4:7389112-7389131 None:intergenic 40.0%
! CAGTCGTTGAGAGTTTTACA+AGG - chr2.4:7389126-7389145 None:intergenic 40.0%
!! CTACTCTTTCTGAGATGCTA+TGG - chr2.4:7389410-7389429 None:intergenic 40.0%
ATTAGAATCACCGCGAGGAA+CGG + chr2.4:7389480-7389499 MS.gene31249:CDS 45.0%
CACGTTGAATGATTTCAGCG+AGG + chr2.4:7389344-7389363 MS.gene31249:CDS 45.0%
CCAGACATAGACCATGTAAC+TGG - chr2.4:7389660-7389679 None:intergenic 45.0%
CCAGTTACATGGTCTATGTC+TGG + chr2.4:7389657-7389676 MS.gene31249:CDS 45.0%
CGTGAGTAATGATGCTTGTG+TGG - chr2.4:7389328-7389347 None:intergenic 45.0%
GACCAGTGTGATTCAGTGAA+TGG + chr2.4:7389528-7389547 MS.gene31249:CDS 45.0%
GATTTACACTTGTCGCCACT+TGG - chr2.4:7389237-7389256 None:intergenic 45.0%
GCTTGTGTGGAAGATGAAAC+TGG - chr2.4:7389315-7389334 None:intergenic 45.0%
GGCGACAAGTGTAAATCTTC+CGG + chr2.4:7389240-7389259 MS.gene31249:CDS 45.0%
TACAACGGAGGTTCAAGATG+TGG + chr2.4:7389450-7389469 MS.gene31249:CDS 45.0%
TAGCTGTGTGGAATGCGTTA+GGG + chr2.4:7389610-7389629 MS.gene31249:CDS 45.0%
TGTGTGGAAGATGAAACTGG+TGG - chr2.4:7389312-7389331 None:intergenic 45.0%
TTGAATGATTTCAGCGAGGG+TGG + chr2.4:7389348-7389367 MS.gene31249:CDS 45.0%
! TTGATGGATCTGTAGCTGTG+TGG + chr2.4:7389598-7389617 MS.gene31249:CDS 45.0%
!! GTGGAGAGCACTTGAATTGA+GGG - chr2.4:7389293-7389312 None:intergenic 45.0%
!! GTTGGATACTGATGATGGTG+TGG + chr2.4:7389632-7389651 MS.gene31249:CDS 45.0%
AAAACTCTCAACGACTGCGC+TGG + chr2.4:7389129-7389148 MS.gene31249:CDS 50.0%
AATTGCTCGTCGCACTGAGA+TGG - chr2.4:7389387-7389406 None:intergenic 50.0%
ATATGTTGGTCCCAACGTCG+GGG - chr2.4:7389191-7389210 None:intergenic 50.0%
CATATGTTGGTCCCAACGTC+GGG - chr2.4:7389192-7389211 None:intergenic 50.0%
GCATATGTTGGTCCCAACGT+CGG - chr2.4:7389193-7389212 None:intergenic 50.0%
GGATGTGATGAGGAACATGC+AGG + chr2.4:7389549-7389568 MS.gene31249:CDS 50.0%
GTAGCTGTGTGGAATGCGTT+AGG + chr2.4:7389609-7389628 MS.gene31249:CDS 50.0%
TGAACCTCCGTTGTACCATC+CGG - chr2.4:7389445-7389464 None:intergenic 50.0%
TGTGTGGAATGCGTTAGGGT+TGG + chr2.4:7389614-7389633 MS.gene31249:CDS 50.0%
TTACACTTGTCGCCACTTGG+TGG - chr2.4:7389234-7389253 None:intergenic 50.0%
TTAGAATCACCGCGAGGAAC+GGG + chr2.4:7389481-7389500 MS.gene31249:CDS 50.0%
! ATGGTGTGGTGCCAGTTACA+TGG + chr2.4:7389646-7389665 MS.gene31249:CDS 50.0%
!! GGACGGTTTGGTGCATATGT+TGG - chr2.4:7389205-7389224 None:intergenic 50.0%
!! GGTGGAGAGCACTTGAATTG+AGG - chr2.4:7389294-7389313 None:intergenic 50.0%
CTGTCCACCGGATGGTACAA+CGG + chr2.4:7389435-7389454 MS.gene31249:CDS 55.0%
GTTGTACCATCCGGTGGACA+GGG - chr2.4:7389436-7389455 None:intergenic 55.0%
TGATTCCCCGTCGCACTCTA+AGG - chr2.4:7389268-7389287 None:intergenic 55.0%
! GACGAGTGTGATGGCGAAAG+TGG + chr2.4:7389503-7389522 MS.gene31249:CDS 55.0%
! GAGTGTGATGGCGAAAGTGG+TGG + chr2.4:7389506-7389525 MS.gene31249:CDS 55.0%
ACCTCCGTTGTACCATCCGG+TGG - chr2.4:7389442-7389461 None:intergenic 60.0%
AGAGTAGTGGCCCTGTCCAC+CGG + chr2.4:7389423-7389442 MS.gene31249:CDS 60.0%
CGTTGTACCATCCGGTGGAC+AGG - chr2.4:7389437-7389456 None:intergenic 60.0%
GAGGAACGGGACGAGTGTGA+TGG + chr2.4:7389494-7389513 MS.gene31249:CDS 60.0%
GATTTCAGCGAGGGTGGCGA+TGG + chr2.4:7389354-7389373 MS.gene31249:CDS 60.0%
GCAACGATGACCCCGACGTT+GGG + chr2.4:7389178-7389197 MS.gene31249:CDS 60.0%
TCCACCGGATGGTACAACGG+AGG + chr2.4:7389438-7389457 MS.gene31249:CDS 60.0%
TCCGGCACCTTAGAGTGCGA+CGG + chr2.4:7389258-7389277 MS.gene31249:CDS 60.0%
TGCAACGATGACCCCGACGT+TGG + chr2.4:7389177-7389196 MS.gene31249:CDS 60.0%
! CACTTGTCGCCACTTGGTGG+TGG - chr2.4:7389231-7389250 None:intergenic 60.0%
!! TGTCGCCACTTGGTGGTGGA+GGG - chr2.4:7389227-7389246 None:intergenic 60.0%
!! TTGTCGCCACTTGGTGGTGG+AGG - chr2.4:7389228-7389247 None:intergenic 60.0%
CACACTCGTCCCGTTCCTCG+CGG - chr2.4:7389493-7389512 None:intergenic 65.0%
CCGGCACCTTAGAGTGCGAC+GGG + chr2.4:7389259-7389278 MS.gene31249:CDS 65.0%
CGGCACCTTAGAGTGCGACG+GGG + chr2.4:7389260-7389279 MS.gene31249:CDS 65.0%
TAGTGGCCCTGTCCACCGGA+TGG + chr2.4:7389427-7389446 MS.gene31249:CDS 65.0%
TTCAGCGAGGGTGGCGATGG+AGG + chr2.4:7389357-7389376 MS.gene31249:CDS 65.0%
!! CCACTTGGTGGTGGAGGGGA+CGG - chr2.4:7389222-7389241 None:intergenic 65.0%
!! CCCGTCGCACTCTAAGGTGC+CGG - chr2.4:7389262-7389281 None:intergenic 65.0%
!! GTCGCCACTTGGTGGTGGAG+GGG - chr2.4:7389226-7389245 None:intergenic 65.0%
!! TGGTGGTGGAGGGGACGGTT+TGG - chr2.4:7389217-7389236 None:intergenic 65.0%
CCGTCCCCTCCACCACCAAG+TGG + chr2.4:7389219-7389238 MS.gene31249:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 7389024 7389713 7389024 ID=MS.gene31249
chr2.4 mRNA 7389024 7389713 7389024 ID=MS.gene31249.t1;Parent=MS.gene31249
chr2.4 exon 7389024 7389713 7389024 ID=MS.gene31249.t1.exon1;Parent=MS.gene31249.t1
chr2.4 CDS 7389024 7389713 7389024 ID=cds.MS.gene31249.t1;Parent=MS.gene31249.t1
Gene Sequence

>MS.gene31249

ATGGCTCAGATATCAAATCTTGTTTTTTTAGCTTCCATTTTCCTTTTTAACATCATAAACAGTCCGTTCCTCACAAATGCTATTTCCTCATGCAATGGACCTTGTAAAACTCTCAACGACTGCGCTGGTCAACTCATTTGCATCAACGGAAAATGCAACGATGACCCCGACGTTGGGACCAACATATGCACCAAACCGTCCCCTCCACCACCAAGTGGCGACAAGTGTAAATCTTCCGGCACCTTAGAGTGCGACGGGGAATCATTCCCTCAATTCAAGTGCTCTCCACCAGTTTCATCTTCCACACAAGCATCATTACTCACGTTGAATGATTTCAGCGAGGGTGGCGATGGAGGAGCTCCATCTCAGTGCGACGAGCAATTCCATAGCATCTCAGAAAGAGTAGTGGCCCTGTCCACCGGATGGTACAACGGAGGTTCAAGATGTGGAAAAATGATTAGAATCACCGCGAGGAACGGGACGAGTGTGATGGCGAAAGTGGTGGACCAGTGTGATTCAGTGAATGGATGTGATGAGGAACATGCAGGTCAGCCACCTTGTCGTAACAATATTGTTGATGGATCTGTAGCTGTGTGGAATGCGTTAGGGTTGGATACTGATGATGGTGTGGTGCCAGTTACATGGTCTATGTCTGGATCTAATGAAGCTTATGAAACATTTAATGCCTAA
Protein sequence

>MS.gene31249.t1

MAQISNLVFLASIFLFNIINSPFLTNAISSCNGPCKTLNDCAGQLICINGKCNDDPDVGTNICTKPSPPPPSGDKCKSSGTLECDGESFPQFKCSPPVSSSTQASLLTLNDFSEGGDGGAPSQCDEQFHSISERVVALSTGWYNGGSRCGKMIRITARNGTSVMAKVVDQCDSVNGCDEEHAGQPPCRNNIVDGSVAVWNALGLDTDDGVVPVTWSMSGSNEAYETFNA