AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0188600

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188600 MtrunA17_Chr4g0046521 47.179 195 89 4 30 223 23 204 1.31e-60 189
Msa0188600 MtrunA17_Chr2g0282811 48.187 193 85 3 34 223 28 208 3.21e-60 188
Msa0188600 MtrunA17_Chr2g0282791 46.632 193 91 2 31 223 25 205 6.27e-59 185
Msa0188600 MtrunA17_Chr4g0040531 43.784 185 89 4 41 223 32 203 1.12e-48 158
Msa0188600 MtrunA17_Chr2g0286871 37.963 216 109 4 12 227 1 191 2.28e-44 147
Msa0188600 MtrunA17_Chr5g0419161 39.683 189 99 4 34 219 38 214 1.21e-41 141
Msa0188600 MtrunA17_Chr7g0217511 37.441 211 113 5 12 219 20 214 7.87e-41 139
Msa0188600 MtrunA17_Chr4g0066481 39.344 183 97 4 41 223 29 197 6.31e-38 131
Msa0188600 MtrunA17_Chr4g0066491 39.344 183 97 4 41 223 31 199 7.10e-38 131
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188600 AT3G02430.1 50.673 223 100 3 1 223 1 213 9.12e-70 213
Msa0188600 AT4G24310.1 52.703 222 85 4 2 223 6 207 5.41e-69 211
Msa0188600 AT4G18425.1 49.153 177 76 4 48 223 48 211 1.27e-53 172
Msa0188600 AT5G46090.1 45.312 192 91 4 33 223 34 212 3.33e-52 168
Msa0188600 AT4G28485.2 45.946 185 87 4 40 223 26 198 8.00e-45 149
Msa0188600 AT3G21550.1 42.614 176 84 3 46 221 14 172 4.35e-39 134
Msa0188600 AT1G09157.1 38.889 180 108 2 41 219 61 239 4.87e-37 130
Msa0188600 AT5G39650.1 38.889 180 108 2 41 219 62 240 2.99e-36 128
Msa0188600 AT3G21520.1 38.418 177 94 3 44 220 26 187 4.25e-36 127
Msa0188600 AT5G27370.1 37.705 183 103 5 44 219 8 186 1.57e-29 109
Msa0188600 AT4G28485.1 44.545 110 50 2 114 223 65 163 6.26e-20 83.6

Find 57 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCAGATTGCTTATTAT+TGG 0.102422 2_1:-3805596 None:intergenic
CATGTATTGTAGTAATTATT+TGG 0.171435 2_1:-3806256 None:intergenic
TGTTCTTTGCTGTTGCATTA+AGG 0.305960 2_1:+3806070 Msa0188600:CDS
GAATTGGGTGCAGGTGTAAC+AGG 0.307857 2_1:-3806234 None:intergenic
GATATTGTGCCACTCGGAAT+TGG 0.345690 2_1:+3806153 Msa0188600:CDS
TTGTAGTAATTATTTGGAAT+TGG 0.347051 2_1:-3806250 None:intergenic
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2_1:-3805762 None:intergenic
TGTAGTAATTATTTGGAATT+GGG 0.358228 2_1:-3806249 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2_1:-3806119 None:intergenic
GTTCTTTGCTGTTGCATTAA+GGG 0.365115 2_1:+3806071 Msa0188600:CDS
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2_1:+3805855 Msa0188600:CDS
CCATGGCATCGCAACCTTCA+AGG 0.392282 2_1:+3805912 Msa0188600:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2_1:+3805691 Msa0188600:CDS
AAATGCATGTACAAAGTCAA+TGG 0.433016 2_1:-3806034 None:intergenic
AGTAGTATCTGGAGCATTAA+CGG 0.435471 2_1:+3805690 Msa0188600:CDS
CGACGGTCAGTAGTAGTATC+TGG 0.437746 2_1:+3805679 Msa0188600:CDS
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2_1:-3806120 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2_1:+3805920 Msa0188600:CDS
GCAGCAGCACATGGAATTAG+TGG 0.477735 2_1:+3805646 Msa0188600:CDS
AATTATTTGGAATTGGGTGC+AGG 0.485423 2_1:-3806243 None:intergenic
GCAACCACGCCGTGTGACTA+AGG 0.489093 2_1:+3806122 Msa0188600:CDS
GCATCAGCAGCAGCAGCACA+TGG 0.489150 2_1:+3805637 Msa0188600:CDS
AATAATAAGCAATCTGAAGC+AGG 0.489383 2_1:+3805598 Msa0188600:CDS
CATGGCATCGCAACCTTCAA+GGG 0.499059 2_1:+3805913 Msa0188600:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2_1:-3805775 None:intergenic
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2_1:-3805926 None:intergenic
TTATACTTGCTCAACTCAGC+TGG 0.520275 2_1:-3806003 None:intergenic
GGGAAGTAAGTTTGCCAAGT+TGG 0.532415 2_1:-3805719 None:intergenic
CCAACCACAAGACATGGGAT+TGG 0.533310 2_1:+3806207 Msa0188600:CDS
AATGCATGTACAAAGTCAAT+GGG 0.533496 2_1:-3806033 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2_1:-3805753 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.539398 2_1:+3805705 Msa0188600:CDS
TCCATGACATTGACATTGAC+GGG 0.550083 2_1:-3805958 None:intergenic
AGTTGAGCAAGTATAAGATC+AGG 0.557038 2_1:+3806010 Msa0188600:CDS
CCAATCCCATGTCTTGTGGT+TGG 0.557682 2_1:-3806207 None:intergenic
GTAGCCAATCCCATGTCTTG+TGG 0.558071 2_1:-3806211 None:intergenic
GTCCATGACATTGACATTGA+CGG 0.563837 2_1:-3805959 None:intergenic
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2_1:-3805912 None:intergenic
ACCCGTCAATGTCAATGTCA+TGG 0.570259 2_1:+3805957 Msa0188600:CDS
ACAGTGAATAATGCATCAGA+TGG 0.586121 2_1:+3805880 Msa0188600:CDS
TTGGCAAACTTACTTCCCAC+AGG 0.590824 2_1:+3805724 Msa0188600:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2_1:-3805740 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2_1:-3805834 None:intergenic
GTTCTTGATATTGTGCCACT+CGG 0.614142 2_1:+3806147 Msa0188600:CDS
AATAAGCAATCTGAAGCAGG+TGG 0.615428 2_1:+3805601 Msa0188600:CDS
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2_1:-3805806 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2_1:-3806131 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2_1:-3805861 None:intergenic
AATTGGGTGCAGGTGTAACA+GGG 0.642036 2_1:-3806233 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2_1:-3806126 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2_1:+3805772 Msa0188600:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2_1:+3805692 Msa0188600:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2_1:+3805895 Msa0188600:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2_1:+3806125 Msa0188600:CDS
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2_1:-3805739 None:intergenic
TTAGTGGTAGACGACGACGA+CGG 0.728627 2_1:+3805662 Msa0188600:CDS
CATAGGAATCCAATTCCGAG+TGG 0.746885 2_1:-3806162 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGCTTCAGATTGCTTATTAT+TGG - chr2_1:3805599-3805618 None:intergenic 30.0%
! AATAATAAGCAATCTGAAGC+AGG + chr2_1:3805598-3805617 Msa0188600:CDS 30.0%
AATGCATGTACAAAGTCAAT+GGG - chr2_1:3806036-3806055 None:intergenic 30.0%
AAATGCATGTACAAAGTCAA+TGG - chr2_1:3806037-3806056 None:intergenic 30.0%
! AGTAGTATCTGGAGCATTAA+CGG + chr2_1:3805690-3805709 Msa0188600:CDS 35.0%
ACAGTGAATAATGCATCAGA+TGG + chr2_1:3805880-3805899 Msa0188600:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG + chr2_1:3806010-3806029 Msa0188600:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG + chr2_1:3806070-3806089 Msa0188600:CDS 35.0%
!! GTTCTTTGCTGTTGCATTAA+GGG + chr2_1:3806071-3806090 Msa0188600:CDS 35.0%
! TTTTTCCAACCACAAGACAT+GGG + chr2_1:3806202-3806221 Msa0188600:CDS 35.0%
! AATAAGCAATCTGAAGCAGG+TGG + chr2_1:3805601-3805620 Msa0188600:CDS 40.0%
! GTAGTATCTGGAGCATTAAC+GGG + chr2_1:3805691-3805710 Msa0188600:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG + chr2_1:3805692-3805711 Msa0188600:CDS 40.0%
AAGTGTGAGAATGCGAGTAA+CGG - chr2_1:3805809-3805828 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG - chr2_1:3805837-3805856 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG + chr2_1:3805855-3805874 Msa0188600:CDS 40.0%
TCAGATGGAAGAATCTACCA+TGG + chr2_1:3805895-3805914 Msa0188600:CDS 40.0%
TCCATGACATTGACATTGAC+GGG - chr2_1:3805961-3805980 None:intergenic 40.0%
GTCCATGACATTGACATTGA+CGG - chr2_1:3805962-3805981 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG - chr2_1:3806006-3806025 None:intergenic 40.0%
! GTTCTTGATATTGTGCCACT+CGG + chr2_1:3806147-3806166 Msa0188600:CDS 40.0%
CGACAAAAAGCAAAGTGCAT+AGG - chr2_1:3806182-3806201 None:intergenic 40.0%
! GTTTTTCCAACCACAAGACA+TGG + chr2_1:3806201-3806220 Msa0188600:CDS 40.0%
GGGAAGTAAGTTTGCCAAGT+TGG - chr2_1:3805722-3805741 None:intergenic 45.0%
TTGGCAAACTTACTTCCCAC+AGG + chr2_1:3805724-3805743 Msa0188600:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG - chr2_1:3805742-3805761 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG + chr2_1:3805772-3805791 Msa0188600:CDS 45.0%
AAATAGCCAGAGACCCTTGA+AGG - chr2_1:3805929-3805948 None:intergenic 45.0%
ACCCGTCAATGTCAATGTCA+TGG + chr2_1:3805957-3805976 Msa0188600:CDS 45.0%
CAAGAACCTCCTTAGTCACA+CGG - chr2_1:3806134-3806153 None:intergenic 45.0%
! GATATTGTGCCACTCGGAAT+TGG + chr2_1:3806153-3806172 Msa0188600:CDS 45.0%
CATAGGAATCCAATTCCGAG+TGG - chr2_1:3806165-3806184 None:intergenic 45.0%
AATTGGGTGCAGGTGTAACA+GGG - chr2_1:3806236-3806255 None:intergenic 45.0%
GCAGCAGCACATGGAATTAG+TGG + chr2_1:3805646-3805665 Msa0188600:CDS 50.0%
TTAGTGGTAGACGACGACGA+CGG + chr2_1:3805662-3805681 Msa0188600:CDS 50.0%
CGACGGTCAGTAGTAGTATC+TGG + chr2_1:3805679-3805698 Msa0188600:CDS 50.0%
ATTAACGGGGACAGCCAACT+TGG + chr2_1:3805705-3805724 Msa0188600:CDS 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG - chr2_1:3805743-3805762 None:intergenic 50.0%
! GCGTGAGAATCTGGAATGCT+AGG - chr2_1:3805756-3805775 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG - chr2_1:3805765-3805784 None:intergenic 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG - chr2_1:3805778-3805797 None:intergenic 50.0%
CTGTGTCCGTGAAACAAGCA+AGG - chr2_1:3805864-3805883 None:intergenic 50.0%
CATGGCATCGCAACCTTCAA+GGG + chr2_1:3805913-3805932 Msa0188600:CDS 50.0%
CCAATCCCATGTCTTGTGGT+TGG - chr2_1:3806210-3806229 None:intergenic 50.0%
CCAACCACAAGACATGGGAT+TGG + chr2_1:3806207-3806226 Msa0188600:CDS 50.0%
GTAGCCAATCCCATGTCTTG+TGG - chr2_1:3806214-3806233 None:intergenic 50.0%
GAATTGGGTGCAGGTGTAAC+AGG - chr2_1:3806237-3806256 None:intergenic 50.0%
CCTTGAAGGTTGCGATGCCA+TGG - chr2_1:3805915-3805934 None:intergenic 55.0%
CCATGGCATCGCAACCTTCA+AGG + chr2_1:3805912-3805931 Msa0188600:CDS 55.0%
TCGCAACCTTCAAGGGTCTC+TGG + chr2_1:3805920-3805939 Msa0188600:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG - chr2_1:3806123-3806142 None:intergenic 55.0%
GCATCAGCAGCAGCAGCACA+TGG + chr2_1:3805637-3805656 Msa0188600:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG - chr2_1:3806122-3806141 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG + chr2_1:3806122-3806141 Msa0188600:CDS 60.0%
ACCACGCCGTGTGACTAAGG+AGG + chr2_1:3806125-3806144 Msa0188600:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG - chr2_1:3806129-3806148 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 3805574 3806263 3805574 ID=Msa0188600;Name=Msa0188600
chr2_1 mRNA 3805574 3806263 3805574 ID=Msa0188600-mRNA-1;Parent=Msa0188600;Name=Msa0188600-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|229
chr2_1 exon 3805574 3806263 3805574 ID=Msa0188600-mRNA-1:exon:1608;Parent=Msa0188600-mRNA-1
chr2_1 CDS 3805574 3806263 3805574 ID=Msa0188600-mRNA-1:cds;Parent=Msa0188600-mRNA-1
Gene Sequence

>Msa0188600

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGGTGGATCATCATCAGCAGCATCAGCAGCAGCAGCACATGGAATTAGTGGTAGACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCAAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCAATGTCAATGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGGATAACAATGTGTTGACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACAAGACATGGGATTGGCTACCCTGTTACACCTGCACCCAATTCCAAATAA
Protein sequence

>Msa0188600

MSVTQRRSNNKQSEAGGSSSAASAAAAHGISGRRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVNVNVMDSSSTIILPAELSKYKIRPIDFVHAFLSVFVFFAVALRDNNVLTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPAPNSK*