AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0230810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230810 MtrunA17_Chr4g0046521 49.457 184 79 4 40 222 34 204 3.10e-60 188
Msa0230810 MtrunA17_Chr2g0282811 48.691 191 84 3 34 222 30 208 3.37e-60 188
Msa0230810 MtrunA17_Chr2g0282791 47.644 191 86 3 34 222 27 205 1.68e-58 184
Msa0230810 MtrunA17_Chr4g0040531 43.784 185 89 4 40 222 32 203 1.06e-48 159
Msa0230810 MtrunA17_Chr2g0286871 41.899 179 89 3 44 222 24 187 5.68e-43 144
Msa0230810 MtrunA17_Chr5g0419161 39.683 189 100 4 32 218 38 214 3.12e-41 140
Msa0230810 MtrunA17_Chr7g0217511 39.153 189 101 4 32 218 38 214 3.99e-39 135
Msa0230810 MtrunA17_Chr4g0066491 37.186 199 111 4 24 222 15 199 4.70e-38 132
Msa0230810 MtrunA17_Chr4g0066481 39.344 183 97 4 40 222 29 197 7.07e-38 131
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230810 AT3G02430.1 52.995 217 92 3 6 222 7 213 1.03e-71 218
Msa0230810 AT4G24310.1 53.394 221 84 4 2 222 6 207 9.70e-70 213
Msa0230810 AT4G18425.1 49.153 177 76 4 47 222 48 211 1.67e-53 172
Msa0230810 AT5G46090.1 48.588 177 77 4 47 222 49 212 4.79e-52 168
Msa0230810 AT4G28485.2 45.178 197 93 5 29 222 14 198 2.95e-45 150
Msa0230810 AT3G21550.1 42.614 176 84 3 45 220 14 172 4.99e-39 134
Msa0230810 AT1G09157.1 38.889 180 108 2 40 218 61 239 4.75e-37 130
Msa0230810 AT3G21520.1 38.418 177 94 3 43 219 26 187 3.87e-36 127
Msa0230810 AT5G39650.1 38.889 180 108 2 40 218 62 240 4.75e-36 128
Msa0230810 AT5G27370.1 37.705 183 103 5 43 218 8 186 1.79e-29 109
Msa0230810 AT4G28485.1 44.545 110 50 2 113 222 65 163 6.18e-20 84.0

Find 58 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCAGATTGCTTATTAT+TGG 0.102422 2_2:+3024939 None:intergenic
GTACTCCTAGTAATTATATT+TGG 0.194804 2_2:+3024264 None:intergenic
CTAGTAATTATATTTGGAAT+TGG 0.267098 2_2:+3024270 None:intergenic
TGTTCTTTGCTGTTGCATTA+AGG 0.305960 2_2:-3024468 Msa0230810:CDS
GGTGCAGGTGTAGGTGTAAC+AGG 0.338425 2_2:+3024304 None:intergenic
GATATTGTGCCACTCGGAAT+TGG 0.345690 2_2:-3024385 Msa0230810:CDS
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2_2:+3024776 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2_2:+3024419 None:intergenic
GTTCTTTGCTGTTGCATTAA+GGG 0.365115 2_2:-3024467 Msa0230810:CDS
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2_2:-3024683 Msa0230810:CDS
TAGTAATTATATTTGGAATT+GGG 0.375012 2_2:+3024271 None:intergenic
CCATGGCATCGCAACCTTCA+AGG 0.392282 2_2:-3024626 Msa0230810:CDS
CGGTCAGTAGTAGTAGTATC+TGG 0.402996 2_2:-3024859 Msa0230810:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2_2:-3024847 Msa0230810:CDS
AAATGCATGTACAAAGTCAA+TGG 0.433016 2_2:+3024504 None:intergenic
AGTAGTATCTGGAGCATTAA+CGG 0.436177 2_2:-3024848 Msa0230810:CDS
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2_2:+3024418 None:intergenic
TTGGAATTGGGTGCAGCAGC+AGG 0.459846 2_2:+3024283 None:intergenic
TTGGGTGCAGCAGCAGGTGC+AGG 0.468002 2_2:+3024289 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2_2:-3024618 Msa0230810:CDS
GCAGCAGCACATGGAATTAG+TGG 0.477735 2_2:-3024895 Msa0230810:CDS
CAATTCCAAATATAATTACT+AGG 0.486361 2_2:-3024269 None:intergenic
GCAGCAGCAGGTGCAGGTGT+AGG 0.488422 2_2:+3024295 None:intergenic
GCAACCACGCCGTGTGACTA+AGG 0.489093 2_2:-3024416 Msa0230810:CDS
CATGGCATCGCAACCTTCAA+GGG 0.499059 2_2:-3024625 Msa0230810:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2_2:+3024763 None:intergenic
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2_2:+3024612 None:intergenic
CCAACCACTAGACATGGGAT+TGG 0.514072 2_2:-3024331 Msa0230810:CDS
TTATACTTGCTCAACTCAGC+TGG 0.520275 2_2:+3024535 None:intergenic
GGGAAGTAAGTTTGCCAAGT+TGG 0.532415 2_2:+3024819 None:intergenic
AATGCATGTACAAAGTCAAT+GGG 0.533496 2_2:+3024505 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2_2:+3024785 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.539398 2_2:-3024833 Msa0230810:CDS
AATAAGCAATCTGAAGCAGA+TGG 0.548858 2_2:-3024934 Msa0230810:CDS
TCCATGACATTGACATTGAC+GGG 0.550083 2_2:+3024580 None:intergenic
AGTTGAGCAAGTATAAGATC+AGG 0.557038 2_2:-3024528 Msa0230810:CDS
CCAATCCCATGTCTAGTGGT+TGG 0.561333 2_2:+3024331 None:intergenic
GTCCATGACATTGACATTGA+CGG 0.563837 2_2:+3024579 None:intergenic
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2_2:+3024626 None:intergenic
ACCCGTCAATGTCAATGTCA+TGG 0.570259 2_2:-3024581 Msa0230810:CDS
ACAGTGAATAATGCATCAGA+TGG 0.586121 2_2:-3024658 Msa0230810:CDS
TTGGCAAACTTACTTCCCAC+AGG 0.590824 2_2:-3024814 Msa0230810:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2_2:+3024798 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2_2:+3024704 None:intergenic
GTTCTTGATATTGTGCCACT+CGG 0.614142 2_2:-3024391 Msa0230810:CDS
GTAGCCAATCCCATGTCTAG+TGG 0.615835 2_2:+3024327 None:intergenic
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2_2:+3024732 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2_2:+3024407 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2_2:+3024677 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2_2:+3024412 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2_2:-3024766 Msa0230810:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2_2:-3024846 Msa0230810:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2_2:-3024643 Msa0230810:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2_2:-3024413 Msa0230810:CDS
GTGCAGGTGTAGGTGTAACA+GGG 0.699596 2_2:+3024305 None:intergenic
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2_2:+3024799 None:intergenic
TTAGTGGTAGACGACGACGA+CGG 0.728627 2_2:-3024879 Msa0230810:CDS
CATAGGAATCCAATTCCGAG+TGG 0.746885 2_2:+3024376 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGTAATTATATTTGGAATT+GGG + chr2_2:3024963-3024982 None:intergenic 15.0%
!!! CTAGTAATTATATTTGGAAT+TGG + chr2_2:3024964-3024983 None:intergenic 20.0%
TGCTTCAGATTGCTTATTAT+TGG + chr2_2:3024295-3024314 None:intergenic 30.0%
AATGCATGTACAAAGTCAAT+GGG + chr2_2:3024729-3024748 None:intergenic 30.0%
AAATGCATGTACAAAGTCAA+TGG + chr2_2:3024730-3024749 None:intergenic 30.0%
! AATAAGCAATCTGAAGCAGA+TGG - chr2_2:3024297-3024316 Msa0230810:CDS 35.0%
! AGTAGTATCTGGAGCATTAA+CGG - chr2_2:3024383-3024402 Msa0230810:CDS 35.0%
ACAGTGAATAATGCATCAGA+TGG - chr2_2:3024573-3024592 Msa0230810:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG - chr2_2:3024703-3024722 Msa0230810:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG - chr2_2:3024763-3024782 Msa0230810:CDS 35.0%
!! GTTCTTTGCTGTTGCATTAA+GGG - chr2_2:3024764-3024783 Msa0230810:CDS 35.0%
! TTTTTCCAACCACTAGACAT+GGG - chr2_2:3024895-3024914 Msa0230810:CDS 35.0%
! GTAGTATCTGGAGCATTAAC+GGG - chr2_2:3024384-3024403 Msa0230810:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG - chr2_2:3024385-3024404 Msa0230810:CDS 40.0%
AAGTGTGAGAATGCGAGTAA+CGG + chr2_2:3024502-3024521 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG + chr2_2:3024530-3024549 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG - chr2_2:3024548-3024567 Msa0230810:CDS 40.0%
TCAGATGGAAGAATCTACCA+TGG - chr2_2:3024588-3024607 Msa0230810:CDS 40.0%
TCCATGACATTGACATTGAC+GGG + chr2_2:3024654-3024673 None:intergenic 40.0%
GTCCATGACATTGACATTGA+CGG + chr2_2:3024655-3024674 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG + chr2_2:3024699-3024718 None:intergenic 40.0%
! GTTCTTGATATTGTGCCACT+CGG - chr2_2:3024840-3024859 Msa0230810:CDS 40.0%
CGACAAAAAGCAAAGTGCAT+AGG + chr2_2:3024875-3024894 None:intergenic 40.0%
! GTTTTTCCAACCACTAGACA+TGG - chr2_2:3024894-3024913 Msa0230810:CDS 40.0%
CGGTCAGTAGTAGTAGTATC+TGG - chr2_2:3024372-3024391 Msa0230810:CDS 45.0%
GGGAAGTAAGTTTGCCAAGT+TGG + chr2_2:3024415-3024434 None:intergenic 45.0%
TTGGCAAACTTACTTCCCAC+AGG - chr2_2:3024417-3024436 Msa0230810:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG + chr2_2:3024435-3024454 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG - chr2_2:3024465-3024484 Msa0230810:CDS 45.0%
AAATAGCCAGAGACCCTTGA+AGG + chr2_2:3024622-3024641 None:intergenic 45.0%
ACCCGTCAATGTCAATGTCA+TGG - chr2_2:3024650-3024669 Msa0230810:CDS 45.0%
CAAGAACCTCCTTAGTCACA+CGG + chr2_2:3024827-3024846 None:intergenic 45.0%
! GATATTGTGCCACTCGGAAT+TGG - chr2_2:3024846-3024865 Msa0230810:CDS 45.0%
CATAGGAATCCAATTCCGAG+TGG + chr2_2:3024858-3024877 None:intergenic 45.0%
GCAGCAGCACATGGAATTAG+TGG - chr2_2:3024336-3024355 Msa0230810:CDS 50.0%
TTAGTGGTAGACGACGACGA+CGG - chr2_2:3024352-3024371 Msa0230810:CDS 50.0%
ATTAACGGGGACAGCCAACT+TGG - chr2_2:3024398-3024417 Msa0230810:CDS 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG + chr2_2:3024436-3024455 None:intergenic 50.0%
! GCGTGAGAATCTGGAATGCT+AGG + chr2_2:3024449-3024468 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG + chr2_2:3024458-3024477 None:intergenic 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG + chr2_2:3024471-3024490 None:intergenic 50.0%
CTGTGTCCGTGAAACAAGCA+AGG + chr2_2:3024557-3024576 None:intergenic 50.0%
CATGGCATCGCAACCTTCAA+GGG - chr2_2:3024606-3024625 Msa0230810:CDS 50.0%
CCAATCCCATGTCTAGTGGT+TGG + chr2_2:3024903-3024922 None:intergenic 50.0%
CCAACCACTAGACATGGGAT+TGG - chr2_2:3024900-3024919 Msa0230810:CDS 50.0%
GTAGCCAATCCCATGTCTAG+TGG + chr2_2:3024907-3024926 None:intergenic 50.0%
GTGCAGGTGTAGGTGTAACA+GGG + chr2_2:3024929-3024948 None:intergenic 50.0%
CCTTGAAGGTTGCGATGCCA+TGG + chr2_2:3024608-3024627 None:intergenic 55.0%
CCATGGCATCGCAACCTTCA+AGG - chr2_2:3024605-3024624 Msa0230810:CDS 55.0%
TCGCAACCTTCAAGGGTCTC+TGG - chr2_2:3024613-3024632 Msa0230810:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG + chr2_2:3024816-3024835 None:intergenic 55.0%
GGTGCAGGTGTAGGTGTAAC+AGG + chr2_2:3024930-3024949 None:intergenic 55.0%
TTGGAATTGGGTGCAGCAGC+AGG + chr2_2:3024951-3024970 None:intergenic 55.0%
TCAGCAGCAGCAGCAGCACA+TGG - chr2_2:3024327-3024346 Msa0230810:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG + chr2_2:3024815-3024834 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG - chr2_2:3024815-3024834 Msa0230810:CDS 60.0%
ACCACGCCGTGTGACTAAGG+AGG - chr2_2:3024818-3024837 Msa0230810:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG + chr2_2:3024822-3024841 None:intergenic 60.0%
GCAGCAGCAGGTGCAGGTGT+AGG + chr2_2:3024939-3024958 None:intergenic 65.0%
TTGGGTGCAGCAGCAGGTGC+AGG + chr2_2:3024945-3024964 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 3024270 3024983 3024270 ID=Msa0230810;Name=Msa0230810
chr2_2 mRNA 3024270 3024983 3024270 ID=Msa0230810-mRNA-1;Parent=Msa0230810;Name=Msa0230810-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|237
chr2_2 exon 3024270 3024983 3024270 ID=Msa0230810-mRNA-1:exon:1117;Parent=Msa0230810-mRNA-1
chr2_2 CDS 3024270 3024983 3024270 ID=Msa0230810-mRNA-1:cds;Parent=Msa0230810-mRNA-1
Gene Sequence

>Msa0230810

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGATGGATCATCATCAGCAGCAGCAGCAGCACATGGAATTAGTGGTAGACGACGACGACGGTCAGTAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCAAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCAATGTCAATGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGGATAACAATGTGTTGACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACTAGACATGGGATTGGCTACCCTGTTACACCTACACCTGCACCTGCTGCTGCACCCAATTCCAAATATAATTACTAG
Protein sequence

>Msa0230810

MSVTQRRSNNKQSEADGSSSAAAAAHGISGRRRRRSVVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVNVNVMDSSSTIILPAELSKYKIRPIDFVHAFLSVFVFFAVALRDNNVLTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPTPAPAAAPNSKYNY*