AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060630.t1 MTR_1g070355 46.117 206 97 1 39 230 19 224 1.11e-57 192
MS.gene060630.t1 MTR_6g022080 35.503 169 109 0 62 230 67 235 4.24e-35 125
MS.gene060630.t1 MTR_5g076070 35.263 190 116 2 42 230 20 203 3.74e-32 118
MS.gene060630.t1 MTR_0060s0090 58.621 87 36 0 79 165 55 141 4.20e-31 112
MS.gene060630.t1 MTR_6g463250 38.323 167 86 3 1 165 7 158 4.51e-30 110
MS.gene060630.t1 MTR_2g101460 37.342 158 92 1 35 185 3 160 1.24e-26 102
MS.gene060630.t1 MTR_2g101460 42.742 124 71 0 62 185 27 150 5.58e-26 100
MS.gene060630.t1 MTR_6g053140 33.728 169 97 3 5 173 36 189 1.09e-23 94.7
MS.gene060630.t1 MTR_3g448650 36.641 131 76 1 35 158 30 160 2.26e-21 87.8
MS.gene060630.t1 MTR_4g050510 36.029 136 72 2 82 217 81 201 9.28e-21 87.0
MS.gene060630.t1 MTR_7g028855 30.698 215 142 2 9 223 56 263 1.92e-20 89.4
MS.gene060630.t1 MTR_1g052260 36.893 103 65 0 60 162 56 158 5.69e-18 78.2
MS.gene060630.t1 MTR_7g446520 30.000 160 94 1 71 230 79 220 2.24e-17 80.1
MS.gene060630.t1 MTR_8g066350 26.061 165 100 3 22 185 23 166 3.98e-13 65.5
MS.gene060630.t1 MTR_0604s0020 36.486 74 47 0 91 164 3 76 1.69e-11 58.9
MS.gene060630.t1 MTR_3g450850 32.558 129 71 6 86 202 53 177 1.73e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060630.t1 AT1G10240 34.356 163 86 5 72 219 34 190 2.09e-14 72.4
MS.gene060630.t1 AT1G10240 34.356 163 86 5 72 219 34 190 2.09e-14 72.4
MS.gene060630.t1 AT5G28530 31.707 123 81 2 86 206 61 182 3.24e-13 68.9
MS.gene060630.t1 AT5G28530 31.707 123 81 2 86 206 61 182 3.34e-13 68.6
MS.gene060630.t1 AT5G28530 31.707 123 81 2 86 206 61 182 3.82e-13 68.6
MS.gene060630.t1 AT5G28530 31.707 123 81 2 86 206 61 182 3.88e-13 68.6
MS.gene060630.t1 AT5G28530 31.707 123 81 2 86 206 61 182 3.88e-13 68.6
MS.gene060630.t1 AT4G38180 30.573 157 106 3 76 230 69 224 2.28e-11 63.5

Find 53 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAGGCAATCTATGTTTAT+TGG 0.295916 2.2:+16852333 None:intergenic
TACCAGTTCTACTACTGGTT+TGG 0.296108 2.2:-16852231 MS.gene060630:CDS
ATATCAATCTTCAAAATATC+AGG 0.302921 2.2:+16852312 None:intergenic
GCATAGAAAATTGTCAAAAT+TGG 0.303743 2.2:-16851926 MS.gene060630:CDS
GGTGCAATGGCAAACGCTTC+TGG 0.313866 2.2:-16851847 MS.gene060630:CDS
GAATGAGTTGGACGAAGAAT+TGG 0.337521 2.2:-16852406 MS.gene060630:CDS
ATTGGTTCCAAATCACCTTC+GGG 0.363893 2.2:+16852351 None:intergenic
TATTGGTTCCAAATCACCTT+CGG 0.372238 2.2:+16852350 None:intergenic
GAAGGTTTAAGCCATGGAAT+TGG 0.373619 2.2:-16852384 MS.gene060630:CDS
ATTGCACCGTACATCTGATA+TGG 0.395766 2.2:+16851862 None:intergenic
ACCAGTTCTACTACTGGTTT+GGG 0.402961 2.2:-16852230 MS.gene060630:CDS
AATTGGATGTACAGGATATT+CGG 0.403668 2.2:-16851909 MS.gene060630:CDS
TACTGGTTTGGGAGAAGAAA+AGG 0.407808 2.2:-16852219 MS.gene060630:CDS
ATTGTCAAAATTGGATGTAC+AGG 0.424754 2.2:-16851917 MS.gene060630:CDS
TTTATAAGAGTCTGATGATA+AGG 0.436426 2.2:-16852188 MS.gene060630:CDS
GTGAACACACATAGGTTTGT+TGG 0.440149 2.2:+16852145 None:intergenic
TCCCAAACCAGTAGTAGAAC+TGG 0.465930 2.2:+16852229 None:intergenic
CCAACGAATCATATGATGAT+TGG 0.467021 2.2:+16852556 None:intergenic
GGGAGTTGTTTCCAATTCCA+TGG 0.469694 2.2:+16852373 None:intergenic
CTGCCTACCAGTTCTACTAC+TGG 0.479288 2.2:-16852236 MS.gene060630:CDS
GTGGATTAACACCCGAGAAA+AGG 0.491667 2.2:-16852101 MS.gene060630:CDS
ACCTATGTGTGTTCACGTGC+AGG 0.495433 2.2:-16852138 MS.gene060630:CDS
CCAATCATCATATGATTCGT+TGG 0.527741 2.2:-16852556 MS.gene060630:intron
GTACCTCTCAACTTCTTCGA+AGG 0.552253 2.2:+16852278 None:intergenic
ATGGAAGGCGGTTCACAAGT+AGG 0.555935 2.2:-16852600 MS.gene060630:CDS
GAATTGGAAGGTTTAAGCCA+TGG 0.558266 2.2:-16852390 MS.gene060630:CDS
CACAACCATGTGCTGTTGGA+TGG 0.560550 2.2:-16851973 MS.gene060630:CDS
TCTGATGATAAGGAATCGTA+CGG 0.560905 2.2:-16852178 MS.gene060630:CDS
AATTGTGACATACCATCGCC+TGG 0.567274 2.2:+16852008 None:intergenic
ACTCATTCTCTCCCGCATCA+TGG 0.574153 2.2:+16852421 None:intergenic
ATATCAGATGTACGGTGCAA+TGG 0.583654 2.2:-16851860 MS.gene060630:CDS
GAAGTTGAGAGGTACAACTT+TGG 0.585776 2.2:-16852270 MS.gene060630:CDS
TATCAATCTTCAAAATATCA+GGG 0.588637 2.2:+16852313 None:intergenic
ATAAGACCATATCAGATGTA+CGG 0.603816 2.2:-16851868 MS.gene060630:CDS
TGATGCGGGAGAGAATGAGT+TGG 0.604824 2.2:-16852418 MS.gene060630:CDS
GCAATGGCAAACGCTTCTGG+TGG 0.608415 2.2:-16851844 MS.gene060630:CDS
TGGTCACAACCATGTGCTGT+TGG 0.609196 2.2:-16851977 MS.gene060630:CDS
CTGATGATAAGGAATCGTAC+GGG 0.620525 2.2:-16852177 MS.gene060630:CDS
TCATTCCATCCAACAGCACA+TGG 0.625026 2.2:+16851968 None:intergenic
TTGGTTCCAAATCACCTTCG+GGG 0.629437 2.2:+16852352 None:intergenic
TTTCCTTCGAAGAAGTTGAG+AGG 0.631586 2.2:-16852281 MS.gene060630:CDS
TCCTGCACGTGAACACACAT+AGG 0.636134 2.2:+16852137 None:intergenic
TGGTTCCAAATCACCTTCGG+GGG 0.641189 2.2:+16852353 None:intergenic
TCGACATTCACACCAGGCGA+TGG 0.642528 2.2:-16852020 MS.gene060630:CDS
GAGTTGGACGAAGAATTGGA+AGG 0.645890 2.2:-16852402 MS.gene060630:CDS
ATTCGGAGTAATAACAACGT+TGG 0.670677 2.2:-16851892 MS.gene060630:CDS
GCAGGATTTAGAGAAGATCG+TGG 0.673352 2.2:-16852120 MS.gene060630:CDS
TACATGTCGACATTCACACC+AGG 0.674089 2.2:-16852026 MS.gene060630:CDS
AAACCAGTAGTAGAACTGGT+AGG 0.688245 2.2:+16852233 None:intergenic
CTGTTGGATGGAATGATGTG+CGG 0.697681 2.2:-16851961 MS.gene060630:CDS
GCTAGAAATGAAACAAGATG+CGG 0.713432 2.2:-16852069 MS.gene060630:CDS
CAATCTTCAAAATATCAGGG+AGG 0.740535 2.2:+16852316 None:intergenic
AGGAAACAGTCATTCACACG+CGG 0.752259 2.2:-16852580 MS.gene060630:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATCAATCTTCAAAATATC+AGG + chr2.2:16852125-16852144 None:intergenic 20.0%
!! TATCAATCTTCAAAATATCA+GGG + chr2.2:16852124-16852143 None:intergenic 20.0%
!!! CACACAAATTTTTTTGTTAT+TGG + chr2.2:16851930-16851949 None:intergenic 20.0%
!!! TATGTCACAATTTTTGAATT+TGG - chr2.2:16852437-16852456 MS.gene060630:CDS 20.0%
! GCATAGAAAATTGTCAAAAT+TGG - chr2.2:16852508-16852527 MS.gene060630:intron 25.0%
! TTTATAAGAGTCTGATGATA+AGG - chr2.2:16852246-16852265 MS.gene060630:CDS 25.0%
!!! GTTATTGGAAAATTTGCTAA+TGG + chr2.2:16851915-16851934 None:intergenic 25.0%
AATTGGATGTACAGGATATT+CGG - chr2.2:16852525-16852544 MS.gene060630:intron 30.0%
ATAAGACCATATCAGATGTA+CGG - chr2.2:16852566-16852585 MS.gene060630:CDS 30.0%
ATTGTCAAAATTGGATGTAC+AGG - chr2.2:16852517-16852536 MS.gene060630:intron 30.0%
AAAACATCATCACACTCTTG+TGG + chr2.2:16851987-16852006 None:intergenic 35.0%
AAACATCATCACACTCTTGT+GGG + chr2.2:16851986-16852005 None:intergenic 35.0%
ATTCGGAGTAATAACAACGT+TGG - chr2.2:16852542-16852561 MS.gene060630:intron 35.0%
CAATCTTCAAAATATCAGGG+AGG + chr2.2:16852121-16852140 None:intergenic 35.0%
CATCATATGATTCGTTGGTA+AGG - chr2.2:16851883-16851902 MS.gene060630:CDS 35.0%
CCAACGAATCATATGATGAT+TGG + chr2.2:16851881-16851900 None:intergenic 35.0%
CCAATCATCATATGATTCGT+TGG - chr2.2:16851878-16851897 MS.gene060630:CDS 35.0%
GCTAGAAATGAAACAAGATG+CGG - chr2.2:16852365-16852384 MS.gene060630:CDS 35.0%
TCTGATGATAAGGAATCGTA+CGG - chr2.2:16852256-16852275 MS.gene060630:CDS 35.0%
!! TATTGGTTCCAAATCACCTT+CGG + chr2.2:16852087-16852106 None:intergenic 35.0%
AAACCAGTAGTAGAACTGGT+AGG + chr2.2:16852204-16852223 None:intergenic 40.0%
AACATCATCACACTCTTGTG+GGG + chr2.2:16851985-16852004 None:intergenic 40.0%
ATATCAGATGTACGGTGCAA+TGG - chr2.2:16852574-16852593 MS.gene060630:CDS 40.0%
ATTGCACCGTACATCTGATA+TGG + chr2.2:16852575-16852594 None:intergenic 40.0%
CTGATGATAAGGAATCGTAC+GGG - chr2.2:16852257-16852276 MS.gene060630:CDS 40.0%
GAAGGTTTAAGCCATGGAAT+TGG - chr2.2:16852050-16852069 MS.gene060630:CDS 40.0%
GAATTGGAAGGTTTAAGCCA+TGG - chr2.2:16852044-16852063 MS.gene060630:CDS 40.0%
GGGAGGCAATCTATGTTTAT+TGG + chr2.2:16852104-16852123 None:intergenic 40.0%
GTGAACACACATAGGTTTGT+TGG + chr2.2:16852292-16852311 None:intergenic 40.0%
TTGTGTGTGTTCTGCAATCA+TGG - chr2.2:16851943-16851962 MS.gene060630:CDS 40.0%
TTTCCTTCGAAGAAGTTGAG+AGG - chr2.2:16852153-16852172 MS.gene060630:CDS 40.0%
! ATTGGTTCCAAATCACCTTC+GGG + chr2.2:16852086-16852105 None:intergenic 40.0%
! GAAGTTGAGAGGTACAACTT+TGG - chr2.2:16852164-16852183 MS.gene060630:CDS 40.0%
! GAATGAGTTGGACGAAGAAT+TGG - chr2.2:16852028-16852047 MS.gene060630:CDS 40.0%
! TACCAGTTCTACTACTGGTT+TGG - chr2.2:16852203-16852222 MS.gene060630:CDS 40.0%
!! ACCAGTTCTACTACTGGTTT+GGG - chr2.2:16852204-16852223 MS.gene060630:CDS 40.0%
!! TACTGGTTTGGGAGAAGAAA+AGG - chr2.2:16852215-16852234 MS.gene060630:CDS 40.0%
!! TGTTTTAAGCAGCCATGATG+CGG - chr2.2:16852001-16852020 MS.gene060630:CDS 40.0%
AATTGTGACATACCATCGCC+TGG + chr2.2:16852429-16852448 None:intergenic 45.0%
AGGAAACAGTCATTCACACG+CGG - chr2.2:16851854-16851873 MS.gene060630:CDS 45.0%
CTGTTGGATGGAATGATGTG+CGG - chr2.2:16852473-16852492 MS.gene060630:intron 45.0%
GAGTTGGACGAAGAATTGGA+AGG - chr2.2:16852032-16852051 MS.gene060630:CDS 45.0%
GCAGGATTTAGAGAAGATCG+TGG - chr2.2:16852314-16852333 MS.gene060630:CDS 45.0%
GTACCTCTCAACTTCTTCGA+AGG + chr2.2:16852159-16852178 None:intergenic 45.0%
TACATGTCGACATTCACACC+AGG - chr2.2:16852408-16852427 MS.gene060630:CDS 45.0%
TCATTCCATCCAACAGCACA+TGG + chr2.2:16852469-16852488 None:intergenic 45.0%
TCCCAAACCAGTAGTAGAAC+TGG + chr2.2:16852208-16852227 None:intergenic 45.0%
TTGGTTCCAAATCACCTTCG+GGG + chr2.2:16852085-16852104 None:intergenic 45.0%
! AGCACGACGTTTCCTTTTCT+CGG + chr2.2:16852348-16852367 None:intergenic 45.0%
! GGGAGTTGTTTCCAATTCCA+TGG + chr2.2:16852064-16852083 None:intergenic 45.0%
! GTGGATTAACACCCGAGAAA+AGG - chr2.2:16852333-16852352 MS.gene060630:CDS 45.0%
!! GTTTTAAGCAGCCATGATGC+GGG - chr2.2:16852002-16852021 MS.gene060630:CDS 45.0%
ACCTATGTGTGTTCACGTGC+AGG - chr2.2:16852296-16852315 MS.gene060630:CDS 50.0%
ACTCATTCTCTCCCGCATCA+TGG + chr2.2:16852016-16852035 None:intergenic 50.0%
ATGGAAGGCGGTTCACAAGT+AGG - chr2.2:16851834-16851853 MS.gene060630:CDS 50.0%
ATTGGAAACAACTCCCCCGA+AGG - chr2.2:16852068-16852087 MS.gene060630:CDS 50.0%
CTGCCTACCAGTTCTACTAC+TGG - chr2.2:16852198-16852217 MS.gene060630:CDS 50.0%
TCCTGCACGTGAACACACAT+AGG + chr2.2:16852300-16852319 None:intergenic 50.0%
TGATGCGGGAGAGAATGAGT+TGG - chr2.2:16852016-16852035 MS.gene060630:CDS 50.0%
TGGTCACAACCATGTGCTGT+TGG - chr2.2:16852457-16852476 MS.gene060630:intron 50.0%
TGGTTCCAAATCACCTTCGG+GGG + chr2.2:16852084-16852103 None:intergenic 50.0%
! CACAACCATGTGCTGTTGGA+TGG - chr2.2:16852461-16852480 MS.gene060630:intron 50.0%
! GCACGACGTTTCCTTTTCTC+GGG + chr2.2:16852347-16852366 None:intergenic 50.0%
CAACTCCCCCGAAGGTGATT+TGG - chr2.2:16852076-16852095 MS.gene060630:CDS 55.0%
GCAATGGCAAACGCTTCTGG+TGG - chr2.2:16852590-16852609 MS.gene060630:CDS 55.0%
GGTGCAATGGCAAACGCTTC+TGG - chr2.2:16852587-16852606 MS.gene060630:CDS 55.0%
TCGACATTCACACCAGGCGA+TGG - chr2.2:16852414-16852433 MS.gene060630:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 16851834 16852622 16851834 ID=MS.gene060630
chr2.2 mRNA 16851834 16852622 16851834 ID=MS.gene060630.t1;Parent=MS.gene060630
chr2.2 exon 16852557 16852622 16852557 ID=MS.gene060630.t1.exon1;Parent=MS.gene060630.t1
chr2.2 CDS 16852557 16852622 16852557 ID=cds.MS.gene060630.t1;Parent=MS.gene060630.t1
chr2.2 exon 16851834 16852463 16851834 ID=MS.gene060630.t1.exon2;Parent=MS.gene060630.t1
chr2.2 CDS 16851834 16852463 16851834 ID=cds.MS.gene060630.t1;Parent=MS.gene060630.t1
Gene Sequence

>MS.gene060630

ATGGAAGGCGGTTCACAAGTAGGAAACAGTCATTCACACGCGGACCAATCATCATATGATTCGTTGGTAAGGCTCAATCCATTAGCAAATTTTCCAATAACAAAAAAATTTGTGTGTGTTCTGCAATCATGGTGATTGTGACTTTTTTCCCCACAAGAGTGTGATGATGTTTTAAGCAGCCATGATGCGGGAGAGAATGAGTTGGACGAAGAATTGGAAGGTTTAAGCCATGGAATTGGAAACAACTCCCCCGAAGGTGATTTGGAACCAATAAACATAGATTGCCTCCCTGATATTTTGAAGATTGATATGAACAACATTTCCTTCGAAGAAGTTGAGAGGTACAACTTTGGTGACTTAGATGCTGCCTACCAGTTCTACTACTGGTTTGGGAGAAGAAAAGGATTCTCTATTTATAAGAGTCTGATGATAAGGAATCGTACGGGAGACATTTTCCAACAAACCTATGTGTGTTCACGTGCAGGATTTAGAGAAGATCGTGGATTAACACCCGAGAAAAGGAAACGTCGTGCTAGAAATGAAACAAGATGCGGATGTCAAGCAAACTTCAGAGTACATGTCGACATTCACACCAGGCGATGGTATGTCACAATTTTTGAATTTGGTCACAACCATGTGCTGTTGGATGGAATGATGTGCGGTCTACTAGCAGCGCATAGAAAATTGTCAAAATTGGATGTACAGGATATTCGGAGTAATAACAACGTTGGTATAAGACCATATCAGATGTACGGTGCAATGGCAAACGCTTCTGGTGGTTTCCACTAG
Protein sequence

>MS.gene060630.t1

MEGGSQVGNSHSHADQSSYDSLCDDVLSSHDAGENELDEELEGLSHGIGNNSPEGDLEPINIDCLPDILKIDMNNISFEEVERYNFGDLDAAYQFYYWFGRRKGFSIYKSLMIRNRTGDIFQQTYVCSRAGFREDRGLTPEKRKRRARNETRCGCQANFRVHVDIHTRRWYVTIFEFGHNHVLLDGMMCGLLAAHRKLSKLDVQDIRSNNNVGIRPYQMYGAMANASGGFH