AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60649


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60649.t1 MTR_1g099320 97.980 297 6 0 1 297 1 297 0.0 598
MS.gene60649.t1 MTR_1g099350 70.805 298 79 4 1 297 1 291 7.57e-149 419
MS.gene60649.t1 MTR_0027s0260 67.241 290 89 4 5 293 10 294 1.69e-139 395
MS.gene60649.t1 MTR_8g055940 66.096 292 94 3 3 293 6 293 1.59e-136 388
MS.gene60649.t1 MTR_1g099310 64.846 293 97 6 7 297 8 296 4.74e-134 382
MS.gene60649.t1 MTR_5g043550 63.605 294 102 3 1 293 1 290 9.25e-133 378
MS.gene60649.t1 MTR_1g099290 63.509 285 99 5 13 295 15 296 2.20e-124 367
MS.gene60649.t1 MTR_7g116350 61.986 292 95 2 7 297 8 284 5.77e-124 373
MS.gene60649.t1 MTR_8g467650 62.284 289 105 3 7 293 8 294 5.96e-123 353
MS.gene60649.t1 MTR_2g102020 57.667 300 116 5 8 297 15 313 8.94e-120 347
MS.gene60649.t1 MTR_7g116850 56.701 291 121 4 11 297 37 326 2.95e-113 330
MS.gene60649.t1 MTR_2g040740 55.634 284 118 4 14 293 16 295 8.34e-105 308
MS.gene60649.t1 MTR_2g040830 53.333 285 124 5 14 293 16 296 1.04e-97 291
MS.gene60649.t1 MTR_2g040690 52.632 285 126 5 14 293 18 298 3.89e-97 289
MS.gene60649.t1 MTR_6g023340 51.237 283 129 7 21 297 23 302 2.18e-93 279
MS.gene60649.t1 MTR_2g040650 48.421 285 134 6 14 293 16 292 4.81e-86 261
MS.gene60649.t1 MTR_2g040870 50.993 151 70 2 16 166 15 161 1.07e-40 139
MS.gene60649.t1 MTR_2g040880 52.212 113 49 3 186 293 1 113 1.57e-35 125
MS.gene60649.t1 MTR_2g040890 42.683 164 83 6 9 166 8 166 4.30e-35 125
MS.gene60649.t1 MTR_2g040850 44.371 151 74 3 2 145 3 150 1.18e-30 115
MS.gene60649.t1 MTR_2g040900 46.774 124 60 4 180 297 18 141 8.30e-28 106
MS.gene60649.t1 MTR_4g077310 52.809 89 38 4 207 293 3 89 2.17e-23 92.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60649.t1 AT5G24090 63.667 300 105 3 1 297 4 302 1.05e-142 404

Find 59 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTGAATTCATGGAATAAA+TGG 0.244707 1.2:-69977804 MS.gene60649:CDS
AACTTGGTTCCACCGAAAAT+TGG 0.244758 1.2:-69978014 MS.gene60649:CDS
CTTAAAGGGTATAGTAGATA+TGG 0.254089 1.2:-69977973 MS.gene60649:CDS
CTTTCTATTGGTGGTGGAAT+TGG 0.283448 1.2:-69978168 MS.gene60649:CDS
AGGTTCCTTCGTTGCCATTT+TGG 0.290608 1.2:+69978373 None:intergenic
GCAATCTATTGGGGCCAAAA+TGG 0.300822 1.2:-69978387 MS.gene60649:CDS
GGGTATAGCACTTCTATTAT+TGG 0.304491 1.2:-69977607 MS.gene60649:CDS
TGACCTGCGAGATTCATTTC+AGG 0.305610 1.2:+69978273 None:intergenic
TAACCAACCTTGTGAATTCA+TGG 0.337959 1.2:-69977813 MS.gene60649:CDS
CTGGTGGCATAGCAATCTAT+TGG 0.352724 1.2:-69978398 MS.gene60649:CDS
AATCCACCTTGTCAATATAA+TGG 0.353574 1.2:-69977841 MS.gene60649:CDS
GACCGTTACCGAATTTGTTT+AGG 0.359199 1.2:+69978301 None:intergenic
TTGGGCACTGCACTTGAAAC+AGG 0.362436 1.2:-69977898 MS.gene60649:CDS
CCGGCGTCTACGGCGGCGGC+CGG 0.373512 1.2:-69977742 MS.gene60649:CDS
TGGTGGCATAGCAATCTATT+GGG 0.384033 1.2:-69978397 MS.gene60649:CDS
GAAAATTGGCAACACCTTGC+AGG 0.393402 1.2:-69978000 MS.gene60649:CDS
AAACTTTGATTCCTTTACTT+TGG 0.396936 1.2:+69978193 None:intergenic
ATAGCTTTCCTAAACAAATT+CGG 0.403876 1.2:-69978309 MS.gene60649:CDS
TGCCGGAATAAAACCACTTC+CGG 0.411953 1.2:+69977723 None:intergenic
GGTTGCACATGCTTCGGATA+AGG 0.416487 1.2:+69978353 None:intergenic
GCTGCCGGCGTCTACGGCGG+CGG 0.417348 1.2:-69977746 MS.gene60649:CDS
TCTACGGCGGCGGCCGGAAG+TGG 0.426613 1.2:-69977736 MS.gene60649:CDS
AAGTCATCTTCAAGACCATT+AGG 0.427426 1.2:-69978072 MS.gene60649:CDS
TCTAAAACAGCATCACCTAA+TGG 0.445847 1.2:+69978057 None:intergenic
AGGTTTCATGATTTGCAGAC+TGG 0.456803 1.2:-69977628 MS.gene60649:CDS
TTTAGGGCTGCCGGCGTCTA+CGG 0.464209 1.2:-69977752 MS.gene60649:CDS
TTATCCGAAGCATGTGCAAC+CGG 0.472372 1.2:-69978351 MS.gene60649:CDS
CTTGTTGCAACTTCCCATGC+TGG 0.478479 1.2:-69978417 MS.gene60649:CDS
AGTATGGAGGAGTGATGCTT+TGG 0.487463 1.2:-69977654 MS.gene60649:CDS
ATCAAAGATTGCCAAAGTAA+AGG 0.491893 1.2:-69978204 MS.gene60649:CDS
GACCTGCGAGATTCATTTCA+GGG 0.492299 1.2:+69978274 None:intergenic
ATTCCATGAATTCACAAGGT+TGG 0.498536 1.2:+69977810 None:intergenic
GATTGCTATGCCACCAGCAT+GGG 0.506152 1.2:+69978404 None:intergenic
TCTGAAGTCAACACATCTGC+CGG 0.541684 1.2:+69977706 None:intergenic
CCGGCCGCCGCCGTAGACGC+CGG 0.543064 1.2:+69977742 None:intergenic
TTATCTGGAATTGGACATTG+AGG 0.543911 1.2:+69977925 None:intergenic
CTTCCCTCTTGGAACAGTAC+TGG 0.543952 1.2:+69977780 None:intergenic
GGTTTCATGATTTGCAGACT+GGG 0.544792 1.2:-69977627 MS.gene60649:CDS
GAGGAGTGATGCTTTGGTCA+AGG 0.544888 1.2:-69977648 MS.gene60649:CDS
GTGCATGAATTTGGAAGTGA+CGG 0.553793 1.2:+69978243 None:intergenic
TTATGGAACACTTTCTTGGG+TGG 0.560429 1.2:-69978096 MS.gene60649:CDS
ACCCCTGAAATGAATCTCGC+AGG 0.567411 1.2:-69978276 MS.gene60649:CDS
TTCCTAAACAAATTCGGTAA+CGG 0.579160 1.2:-69978303 MS.gene60649:CDS
TGGGGCCAAAATGGCAACGA+AGG 0.591522 1.2:-69978378 MS.gene60649:CDS
AGATTGCTATGCCACCAGCA+TGG 0.592121 1.2:+69978403 None:intergenic
TGCATGAATTTGGAAGTGAC+GGG 0.593382 1.2:+69978244 None:intergenic
GTTGCAACTTCCCATGCTGG+TGG 0.594762 1.2:-69978414 MS.gene60649:CDS
AGGGCTGCCGGCGTCTACGG+CGG 0.600947 1.2:-69977749 MS.gene60649:CDS
TTAGGAAAGCTATGTTAACA+TGG 0.604430 1.2:+69978319 None:intergenic
ATTTATTCCATGAATTCACA+AGG 0.612674 1.2:+69977806 None:intergenic
TTGCCATTATATTGACAAGG+TGG 0.613084 1.2:+69977838 None:intergenic
ACCCTTTAAGAAAACCTGCA+AGG 0.616480 1.2:+69977986 None:intergenic
ACCTGCGAGATTCATTTCAG+GGG 0.619333 1.2:+69978275 None:intergenic
ATGTTGCCATTATATTGACA+AGG 0.624746 1.2:+69977835 None:intergenic
TAGGAAAGCTATGTTAACAT+GGG 0.626283 1.2:+69978320 None:intergenic
GGGAAGTTGCAACAAGAGTG+AGG 0.646970 1.2:+69978424 None:intergenic
GGTGGCATAGCAATCTATTG+GGG 0.654630 1.2:-69978396 MS.gene60649:CDS
GGACCAGTACTGTTCCAAGA+GGG 0.670941 1.2:-69977783 MS.gene60649:CDS
TGGACCAGTACTGTTCCAAG+AGG 0.699480 1.2:-69977784 MS.gene60649:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAGAAGTCAAAAAAGTA+TGG - chr1.2:69978395-69978414 MS.gene60649:CDS 20.0%
!!! ATAGATTTTGATATTGAACT+TGG - chr1.2:69978035-69978054 MS.gene60649:CDS 20.0%
!!! ATCAAAGTTTTACTTTCTAT+TGG - chr1.2:69977885-69977904 MS.gene60649:CDS 20.0%
!!! GAAACGTTTCAAAATTTTTA+TGG - chr1.2:69977952-69977971 MS.gene60649:CDS 20.0%
! AAACTTTGATTCCTTTACTT+TGG + chr1.2:69977875-69977894 None:intergenic 25.0%
! ATAGCTTTCCTAAACAAATT+CGG - chr1.2:69977756-69977775 MS.gene60649:CDS 25.0%
! ATTTATTCCATGAATTCACA+AGG + chr1.2:69978262-69978281 None:intergenic 25.0%
! GTATAGTAGATATGGAAAAA+AGG - chr1.2:69978100-69978119 MS.gene60649:CDS 25.0%
! TTGTGAATTCATGGAATAAA+TGG - chr1.2:69978261-69978280 MS.gene60649:CDS 25.0%
!! AAAGTTTTACTTTCTATTGG+TGG - chr1.2:69977888-69977907 MS.gene60649:CDS 25.0%
!! ATTTTTATGGAACACTTTCT+TGG - chr1.2:69977965-69977984 MS.gene60649:CDS 25.0%
!! CCAATTCCAGATAAATTTTT+GGG - chr1.2:69978149-69978168 MS.gene60649:CDS 25.0%
!! TCCAATTCCAGATAAATTTT+TGG - chr1.2:69978148-69978167 MS.gene60649:CDS 25.0%
!! TTTTTATGGAACACTTTCTT+GGG - chr1.2:69977966-69977985 MS.gene60649:CDS 25.0%
!!! TTTTTTGACTTCTTAATCAC+AGG + chr1.2:69978392-69978411 None:intergenic 25.0%
AATCCACCTTGTCAATATAA+TGG - chr1.2:69978224-69978243 MS.gene60649:CDS 30.0%
ATCAAAGATTGCCAAAGTAA+AGG - chr1.2:69977861-69977880 MS.gene60649:CDS 30.0%
ATGTTGCCATTATATTGACA+AGG + chr1.2:69978233-69978252 None:intergenic 30.0%
TAGGAAAGCTATGTTAACAT+GGG + chr1.2:69977748-69977767 None:intergenic 30.0%
TTAGGAAAGCTATGTTAACA+TGG + chr1.2:69977749-69977768 None:intergenic 30.0%
TTCCTAAACAAATTCGGTAA+CGG - chr1.2:69977762-69977781 MS.gene60649:CDS 30.0%
! AAGAAGTCAAAAAAGTATGG+AGG - chr1.2:69978398-69978417 MS.gene60649:CDS 30.0%
! CCCAAAAATTTATCTGGAAT+TGG + chr1.2:69978152-69978171 None:intergenic 30.0%
! CTGAATTTTGTGCATGAATT+TGG + chr1.2:69977834-69977853 None:intergenic 30.0%
! CTTAAAGGGTATAGTAGATA+TGG - chr1.2:69978092-69978111 MS.gene60649:CDS 30.0%
! TATGGAAAAAAGGTGTATCT+TGG - chr1.2:69978110-69978129 MS.gene60649:CDS 30.0%
!!! AGGTCTTTTTGACTTTGTTT+GGG - chr1.2:69978187-69978206 MS.gene60649:CDS 30.0%
!!! CAAGAGGGAAGTTATTTTTA+GGG - chr1.2:69978297-69978316 MS.gene60649:CDS 30.0%
AAGTCATCTTCAAGACCATT+AGG - chr1.2:69977993-69978012 MS.gene60649:CDS 35.0%
ATTCCATGAATTCACAAGGT+TGG + chr1.2:69978258-69978277 None:intergenic 35.0%
CCTAAAAATAACTTCCCTCT+TGG + chr1.2:69978299-69978318 None:intergenic 35.0%
GGGTATAGCACTTCTATTAT+TGG - chr1.2:69978458-69978477 MS.gene60649:CDS 35.0%
TAACCAACCTTGTGAATTCA+TGG - chr1.2:69978252-69978271 MS.gene60649:CDS 35.0%
TTGCCATTATATTGACAAGG+TGG + chr1.2:69978230-69978249 None:intergenic 35.0%
! ACCTTGCAGGTTTTCTTAAA+GGG - chr1.2:69978078-69978097 MS.gene60649:CDS 35.0%
! GTTTTACTTTCTATTGGTGG+TGG - chr1.2:69977891-69977910 MS.gene60649:CDS 35.0%
! TCTAAAACAGCATCACCTAA+TGG + chr1.2:69978011-69978030 None:intergenic 35.0%
! TTATCTGGAATTGGACATTG+AGG + chr1.2:69978143-69978162 None:intergenic 35.0%
!!! CAGGTCTTTTTGACTTTGTT+TGG - chr1.2:69978186-69978205 MS.gene60649:CDS 35.0%
!!! CCAAGAGGGAAGTTATTTTT+AGG - chr1.2:69978296-69978315 MS.gene60649:CDS 35.0%
!!! GTTAACATGGGAGTATTTTC+CGG + chr1.2:69977736-69977755 None:intergenic 35.0%
!!! TTAGGTGATGCTGTTTTAGA+TGG - chr1.2:69978011-69978030 MS.gene60649:CDS 35.0%
AACTTGGTTCCACCGAAAAT+TGG - chr1.2:69978051-69978070 MS.gene60649:CDS 40.0%
GCAGTGCCCAAAAATTTATC+TGG + chr1.2:69978158-69978177 None:intergenic 40.0%
GTGCATGAATTTGGAAGTGA+CGG + chr1.2:69977825-69977844 None:intergenic 40.0%
TGCATGAATTTGGAAGTGAC+GGG + chr1.2:69977824-69977843 None:intergenic 40.0%
TGGTGGCATAGCAATCTATT+GGG - chr1.2:69977668-69977687 MS.gene60649:CDS 40.0%
TTATGGAACACTTTCTTGGG+TGG - chr1.2:69977969-69977988 MS.gene60649:CDS 40.0%
! ACCCTTTAAGAAAACCTGCA+AGG + chr1.2:69978082-69978101 None:intergenic 40.0%
! AGGTTTCATGATTTGCAGAC+TGG - chr1.2:69978437-69978456 MS.gene60649:CDS 40.0%
! CACCTTGCAGGTTTTCTTAA+AGG - chr1.2:69978077-69978096 MS.gene60649:CDS 40.0%
! GACCGTTACCGAATTTGTTT+AGG + chr1.2:69977767-69977786 None:intergenic 40.0%
! GGTTTCATGATTTGCAGACT+GGG - chr1.2:69978438-69978457 MS.gene60649:CDS 40.0%
!! CTTTCTATTGGTGGTGGAAT+TGG - chr1.2:69977897-69977916 MS.gene60649:CDS 40.0%
!!! GAAGTTATTTTTAGGGCTGC+CGG - chr1.2:69978304-69978323 MS.gene60649:CDS 40.0%
!!! TGCAAGGTGTTGCCAATTTT+CGG + chr1.2:69978066-69978085 None:intergenic 40.0%
ACCTGCGAGATTCATTTCAG+GGG + chr1.2:69977793-69977812 None:intergenic 45.0%
AGTATGGAGGAGTGATGCTT+TGG - chr1.2:69978411-69978430 MS.gene60649:CDS 45.0%
CTGGTGGCATAGCAATCTAT+TGG - chr1.2:69977667-69977686 MS.gene60649:CDS 45.0%
GAAAATTGGCAACACCTTGC+AGG - chr1.2:69978065-69978084 MS.gene60649:CDS 45.0%
GACCTGCGAGATTCATTTCA+GGG + chr1.2:69977794-69977813 None:intergenic 45.0%
GCAATCTATTGGGGCCAAAA+TGG - chr1.2:69977678-69977697 MS.gene60649:CDS 45.0%
GGTGGCATAGCAATCTATTG+GGG - chr1.2:69977669-69977688 MS.gene60649:CDS 45.0%
TGACCTGCGAGATTCATTTC+AGG + chr1.2:69977795-69977814 None:intergenic 45.0%
TGCCGGAATAAAACCACTTC+CGG + chr1.2:69978345-69978364 None:intergenic 45.0%
TTATCCGAAGCATGTGCAAC+CGG - chr1.2:69977714-69977733 MS.gene60649:CDS 45.0%
! TCTGAAGTCAACACATCTGC+CGG + chr1.2:69978362-69978381 None:intergenic 45.0%
! TTTTCCGGTTGCACATGCTT+CGG + chr1.2:69977721-69977740 None:intergenic 45.0%
!! AGGTTCCTTCGTTGCCATTT+TGG + chr1.2:69977695-69977714 None:intergenic 45.0%
!!! AAGGTGTTGCCAATTTTCGG+TGG + chr1.2:69978063-69978082 None:intergenic 45.0%
ACCCCTGAAATGAATCTCGC+AGG - chr1.2:69977789-69977808 MS.gene60649:CDS 50.0%
AGATTGCTATGCCACCAGCA+TGG + chr1.2:69977665-69977684 None:intergenic 50.0%
CTTCCCTCTTGGAACAGTAC+TGG + chr1.2:69978288-69978307 None:intergenic 50.0%
CTTGTTGCAACTTCCCATGC+TGG - chr1.2:69977648-69977667 MS.gene60649:CDS 50.0%
GAGGAGTGATGCTTTGGTCA+AGG - chr1.2:69978417-69978436 MS.gene60649:CDS 50.0%
GATTGCTATGCCACCAGCAT+GGG + chr1.2:69977664-69977683 None:intergenic 50.0%
GGACCAGTACTGTTCCAAGA+GGG - chr1.2:69978282-69978301 MS.gene60649:CDS 50.0%
GGGAAGTTGCAACAAGAGTG+AGG + chr1.2:69977644-69977663 None:intergenic 50.0%
GGTTGCACATGCTTCGGATA+AGG + chr1.2:69977715-69977734 None:intergenic 50.0%
TGGACCAGTACTGTTCCAAG+AGG - chr1.2:69978281-69978300 MS.gene60649:CDS 50.0%
! TTGGGCACTGCACTTGAAAC+AGG - chr1.2:69978167-69978186 MS.gene60649:CDS 50.0%
!!! GGCCGGAAGTGGTTTTATTC+CGG - chr1.2:69978340-69978359 MS.gene60649:CDS 50.0%
GTTGCAACTTCCCATGCTGG+TGG - chr1.2:69977651-69977670 MS.gene60649:CDS 55.0%
TGGGGCCAAAATGGCAACGA+AGG - chr1.2:69977687-69977706 MS.gene60649:CDS 55.0%
! TTTAGGGCTGCCGGCGTCTA+CGG - chr1.2:69978313-69978332 MS.gene60649:CDS 60.0%
AGGGCTGCCGGCGTCTACGG+CGG - chr1.2:69978316-69978335 MS.gene60649:CDS 75.0%
TCTACGGCGGCGGCCGGAAG+TGG - chr1.2:69978329-69978348 MS.gene60649:CDS 75.0%
! GCTGCCGGCGTCTACGGCGG+CGG - chr1.2:69978319-69978338 MS.gene60649:CDS 80.0%
! CCGGCCGCCGCCGTAGACGC+CGG + chr1.2:69978326-69978345 None:intergenic 85.0%
! CCGGCGTCTACGGCGGCGGC+CGG - chr1.2:69978323-69978342 MS.gene60649:CDS 85.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 69977597 69978490 69977597 ID=MS.gene60649
chr1.2 mRNA 69977597 69978490 69977597 ID=MS.gene60649.t1;Parent=MS.gene60649
chr1.2 exon 69977597 69978490 69977597 ID=MS.gene60649.t1.exon1;Parent=MS.gene60649.t1
chr1.2 CDS 69977597 69978490 69977597 ID=cds.MS.gene60649.t1;Parent=MS.gene60649.t1
Gene Sequence

>MS.gene60649

ATGGCAAAAAACTCTCACACTTTGTTGTCTCTTATTCTTCTATTCCTCACTCTTGTTGCAACTTCCCATGCTGGTGGCATAGCAATCTATTGGGGCCAAAATGGCAACGAAGGAACCTTATCCGAAGCATGTGCAACCGGAAAATACTCCCATGTTAACATAGCTTTCCTAAACAAATTCGGTAACGGTCAAACCCCTGAAATGAATCTCGCAGGTCACTGCAACCCGTCACTTCCAAATTCATGCACAAAATTCAGCTCAGAAATCAAAGATTGCCAAAGTAAAGGAATCAAAGTTTTACTTTCTATTGGTGGTGGAATTGGAAGCTACTCTTTATCTTCAATTGAAGATGCAAGAAACGTTTCAAAATTTTTATGGAACACTTTCTTGGGTGGCAAGTCATCTTCAAGACCATTAGGTGATGCTGTTTTAGATGGAATAGATTTTGATATTGAACTTGGTTCCACCGAAAATTGGCAACACCTTGCAGGTTTTCTTAAAGGGTATAGTAGATATGGAAAAAAGGTGTATCTTGGTGCAGCTCCTCAATGTCCAATTCCAGATAAATTTTTGGGCACTGCACTTGAAACAGGTCTTTTTGACTTTGTTTGGGTACAATTTTACAATAATCCACCTTGTCAATATAATGGCAACATAACCAACCTTGTGAATTCATGGAATAAATGGACCAGTACTGTTCCAAGAGGGAAGTTATTTTTAGGGCTGCCGGCGTCTACGGCGGCGGCCGGAAGTGGTTTTATTCCGGCAGATGTGTTGACTTCAGAAATATTACCTGTGATTAAGAAGTCAAAAAAGTATGGAGGAGTGATGCTTTGGTCAAGGTTTCATGATTTGCAGACTGGGTATAGCACTTCTATTATTGGAAGCGTGTGA

Protein sequence

>MS.gene60649.t1

MAKNSHTLLSLILLFLTLVATSHAGGIAIYWGQNGNEGTLSEACATGKYSHVNIAFLNKFGNGQTPEMNLAGHCNPSLPNSCTKFSSEIKDCQSKGIKVLLSIGGGIGSYSLSSIEDARNVSKFLWNTFLGGKSSSRPLGDAVLDGIDFDIELGSTENWQHLAGFLKGYSRYGKKVYLGAAPQCPIPDKFLGTALETGLFDFVWVQFYNNPPCQYNGNITNLVNSWNKWTSTVPRGKLFLGLPASTAAAGSGFIPADVLTSEILPVIKKSKKYGGVMLWSRFHDLQTGYSTSIIGSV