AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280006312.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006312.01.T01 MTR_2g014550 48.352 182 89 3 31 208 28 208 2.79e-56 178
MsG0280006312.01.T01 MTR_2g014520 48.352 182 89 3 31 208 25 205 1.69e-55 176
MsG0280006312.01.T01 MTR_4g088335 46.995 183 92 3 30 208 23 204 2.45e-55 175
MsG0280006312.01.T01 MTR_4g078870 44.509 173 90 4 41 208 32 203 8.94e-46 150
MsG0280006312.01.T01 MTR_2g020850 40.099 202 109 3 12 212 1 191 1.09e-44 148
MsG0280006312.01.T01 MTR_5g044580 37.383 214 115 5 9 204 2 214 2.01e-38 132
MsG0280006312.01.T01 MTR_7g010890 39.000 200 110 5 12 204 20 214 4.91e-38 131
MsG0280006312.01.T01 MTR_4g118470 40.588 170 98 3 41 208 29 197 1.13e-36 128
MsG0280006312.01.T01 MTR_4g118480 40.588 170 98 3 41 208 27 195 1.81e-36 127
MsG0280006312.01.T02 MTR_4g088335 47.120 191 90 5 30 218 23 204 1.36e-56 179
MsG0280006312.01.T02 MTR_2g014550 47.090 189 91 3 31 218 28 208 1.97e-56 179
MsG0280006312.01.T02 MTR_2g014520 47.090 189 91 3 31 218 25 205 1.27e-55 176
MsG0280006312.01.T02 MTR_4g078870 44.199 181 89 5 41 218 32 203 9.19e-46 151
MsG0280006312.01.T02 MTR_2g020850 39.151 212 107 5 12 222 1 191 1.08e-42 143
MsG0280006312.01.T02 MTR_5g044580 40.541 185 98 5 34 214 38 214 2.36e-39 135
MsG0280006312.01.T02 MTR_7g010890 37.681 207 113 6 12 214 20 214 2.69e-38 132
MsG0280006312.01.T02 MTR_4g118470 39.106 179 98 4 41 218 29 197 4.00e-36 127
MsG0280006312.01.T02 MTR_4g118480 39.106 179 98 4 41 218 27 195 5.41e-36 126
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006312.01.T01 AT3G02430 51.869 214 96 3 1 208 1 213 1.01e-68 210
MsG0280006312.01.T01 AT4G24310 53.953 215 78 5 2 208 6 207 2.51e-66 203
MsG0280006312.01.T01 AT4G18425 49.697 165 78 4 48 208 48 211 1.96e-49 160
MsG0280006312.01.T01 AT5G46090 48.485 165 80 4 48 208 49 212 4.52e-47 154
MsG0280006312.01.T01 AT4G28485 43.011 186 97 5 31 208 14 198 8.85e-42 140
MsG0280006312.01.T01 AT3G21550 44.444 162 86 3 46 206 14 172 1.88e-37 129
MsG0280006312.01.T01 AT3G21520 40.491 163 95 2 44 205 26 187 1.08e-36 127
MsG0280006312.01.T01 AT1G09157 38.674 181 92 4 41 204 61 239 4.37e-33 119
MsG0280006312.01.T01 AT5G39650 37.778 180 95 3 41 204 62 240 6.80e-32 116
MsG0280006312.01.T01 AT5G27370 38.333 180 91 7 44 204 8 186 7.38e-28 104
MsG0280006312.01.T01 AT4G28485 41.414 99 54 2 114 208 65 163 3.81e-17 75.9
MsG0280006312.01.T02 AT3G02430 51.598 219 99 4 1 218 1 213 1.63e-68 209
MsG0280006312.01.T02 AT4G24310 54.545 220 79 7 2 218 6 207 4.24e-66 203
MsG0280006312.01.T02 AT4G18425 49.711 173 76 5 48 218 48 211 1.12e-50 164
MsG0280006312.01.T02 AT5G46090 48.555 173 78 5 48 218 49 212 2.35e-48 158
MsG0280006312.01.T02 AT4G28485 46.409 181 87 5 40 218 26 198 2.66e-41 139
MsG0280006312.01.T02 AT3G21550 43.023 172 84 4 46 216 14 172 1.90e-36 127
MsG0280006312.01.T02 AT1G09157 38.889 180 103 3 41 214 61 239 2.16e-34 123
MsG0280006312.01.T02 AT5G39650 39.444 180 102 4 41 214 62 240 8.86e-34 121
MsG0280006312.01.T02 AT3G21520 38.150 173 95 3 44 215 26 187 1.57e-33 120
MsG0280006312.01.T02 AT5G27370 37.778 180 102 6 44 214 8 186 3.73e-28 105
MsG0280006312.01.T02 AT4G28485 45.283 106 50 3 114 218 65 163 1.02e-16 75.1

