AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene072079

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072079.t1 MTR_4g088335 48.168 191 89 4 31 220 23 204 4.14e-61 190
MS.gene072079.t1 MTR_2g014550 49.733 187 83 3 37 220 30 208 8.08e-61 190
MS.gene072079.t1 MTR_2g014520 47.619 189 91 2 32 220 25 205 1.97e-59 186
MS.gene072079.t1 MTR_4g078870 44.751 181 89 4 42 220 32 203 4.02e-49 160
MS.gene072079.t1 MTR_2g020850 39.303 201 111 3 24 224 2 191 1.50e-45 150
MS.gene072079.t1 MTR_5g044580 40.541 185 99 4 35 216 38 214 3.33e-42 142
MS.gene072079.t1 MTR_7g010890 37.681 207 114 5 13 216 20 214 3.94e-41 140
MS.gene072079.t1 MTR_4g118470 39.106 179 99 3 42 220 29 197 2.09e-39 135
MS.gene072079.t1 MTR_4g118480 39.106 179 99 3 42 220 27 195 3.14e-39 135
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072079.t1 AT3G02430 53.023 215 93 4 6 220 7 213 4.33e-70 214
MS.gene072079.t1 AT4G24310 54.338 219 83 5 2 220 6 207 5.52e-70 213
MS.gene072079.t1 AT4G18425 50.289 173 76 4 49 220 48 211 2.08e-54 174
MS.gene072079.t1 AT5G46090 46.277 188 91 4 34 220 34 212 7.89e-53 169
MS.gene072079.t1 AT4G28485 43.269 208 106 5 14 220 2 198 1.40e-45 150
MS.gene072079.t1 AT3G21550 43.605 172 84 3 47 218 14 172 6.61e-40 135
MS.gene072079.t1 AT1G09157 38.889 180 104 2 42 216 61 239 3.30e-37 130
MS.gene072079.t1 AT3G21520 38.728 173 95 2 45 217 26 187 6.32e-37 129
MS.gene072079.t1 AT5G39650 39.444 180 103 3 42 216 62 240 1.35e-36 129
MS.gene072079.t1 AT5G27370 37.778 180 103 5 45 216 8 186 3.35e-30 110
MS.gene072079.t1 AT4G28485 46.226 106 50 2 115 220 65 163 1.68e-20 85.1

Find 55 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 2.4:-76385100 None:intergenic
TATTGTAGTACTTAATTATT+TGG 0.108939 2.4:-76385751 None:intergenic
AGTACTTAATTATTTGGAAT+TGG 0.286533 2.4:-76385745 None:intergenic
TGTTCTTTGCTGTTGCATTA+AGG 0.305960 2.4:+76385565 MS.gene072079:CDS
GAATTGGGTGCAGGTGTAAC+AGG 0.307857 2.4:-76385729 None:intergenic
GATATTGTGCCACTCGGAAT+TGG 0.345690 2.4:+76385648 MS.gene072079:CDS
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2.4:-76385269 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2.4:-76385614 None:intergenic
GTTCTTTGCTGTTGCATTAA+GGG 0.365115 2.4:+76385566 MS.gene072079:CDS
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2.4:+76385362 MS.gene072079:CDS
GTACTTAATTATTTGGAATT+GGG 0.385140 2.4:-76385744 None:intergenic
CCATGGCATCGCAACCTTCA+AGG 0.392282 2.4:+76385419 MS.gene072079:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2.4:+76385198 MS.gene072079:CDS
AAATGCATGTACAAAGTCAA+TGG 0.433016 2.4:-76385529 None:intergenic
AGTAGTATCTGGAGCATTAA+CGG 0.435471 2.4:+76385197 MS.gene072079:CDS
CGACGGTCAGTAGTAGTATC+TGG 0.437746 2.4:+76385186 MS.gene072079:CDS
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2.4:-76385615 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2.4:+76385427 MS.gene072079:CDS
GCAGCAGCACATGGAATTAG+TGG 0.477735 2.4:+76385153 MS.gene072079:CDS
GCAACCACGCCGTGTGACTA+AGG 0.489093 2.4:+76385617 MS.gene072079:CDS
AATTATTTGGAATTGGGTGC+AGG 0.489308 2.4:-76385738 None:intergenic
CATGGCATCGCAACCTTCAA+GGG 0.499059 2.4:+76385420 MS.gene072079:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2.4:-76385282 None:intergenic
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2.4:-76385433 None:intergenic
TTATACTTGCTCAACTCAGC+TGG 0.520275 2.4:-76385498 None:intergenic
GGGAAGTAAGTTTGCCAAGT+TGG 0.532415 2.4:-76385226 None:intergenic
CCAACCACAAGACATGGGAT+TGG 0.533310 2.4:+76385702 MS.gene072079:CDS
AATGCATGTACAAAGTCAAT+GGG 0.533496 2.4:-76385528 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2.4:-76385260 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.539398 2.4:+76385212 MS.gene072079:CDS
AATAAGCAATCTGAAGCAGA+TGG 0.548858 2.4:+76385105 MS.gene072079:CDS
AGTTGAGCAAGTATAAGATC+AGG 0.557038 2.4:+76385505 MS.gene072079:CDS
CCAATCCCATGTCTTGTGGT+TGG 0.557682 2.4:-76385702 None:intergenic
GTAGCCAATCCCATGTCTTG+TGG 0.558071 2.4:-76385706 None:intergenic
ATTTGATTACTCACCCGTCA+TGG 0.558183 2.4:+76385452 MS.gene072079:CDS
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2.4:-76385419 None:intergenic
GTACTACTACTGTCCATGAC+GGG 0.572356 2.4:-76385465 None:intergenic
ACAGTGAATAATGCATCAGA+TGG 0.586121 2.4:+76385387 MS.gene072079:CDS
TTGGCAAACTTACTTCCCAC+AGG 0.590824 2.4:+76385231 MS.gene072079:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2.4:-76385247 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2.4:-76385341 None:intergenic
GTTCTTGATATTGTGCCACT+CGG 0.614142 2.4:+76385642 MS.gene072079:CDS
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2.4:-76385313 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2.4:-76385626 None:intergenic
TGTACTACTACTGTCCATGA+CGG 0.632264 2.4:-76385466 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2.4:-76385368 None:intergenic
AATTGGGTGCAGGTGTAACA+GGG 0.642036 2.4:-76385728 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2.4:-76385621 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2.4:+76385279 MS.gene072079:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2.4:+76385199 MS.gene072079:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2.4:+76385402 MS.gene072079:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2.4:+76385620 MS.gene072079:CDS
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2.4:-76385246 None:intergenic
TTAGTGGTAGACGACGACGA+CGG 0.728627 2.4:+76385169 MS.gene072079:CDS
CATAGGAATCCAATTCCGAG+TGG 0.746885 2.4:-76385657 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAATGCATGTACAAAGTCAA+TGG - chr2.4:76385532-76385551 None:intergenic 30.0%
AATGCATGTACAAAGTCAAT+GGG - chr2.4:76385531-76385550 None:intergenic 30.0%
TGCTTCAGATTGCTTATTAT+TGG - chr2.4:76385103-76385122 None:intergenic 30.0%
ACAGTGAATAATGCATCAGA+TGG + chr2.4:76385387-76385406 MS.gene072079:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG + chr2.4:76385505-76385524 MS.gene072079:CDS 35.0%
CGACAAAAAGTAAAGTGCAT+AGG - chr2.4:76385677-76385696 None:intergenic 35.0%
! AATAAGCAATCTGAAGCAGA+TGG + chr2.4:76385105-76385124 MS.gene072079:CDS 35.0%
! AGTAGTATCTGGAGCATTAA+CGG + chr2.4:76385197-76385216 MS.gene072079:CDS 35.0%
! TTTTTCCAACCACAAGACAT+GGG + chr2.4:76385697-76385716 MS.gene072079:CDS 35.0%
!! GTTCTTTGCTGTTGCATTAA+GGG + chr2.4:76385566-76385585 MS.gene072079:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG + chr2.4:76385565-76385584 MS.gene072079:CDS 35.0%
AAGTGTGAGAATGCGAGTAA+CGG - chr2.4:76385316-76385335 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG - chr2.4:76385344-76385363 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG + chr2.4:76385362-76385381 MS.gene072079:CDS 40.0%
ATTTGATTACTCACCCGTCA+TGG + chr2.4:76385452-76385471 MS.gene072079:CDS 40.0%
TCAGATGGAAGAATCTACCA+TGG + chr2.4:76385402-76385421 MS.gene072079:CDS 40.0%
TGTACTACTACTGTCCATGA+CGG - chr2.4:76385469-76385488 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG - chr2.4:76385501-76385520 None:intergenic 40.0%
! GTAGTATCTGGAGCATTAAC+GGG + chr2.4:76385198-76385217 MS.gene072079:CDS 40.0%
! GTTCTTGATATTGTGCCACT+CGG + chr2.4:76385642-76385661 MS.gene072079:CDS 40.0%
! GTTTTTCCAACCACAAGACA+TGG + chr2.4:76385696-76385715 MS.gene072079:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG + chr2.4:76385199-76385218 MS.gene072079:CDS 40.0%
AAATAGCCAGAGACCCTTGA+AGG - chr2.4:76385436-76385455 None:intergenic 45.0%
AATTGGGTGCAGGTGTAACA+GGG - chr2.4:76385731-76385750 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG + chr2.4:76385279-76385298 MS.gene072079:CDS 45.0%
CAAGAACCTCCTTAGTCACA+CGG - chr2.4:76385629-76385648 None:intergenic 45.0%
CATAGGAATCCAATTCCGAG+TGG - chr2.4:76385660-76385679 None:intergenic 45.0%
GGGAAGTAAGTTTGCCAAGT+TGG - chr2.4:76385229-76385248 None:intergenic 45.0%
GTACTACTACTGTCCATGAC+GGG - chr2.4:76385468-76385487 None:intergenic 45.0%
TTGGCAAACTTACTTCCCAC+AGG + chr2.4:76385231-76385250 MS.gene072079:CDS 45.0%
! GATATTGTGCCACTCGGAAT+TGG + chr2.4:76385648-76385667 MS.gene072079:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG - chr2.4:76385249-76385268 None:intergenic 45.0%
ATTAACGGGGACAGCCAACT+TGG + chr2.4:76385212-76385231 MS.gene072079:CDS 50.0%
CATGGCATCGCAACCTTCAA+GGG + chr2.4:76385420-76385439 MS.gene072079:CDS 50.0%
CCAACCACAAGACATGGGAT+TGG + chr2.4:76385702-76385721 MS.gene072079:CDS 50.0%
CCAATCCCATGTCTTGTGGT+TGG - chr2.4:76385705-76385724 None:intergenic 50.0%
CGACGGTCAGTAGTAGTATC+TGG + chr2.4:76385186-76385205 MS.gene072079:CDS 50.0%
CTGTGTCCGTGAAACAAGCA+AGG - chr2.4:76385371-76385390 None:intergenic 50.0%
GAATTGGGTGCAGGTGTAAC+AGG - chr2.4:76385732-76385751 None:intergenic 50.0%
GCAGCAGCACATGGAATTAG+TGG + chr2.4:76385153-76385172 MS.gene072079:CDS 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG - chr2.4:76385285-76385304 None:intergenic 50.0%
GTAGCCAATCCCATGTCTTG+TGG - chr2.4:76385709-76385728 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG - chr2.4:76385272-76385291 None:intergenic 50.0%
TTAGTGGTAGACGACGACGA+CGG + chr2.4:76385169-76385188 MS.gene072079:CDS 50.0%
! GCGTGAGAATCTGGAATGCT+AGG - chr2.4:76385263-76385282 None:intergenic 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG - chr2.4:76385250-76385269 None:intergenic 50.0%
CCATGGCATCGCAACCTTCA+AGG + chr2.4:76385419-76385438 MS.gene072079:CDS 55.0%
CCTTGAAGGTTGCGATGCCA+TGG - chr2.4:76385422-76385441 None:intergenic 55.0%
TCGCAACCTTCAAGGGTCTC+TGG + chr2.4:76385427-76385446 MS.gene072079:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG - chr2.4:76385618-76385637 None:intergenic 55.0%
ACCACGCCGTGTGACTAAGG+AGG + chr2.4:76385620-76385639 MS.gene072079:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG - chr2.4:76385624-76385643 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG + chr2.4:76385617-76385636 MS.gene072079:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG - chr2.4:76385617-76385636 None:intergenic 60.0%
GCAGCAGCAGCAGCAGCACA+TGG + chr2.4:76385144-76385163 MS.gene072079:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 76385078 76385758 76385078 ID=MS.gene072079
chr2.4 mRNA 76385078 76385758 76385078 ID=MS.gene072079.t1;Parent=MS.gene072079
chr2.4 exon 76385078 76385758 76385078 ID=MS.gene072079.t1.exon1;Parent=MS.gene072079.t1
chr2.4 CDS 76385078 76385758 76385078 ID=cds.MS.gene072079.t1;Parent=MS.gene072079.t1
Gene Sequence

>MS.gene072079

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGATGGATCATCATCAGCAGCAGCAGCAGCAGCAGCAGCACATGGAATTAGTGGTAGACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCAAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGGATAACAATGTGTTGACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTACTTTTTGTCGTTTTTCCAACCACAAGACATGGGATTGGCTACCCTGTTACACCTGCACCCAATTCCAAATAA
Protein sequence

>MS.gene072079.t1

MSVTQRRSNNKQSEADGSSSAAAAAAAAHGISGRRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVMDSSSTIILPAELSKYKIRPIDFVHAFLSVFVFFAVALRDNNVLTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPAPNSK