AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002958

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002958.t1 MTR_2g023340 84.825 257 26 3 1 257 1 244 9.65e-148 412
MS.gene002958.t1 MTR_7g113680 49.457 184 86 6 69 251 133 310 9.68e-52 171
MS.gene002958.t1 MTR_1g082660 51.205 166 66 6 69 230 82 236 6.11e-49 162
MS.gene002958.t1 MTR_3g099180 51.678 149 56 2 70 218 37 169 6.54e-44 148
MS.gene002958.t1 MTR_3g099180 51.678 149 56 2 70 218 37 169 7.33e-44 148
MS.gene002958.t1 MTR_2g081600 59.740 77 30 1 89 164 23 99 9.06e-24 93.2
MS.gene002958.t1 MTR_2g081630 59.740 77 30 1 89 164 23 99 1.04e-23 92.8
MS.gene002958.t1 MTR_3g012030 43.590 78 44 0 89 166 9 86 1.12e-12 66.6
MS.gene002958.t1 MTR_8g041420 41.026 78 46 0 89 166 9 86 4.16e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002958.t1 AT1G54830 53.125 160 69 3 69 224 51 208 2.95e-50 164
MS.gene002958.t1 AT1G54830 53.125 160 69 3 69 224 51 208 2.95e-50 164
MS.gene002958.t1 AT1G54830 53.125 160 69 3 69 224 51 208 2.95e-50 164
MS.gene002958.t1 AT1G08970 52.353 170 64 6 70 237 62 216 1.29e-48 160
MS.gene002958.t1 AT1G08970 52.353 170 64 6 70 237 62 216 1.29e-48 160
MS.gene002958.t1 AT1G08970 52.353 170 64 6 70 237 62 216 1.29e-48 160
MS.gene002958.t1 AT1G08970 52.353 170 64 6 70 237 62 216 1.29e-48 160
MS.gene002958.t1 AT1G56170 57.812 128 49 3 67 192 55 179 7.05e-48 157
MS.gene002958.t1 AT1G56170 57.812 128 49 3 67 192 55 179 7.05e-48 157
MS.gene002958.t1 AT3G48590 52.349 149 62 2 70 218 47 186 5.95e-47 156
MS.gene002958.t1 AT5G63470 57.031 128 52 1 70 194 60 187 1.54e-44 150
MS.gene002958.t1 AT5G63470 57.031 128 52 1 70 194 60 187 1.54e-44 150
MS.gene002958.t1 AT5G50480 46.875 160 68 5 66 223 35 179 3.59e-38 132
MS.gene002958.t1 AT5G27910 41.420 169 78 6 65 231 16 165 1.76e-30 112
MS.gene002958.t1 AT5G50490 46.154 104 53 1 65 168 16 116 5.76e-26 100
MS.gene002958.t1 AT5G50470 39.098 133 72 2 66 192 44 173 3.20e-24 97.1
MS.gene002958.t1 AT5G38140 39.806 103 60 1 63 165 44 144 5.36e-22 90.5

Find 52 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCTTAATCTTCTGAATT+TGG 0.149271 2.4:-63931398 None:intergenic
AATGGAGCGTGACATATTTA+TGG 0.230451 2.4:+63931148 MS.gene002958:CDS
ATTGGAACACTTTCACTTCT+TGG 0.249877 2.4:-63931176 None:intergenic
GGCGAGGCACTGATACTATT+TGG 0.252757 2.4:-63930710 None:intergenic
TGGTCCTCCAAGAATGCTTA+TGG 0.263320 2.4:+63931268 MS.gene002958:CDS
GGCATGTGAAATGTTTATTA+TGG 0.268895 2.4:+63930992 MS.gene002958:CDS
TGTCTTCCCATAAGCATTCT+TGG 0.296015 2.4:-63931275 None:intergenic
GTTGTCGGTGAGAGATTTCT+TGG 0.314048 2.4:-63930791 None:intergenic
GAATTTGGCAAATCAGTAGA+AGG 0.372595 2.4:-63931383 None:intergenic
TGGAGCTAGCAACAAGGTCT+TGG 0.374473 2.4:+63931012 MS.gene002958:CDS
ATCTTCTTAATCCTTGCTAA+TGG 0.378288 2.4:-63930909 None:intergenic
GTGCCACCTCAGTATGTTGC+AGG 0.380885 2.4:+63931236 MS.gene002958:CDS
ACAGACATAGGCAGATAATA+AGG 0.391390 2.4:-63931209 None:intergenic
GGAAACATTTGATTTGCAAA+AGG 0.397276 2.4:-63931338 None:intergenic
TAATAAGGAACATTTCCTAT+TGG 0.408920 2.4:-63931194 None:intergenic
CCCGTTGTAAGGAGGTTGAT+TGG 0.412220 2.4:-63931303 None:intergenic
GAAACATTTGATTTGCAAAA+GGG 0.424540 2.4:-63931337 None:intergenic
ACTGTTGATTTCAAAAGTAA+TGG 0.437192 2.4:+63930882 MS.gene002958:CDS
ATGGAGCGTGACATATTTAT+GGG 0.438860 2.4:+63931149 MS.gene002958:CDS
TCTACTCAGGTAGGATGAAA+AGG 0.455810 2.4:-63930760 None:intergenic
AGAAGTGAAAGTGTTCCAAT+AGG 0.456998 2.4:+63931179 MS.gene002958:CDS
GGTCCTCCAAGAATGCTTAT+GGG 0.469493 2.4:+63931269 MS.gene002958:CDS
CCGTTGTAAGGAGGTTGATT+GGG 0.477387 2.4:-63931302 None:intergenic
CCAATCAACCTCCTTACAAC+GGG 0.477395 2.4:+63931303 MS.gene002958:CDS
GGAGCTAGCAACAAGGTCTT+GGG 0.481151 2.4:+63931013 MS.gene002958:CDS
CATGCCTTAGCAAACAGAAT+AGG 0.486382 2.4:-63930975 None:intergenic
CCTAGTTGATATTGTCCCTA+GGG 0.487741 2.4:+63931118 MS.gene002958:CDS
CCCTAGGGACAATATCAACT+AGG 0.511793 2.4:-63931118 None:intergenic
TGTGATGGATGCCCGTTGTA+AGG 0.514096 2.4:-63931314 None:intergenic
TATGTTGCAGGTCCATCATA+TGG 0.515120 2.4:+63931248 MS.gene002958:CDS
AAGATCATGAAAGCAGAAGA+AGG 0.528329 2.4:+63930927 MS.gene002958:CDS
GGCACCTATTCTGTTTGCTA+AGG 0.530640 2.4:+63930971 MS.gene002958:CDS
CTTGGAGTTGAACTCTACTC+AGG 0.542580 2.4:-63930773 None:intergenic
TGATTTGCAAAAGGGTGTGA+TGG 0.553637 2.4:-63931329 None:intergenic
GCACTTGCAGTGTGAAACAA+AGG 0.556863 2.4:-63930732 None:intergenic
TCCTAGTTGATATTGTCCCT+AGG 0.558927 2.4:+63931117 MS.gene002958:CDS
CTTCCCATAAGCATTCTTGG+AGG 0.580142 2.4:-63931272 None:intergenic
CACTTGCAGTGTGAAACAAA+GGG 0.597437 2.4:-63930731 None:intergenic
GTAATGGCTTGCCATTAGCA+AGG 0.597965 2.4:+63930898 MS.gene002958:CDS
CCCAATCAACCTCCTTACAA+CGG 0.599569 2.4:+63931302 MS.gene002958:CDS
ATTCTTGGAGGACCATATGA+TGG 0.609961 2.4:-63931260 None:intergenic
GGTGGCACATGAACAGACAT+AGG 0.629233 2.4:-63931221 None:intergenic
GAGTTGAACTCTACTCAGGT+AGG 0.629918 2.4:-63930769 None:intergenic
AAGGTCTTGGGCTAATACAG+AGG 0.635077 2.4:+63931025 MS.gene002958:CDS
GCAGTGTGAAACAAAGGGCG+AGG 0.647228 2.4:-63930726 None:intergenic
AATTTGGCAAATCAGTAGAA+GGG 0.648246 2.4:-63931382 None:intergenic
GATGGATGCCCGTTGTAAGG+AGG 0.657482 2.4:-63931311 None:intergenic
TTATTATGGAGCTAGCAACA+AGG 0.684039 2.4:+63931006 MS.gene002958:CDS
AGTGAGTATGATATCAGCTG+AGG 0.690629 2.4:+63930950 MS.gene002958:CDS
GGACCTGCAACATACTGAGG+TGG 0.712994 2.4:-63931239 None:intergenic
GATGGACCTGCAACATACTG+AGG 0.735823 2.4:-63931242 None:intergenic
AAAGACACAAGTGAACCCAG+AGG 0.809094 2.4:+63930650 MS.gene002958:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAATAAGGAACATTTCCTAT+TGG - chr2.4:63931197-63931216 None:intergenic 25.0%
!!! ACTGTTGATTTCAAAAGTAA+TGG + chr2.4:63930882-63930901 MS.gene002958:CDS 25.0%
!!! ATTCTTGTTGTTTTTGTTGT+CGG - chr2.4:63930809-63930828 None:intergenic 25.0%
!!! GAAACATTTGATTTGCAAAA+GGG - chr2.4:63931340-63931359 None:intergenic 25.0%
AATTTGGCAAATCAGTAGAA+GGG - chr2.4:63931385-63931404 None:intergenic 30.0%
ATCTTCTTAATCCTTGCTAA+TGG - chr2.4:63930912-63930931 None:intergenic 30.0%
GGCATGTGAAATGTTTATTA+TGG + chr2.4:63930992-63931011 MS.gene002958:CDS 30.0%
!! GGAAACATTTGATTTGCAAA+AGG - chr2.4:63931341-63931360 None:intergenic 30.0%
!! TGGTTTGATTGATTTTGTGT+TGG - chr2.4:63930693-63930712 None:intergenic 30.0%
!!! TATCATTCCTTTTTTCCTCT+GGG - chr2.4:63930668-63930687 None:intergenic 30.0%
!!! TTCATTTTGTTTTGACCAGA+AGG - chr2.4:63930850-63930869 None:intergenic 30.0%
AAGATCATGAAAGCAGAAGA+AGG + chr2.4:63930927-63930946 MS.gene002958:CDS 35.0%
AATGGAGCGTGACATATTTA+TGG + chr2.4:63931148-63931167 MS.gene002958:CDS 35.0%
ACAGACATAGGCAGATAATA+AGG - chr2.4:63931212-63931231 None:intergenic 35.0%
AGAAAAAACTTGACACCTTC+TGG + chr2.4:63930832-63930851 MS.gene002958:CDS 35.0%
ATGGAGCGTGACATATTTAT+GGG + chr2.4:63931149-63931168 MS.gene002958:CDS 35.0%
ATTGGAACACTTTCACTTCT+TGG - chr2.4:63931179-63931198 None:intergenic 35.0%
GAATTTGGCAAATCAGTAGA+AGG - chr2.4:63931386-63931405 None:intergenic 35.0%
TTATTATGGAGCTAGCAACA+AGG + chr2.4:63931006-63931025 MS.gene002958:CDS 35.0%
!! AAGGGTCGTTTTCTTTCTTT+GGG - chr2.4:63931367-63931386 None:intergenic 35.0%
!! AGAAGTGAAAGTGTTCCAAT+AGG + chr2.4:63931179-63931198 MS.gene002958:CDS 35.0%
!!! GTATCATTCCTTTTTTCCTC+TGG - chr2.4:63930669-63930688 None:intergenic 35.0%
!!! TCGTTTTCTTTCTTTGGGAT+TGG - chr2.4:63931362-63931381 None:intergenic 35.0%
AAGTGAACCCAGAGGAAAAA+AGG + chr2.4:63930658-63930677 MS.gene002958:CDS 40.0%
AGTGAGTATGATATCAGCTG+AGG + chr2.4:63930950-63930969 MS.gene002958:CDS 40.0%
ATTCTTGGAGGACCATATGA+TGG - chr2.4:63931263-63931282 None:intergenic 40.0%
CACTTGCAGTGTGAAACAAA+GGG - chr2.4:63930734-63930753 None:intergenic 40.0%
CATGCCTTAGCAAACAGAAT+AGG - chr2.4:63930978-63930997 None:intergenic 40.0%
TATGTTGCAGGTCCATCATA+TGG + chr2.4:63931248-63931267 MS.gene002958:CDS 40.0%
TCTACTCAGGTAGGATGAAA+AGG - chr2.4:63930763-63930782 None:intergenic 40.0%
TGTCCCTAGGGAAAAAACAA+TGG + chr2.4:63931130-63931149 MS.gene002958:CDS 40.0%
TGTCTTCCCATAAGCATTCT+TGG - chr2.4:63931278-63931297 None:intergenic 40.0%
! CCTAGTTGATATTGTCCCTA+GGG + chr2.4:63931118-63931137 MS.gene002958:CDS 40.0%
! TCCTAGTTGATATTGTCCCT+AGG + chr2.4:63931117-63931136 MS.gene002958:CDS 40.0%
! TGATTTGCAAAAGGGTGTGA+TGG - chr2.4:63931332-63931351 None:intergenic 40.0%
!! GAAGGGTCGTTTTCTTTCTT+TGG - chr2.4:63931368-63931387 None:intergenic 40.0%
!!! GCTCCATTGTTTTTTCCCTA+GGG - chr2.4:63931136-63931155 None:intergenic 40.0%
AAAGACACAAGTGAACCCAG+AGG + chr2.4:63930650-63930669 MS.gene002958:CDS 45.0%
AAGGTCTTGGGCTAATACAG+AGG + chr2.4:63931025-63931044 MS.gene002958:CDS 45.0%
CCAATCAACCTCCTTACAAC+GGG + chr2.4:63931303-63931322 MS.gene002958:CDS 45.0%
CCCAATCAACCTCCTTACAA+CGG + chr2.4:63931302-63931321 MS.gene002958:CDS 45.0%
CCCTAGGGACAATATCAACT+AGG - chr2.4:63931121-63931140 None:intergenic 45.0%
CTTCCCATAAGCATTCTTGG+AGG - chr2.4:63931275-63931294 None:intergenic 45.0%
CTTGGAGTTGAACTCTACTC+AGG - chr2.4:63930776-63930795 None:intergenic 45.0%
GAGTTGAACTCTACTCAGGT+AGG - chr2.4:63930772-63930791 None:intergenic 45.0%
GCACTTGCAGTGTGAAACAA+AGG - chr2.4:63930735-63930754 None:intergenic 45.0%
GGTCCTCCAAGAATGCTTAT+GGG + chr2.4:63931269-63931288 MS.gene002958:CDS 45.0%
GTTGTCGGTGAGAGATTTCT+TGG - chr2.4:63930794-63930813 None:intergenic 45.0%
TGGTCCTCCAAGAATGCTTA+TGG + chr2.4:63931268-63931287 MS.gene002958:CDS 45.0%
! CCGTTGTAAGGAGGTTGATT+GGG - chr2.4:63931305-63931324 None:intergenic 45.0%
! GGCACCTATTCTGTTTGCTA+AGG + chr2.4:63930971-63930990 MS.gene002958:CDS 45.0%
! GTAATGGCTTGCCATTAGCA+AGG + chr2.4:63930898-63930917 MS.gene002958:CDS 45.0%
!!! CGCTCCATTGTTTTTTCCCT+AGG - chr2.4:63931137-63931156 None:intergenic 45.0%
GATGGACCTGCAACATACTG+AGG - chr2.4:63931245-63931264 None:intergenic 50.0%
GGAGCTAGCAACAAGGTCTT+GGG + chr2.4:63931013-63931032 MS.gene002958:CDS 50.0%
GGTGGCACATGAACAGACAT+AGG - chr2.4:63931224-63931243 None:intergenic 50.0%
TGGAGCTAGCAACAAGGTCT+TGG + chr2.4:63931012-63931031 MS.gene002958:CDS 50.0%
! CCCGTTGTAAGGAGGTTGAT+TGG - chr2.4:63931306-63931325 None:intergenic 50.0%
!! GGCGAGGCACTGATACTATT+TGG - chr2.4:63930713-63930732 None:intergenic 50.0%
!! TGTGATGGATGCCCGTTGTA+AGG - chr2.4:63931317-63931336 None:intergenic 50.0%
GATGGATGCCCGTTGTAAGG+AGG - chr2.4:63931314-63931333 None:intergenic 55.0%
GCAGTGTGAAACAAAGGGCG+AGG - chr2.4:63930729-63930748 None:intergenic 55.0%
GGACCTGCAACATACTGAGG+TGG - chr2.4:63931242-63931261 None:intergenic 55.0%
GTGCCACCTCAGTATGTTGC+AGG + chr2.4:63931236-63931255 MS.gene002958:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 63930642 63931415 63930642 ID=MS.gene002958
chr2.4 mRNA 63930642 63931415 63930642 ID=MS.gene002958.t1;Parent=MS.gene002958
chr2.4 exon 63930642 63931415 63930642 ID=MS.gene002958.t1.exon1;Parent=MS.gene002958.t1
chr2.4 CDS 63930642 63931415 63930642 ID=cds.MS.gene002958.t1;Parent=MS.gene002958.t1
Gene Sequence

>MS.gene002958

ATGGATCAAAAGACACAAGTGAACCCAGAGGAAAAAAGGAATGATACACCAACACAAAATCAATCAAACCAAATAGTATCAGTGCCTCGCCCTTTGTTTCACACTGCAAGTGCTTCTGCCTTTTCATCCTACCTGAGTAGAGTTCAACTCCAAGAAATCTCTCACCGACAACAAAAACAACAAGAATTGCAGAAAAAACTTGACACCTTCTGGTCAAAACAAAATGAAGAAGTTCAGAAGACTGTTGATTTCAAAAGTAATGGCTTGCCATTAGCAAGGATTAAGAAGATCATGAAAGCAGAAGAAGGAGTGAGTATGATATCAGCTGAGGCACCTATTCTGTTTGCTAAGGCATGTGAAATGTTTATTATGGAGCTAGCAACAAGGTCTTGGGCTAATACAGAGGTGAACAAAAGAAAGACACTTCAAAAGAGTGACATTGCATCTGCTGTCTCAAGTAATGAAGTGTTTGATTTCCTAGTTGATATTGTCCCTAGGGAAAAAACAATGGAGCGTGACATATTTATGGGTATACCAAGAAGTGAAAGTGTTCCAATAGGAAATGTTCCTTATTATCTGCCTATGTCTGTTCATGTGCCACCTCAGTATGTTGCAGGTCCATCATATGGTCCTCCAAGAATGCTTATGGGAAGACATCTTCCCAATCAACCTCCTTACAACGGGCATCCATCACACCCTTTTGCAAATCAAATGTTTCCAATCCCAAAGAAAGAAAACGACCCTTCTACTGATTTGCCAAATTCAGAAGATTAA
Protein sequence

>MS.gene002958.t1

MDQKTQVNPEEKRNDTPTQNQSNQIVSVPRPLFHTASASAFSSYLSRVQLQEISHRQQKQQELQKKLDTFWSKQNEEVQKTVDFKSNGLPLARIKKIMKAEEGVSMISAEAPILFAKACEMFIMELATRSWANTEVNKRKTLQKSDIASAVSSNEVFDFLVDIVPREKTMERDIFMGIPRSESVPIGNVPYYLPMSVHVPPQYVAGPSYGPPRMLMGRHLPNQPPYNGHPSHPFANQMFPIPKKENDPSTDLPNSED