Find 56 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCAGATTGCTTATTAT+TGG 0.102422 2:+342994 None:intergenic
CATGTATTGTAGTAATTATT+TGG 0.171435 2:+342349 None:intergenic
GAATTGGGTGCAGGTGTAAC+AGG 0.307857 2:+342371 None:intergenic
GATATTGTGCCACTCGGAAT+TGG 0.345690 2:-342452 MsG0280006312.01.T02:CDS
TTGTAGTAATTATTTGGAAT+TGG 0.347051 2:+342355 None:intergenic
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2:+342828 None:intergenic
TGTAGTAATTATTTGGAATT+GGG 0.358228 2:+342356 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2:+342486 None:intergenic
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2:-342735 MsG0280006312.01.T02:CDS
TGTTCTTTGCTGTTGCATTA+AGG 0.381421 2:-342532 MsG0280006312.01.T02:CDS
CCATGGCATCGCAACCTTCA+AGG 0.392282 2:-342678 MsG0280006312.01.T02:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2:-342899 MsG0280006312.01.T02:CDS
AAATGCATGTACAAAGTCAA+TGG 0.433016 2:+342568 None:intergenic
AGTAGTATCTGGAGCATTAA+CGG 0.435471 2:-342900 MsG0280006312.01.T02:CDS
CGACGGTCAGTAGTAGTATC+TGG 0.437746 2:-342911 MsG0280006312.01.T02:CDS
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2:+342485 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2:-342670 MsG0280006312.01.T02:CDS
AATTATTTGGAATTGGGTGC+AGG 0.485423 2:+342362 None:intergenic
GCAACCACGCCGTGTGACTA+AGG 0.489093 2:-342483 MsG0280006312.01.T02:CDS
AATAATAAGCAATCTGAAGC+AGG 0.489383 2:-342992 MsG0280006312.01.T02:CDS
CATGGCATCGCAACCTTCAA+GGG 0.499059 2:-342677 MsG0280006312.01.T02:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2:+342815 None:intergenic
GCAGCAGCACATGGAATTAG+TGG 0.505993 2:-342944 MsG0280006312.01.T02:CDS
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2:+342664 None:intergenic
CCAACCACTAGACATGGGAT+TGG 0.514072 2:-342398 MsG0280006312.01.T02:CDS
TTATACTTGCTCAACTCAGC+TGG 0.520275 2:+342599 None:intergenic
GGGAAGTAAGTTAGCCAAGT+TGG 0.532273 2:+342871 None:intergenic
AATGCATGTACAAAGTCAAT+GGG 0.533496 2:+342569 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2:+342837 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.540652 2:-342885 MsG0280006312.01.T02:CDS
AGTTGAGCAAGTATAAGATC+AGG 0.557038 2:-342592 MsG0280006312.01.T02:CDS
ATTTGATTACTCACCCGTCA+TGG 0.558183 2:-342645 MsG0280006312.01.T02:CDS
CCAATCCCATGTCTAGTGGT+TGG 0.561333 2:+342398 None:intergenic
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2:+342678 None:intergenic
GTACTACTACTGTCCATGAC+GGG 0.572356 2:+342632 None:intergenic
GCATCAGCAGCAGCAGCACA+TGG 0.574320 2:-342953 MsG0280006312.01.T02:CDS
ACAGTGAATAATGCATCAGA+TGG 0.586121 2:-342710 MsG0280006312.01.T02:CDS
TTGGCTAACTTACTTCCCAC+AGG 0.590824 2:-342866 MsG0280006312.01.T02:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2:+342850 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2:+342756 None:intergenic
GTTCTTGATATTGTGCCACT+CGG 0.614142 2:-342458 MsG0280006312.01.T02:CDS
AATAAGCAATCTGAAGCAGG+TGG 0.615428 2:-342989 MsG0280006312.01.T02:CDS
GTAGCCAATCCCATGTCTAG+TGG 0.615835 2:+342394 None:intergenic
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2:+342784 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2:+342474 None:intergenic
TGTACTACTACTGTCCATGA+CGG 0.632264 2:+342631 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2:+342729 None:intergenic
AATTGGGTGCAGGTGTAACA+GGG 0.642036 2:+342372 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2:+342479 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2:-342818 MsG0280006312.01.T02:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2:-342898 MsG0280006312.01.T02:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2:-342695 MsG0280006312.01.T02:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2:-342480 MsG0280006312.01.T02:CDS
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2:+342851 None:intergenic
CATAGGAATCCAATTCCGAG+TGG 0.746885 2:+342443 None:intergenic
TTAGTGGTAAACGACGACGA+CGG 0.769975 2:-342928 MsG0280006312.01.T02:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAATGCATGTACAAAGTCAA+TGG + Chr2:342815-342834 None:intergenic 30.0%
AATGCATGTACAAAGTCAAT+GGG + Chr2:342814-342833 None:intergenic 30.0%
TGCTTCAGATTGCTTATTAT+TGG + Chr2:342389-342408 None:intergenic 30.0%
! AATAATAAGCAATCTGAAGC+AGG - Chr2:342388-342407 MsG0280006312.01.T02:CDS 30.0%
ACAGTGAATAATGCATCAGA+TGG - Chr2:342670-342689 MsG0280006312.01.T02:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG - Chr2:342788-342807 MsG0280006312.01.T02:CDS 35.0%
! AGTAGTATCTGGAGCATTAA+CGG - Chr2:342480-342499 MsG0280006312.01.T02:CDS 35.0%
! TTTTTCCAACCACTAGACAT+GGG - Chr2:342977-342996 MsG0280006312.01.T02:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG - Chr2:342848-342867 MsG0280006312.01.T02:CDS 35.0%
AAGTGTGAGAATGCGAGTAA+CGG + Chr2:342599-342618 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG + Chr2:342627-342646 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG - Chr2:342645-342664 MsG0280006312.01.T02:CDS 40.0%
ATTTGATTACTCACCCGTCA+TGG - Chr2:342735-342754 MsG0280006312.01.T02:CDS 40.0%
CGACAAAAAGCAAAGTGCAT+AGG + Chr2:342957-342976 None:intergenic 40.0%
TCAGATGGAAGAATCTACCA+TGG - Chr2:342685-342704 MsG0280006312.01.T02:CDS 40.0%
TGTACTACTACTGTCCATGA+CGG + Chr2:342752-342771 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG + Chr2:342784-342803 None:intergenic 40.0%
! AATAAGCAATCTGAAGCAGG+TGG - Chr2:342391-342410 MsG0280006312.01.T02:CDS 40.0%
! GTAGTATCTGGAGCATTAAC+GGG - Chr2:342481-342500 MsG0280006312.01.T02:CDS 40.0%
! GTTCTTGATATTGTGCCACT+CGG - Chr2:342922-342941 MsG0280006312.01.T02:CDS 40.0%
! GTTTTTCCAACCACTAGACA+TGG - Chr2:342976-342995 MsG0280006312.01.T02:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG - Chr2:342482-342501 MsG0280006312.01.T02:CDS 40.0%
AAATAGCCAGAGACCCTTGA+AGG + Chr2:342719-342738 None:intergenic 45.0%
AATTGGGTGCAGGTGTAACA+GGG + Chr2:343011-343030 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG - Chr2:342562-342581 MsG0280006312.01.T02:CDS 45.0%
CAAGAACCTCCTTAGTCACA+CGG + Chr2:342909-342928 None:intergenic 45.0%
CATAGGAATCCAATTCCGAG+TGG + Chr2:342940-342959 None:intergenic 45.0%
GGGAAGTAAGTTAGCCAAGT+TGG + Chr2:342512-342531 None:intergenic 45.0%
GTACTACTACTGTCCATGAC+GGG + Chr2:342751-342770 None:intergenic 45.0%
TTAGTGGTAAACGACGACGA+CGG - Chr2:342452-342471 MsG0280006312.01.T02:CDS 45.0%
TTGGCTAACTTACTTCCCAC+AGG - Chr2:342514-342533 MsG0280006312.01.T02:CDS 45.0%
! GATATTGTGCCACTCGGAAT+TGG - Chr2:342928-342947 MsG0280006312.01.T02:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG + Chr2:342532-342551 None:intergenic 45.0%
ATTAACGGGGACAGCCAACT+TGG - Chr2:342495-342514 MsG0280006312.01.T02:CDS 50.0%
CATGGCATCGCAACCTTCAA+GGG - Chr2:342703-342722 MsG0280006312.01.T02:CDS 50.0%
CCAACCACTAGACATGGGAT+TGG - Chr2:342982-343001 MsG0280006312.01.T02:CDS 50.0%
CCAATCCCATGTCTAGTGGT+TGG + Chr2:342985-343004 None:intergenic 50.0%
CGACGGTCAGTAGTAGTATC+TGG - Chr2:342469-342488 MsG0280006312.01.T02:CDS 50.0%
CTGTGTCCGTGAAACAAGCA+AGG + Chr2:342654-342673 None:intergenic 50.0%
GAATTGGGTGCAGGTGTAAC+AGG + Chr2:343012-343031 None:intergenic 50.0%
GCAGCAGCACATGGAATTAG+TGG - Chr2:342436-342455 MsG0280006312.01.T02:CDS 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG + Chr2:342568-342587 None:intergenic 50.0%
GTAGCCAATCCCATGTCTAG+TGG + Chr2:342989-343008 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG + Chr2:342555-342574 None:intergenic 50.0%
! GCGTGAGAATCTGGAATGCT+AGG + Chr2:342546-342565 None:intergenic 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG + Chr2:342533-342552 None:intergenic 50.0%
CCATGGCATCGCAACCTTCA+AGG - Chr2:342702-342721 MsG0280006312.01.T02:CDS 55.0%
CCTTGAAGGTTGCGATGCCA+TGG + Chr2:342705-342724 None:intergenic 55.0%
TCGCAACCTTCAAGGGTCTC+TGG - Chr2:342710-342729 MsG0280006312.01.T02:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG + Chr2:342898-342917 None:intergenic 55.0%
ACCACGCCGTGTGACTAAGG+AGG - Chr2:342900-342919 MsG0280006312.01.T02:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG + Chr2:342904-342923 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG - Chr2:342897-342916 MsG0280006312.01.T02:CDS 60.0%
GCATCAGCAGCAGCAGCACA+TGG - Chr2:342427-342446 MsG0280006312.01.T02:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG + Chr2:342897-342916 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 342364 343038 342364 ID=MsG0280006312.01;Name=MsG0280006312.01
Chr2 mRNA 342364 343038 342364 ID=MsG0280006312.01.T01;Parent=MsG0280006312.01;Name=MsG0280006312.01.T01;_AED=0.49;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|214
Chr2 exon 342364 342612 342364 ID=MsG0280006312.01.T01:exon:611;Parent=MsG0280006312.01.T01
Chr2 exon 342643 343038 342643 ID=MsG0280006312.01.T01:exon:610;Parent=MsG0280006312.01.T01
Chr2 CDS 342643 343038 342643 ID=MsG0280006312.01.T01:cds;Parent=MsG0280006312.01.T01
Chr2 CDS 342364 342612 342364 ID=MsG0280006312.01.T01:cds;Parent=MsG0280006312.01.T01
Chr2 mRNA 342364 343038 342364 ID=MsG0280006312.01.T02;Parent=MsG0280006312.01;Name=MsG0280006312.01.T02;_AED=0.49;_eAED=0.49;_QI=0|-1|0|1|-1|0|1|0|224
Chr2 exon 342364 343038 342364 ID=MsG0280006312.01.T02:exon:612;Parent=MsG0280006312.01.T02
Chr2 CDS 342364 343038 342364 ID=MsG0280006312.01.T02:cds;Parent=MsG0280006312.01.T02
Gene Sequence

>MsG0280006312.01.T01

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGGTGGATCATCATCATCAGCATCAGCAGCAGCAGCACATGGAATTAGTGGTAAACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCTAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCATGGACTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGATAACATGTGTTACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACTAGACATGGGATTGGCTACCCTGTTACACCTGCACCCAATTCCAAATAA

>MsG0280006312.01.T02

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGGTGGATCATCATCATCAGCATCAGCAGCAGCAGCACATGGAATTAGTGGTAAACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCTAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGATAACATGTGTTACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACTAGACATGGGATTGGCTACCCTGTTACACCTGCACCCAATTCCAAATAA

Protein sequence

>MsG0280006312.01.T01

MSVTQRRSNNKQSEAGGSSSSASAAAAHGISGKRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVMDLSKYKIRPIDFVHAFLSVFVFFAVALRITCVTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPAPNSK*

>MsG0280006312.01.T02

MSVTQRRSNNKQSEAGGSSSSASAAAAHGISGKRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVMDSSSTIILPAELSKYKIRPIDFVHAFLSVFVFFAVALRITCVTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPAPNSK*