AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene011104

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene011104.t1 MTR_7g029400 91.146 192 15 2 1 190 1 192 5.89e-130 363
MS.gene011104.t1 MTR_8g015250 92.105 190 6 1 1 190 1 181 3.36e-128 358
MS.gene011104.t1 MTR_6g016375 47.030 202 73 5 1 184 1 186 9.74e-47 152
MS.gene011104.t1 MTR_7g017880 61.194 134 50 2 54 186 58 190 5.76e-44 145
MS.gene011104.t1 MTR_4g070860 53.425 73 34 0 79 151 26 98 3.85e-19 80.1
MS.gene011104.t1 MTR_1g022495 40.206 97 57 1 57 153 5 100 1.25e-16 73.6
MS.gene011104.t1 MTR_3g117120 49.315 73 37 0 79 151 26 98 3.53e-16 72.4
MS.gene011104.t1 MTR_8g086020 35.294 102 66 0 50 151 2 103 3.88e-15 69.7
MS.gene011104.t1 MTR_4g097440 44.706 85 47 0 71 155 63 147 4.45e-15 70.1
MS.gene011104.t1 MTR_5g015090 46.835 79 42 0 80 158 58 136 1.49e-13 65.5
MS.gene011104.t1 MTR_1g087040 43.478 92 46 3 60 151 10 95 7.53e-13 63.5
MS.gene011104.t1 MTR_3g109310 41.489 94 52 1 78 168 121 214 1.17e-11 62.4
MS.gene011104.t1 MTR_5g028850 40.426 94 51 2 58 146 280 373 1.30e-11 62.8
MS.gene011104.t1 MTR_5g028850 40.426 94 51 2 58 146 278 371 1.34e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene011104.t1 AT3G30530 70.690 116 32 1 61 174 57 172 5.99e-52 164
MS.gene011104.t1 AT1G13600 46.409 181 78 5 2 170 4 177 2.03e-41 139
MS.gene011104.t1 AT5G38800 55.469 128 55 1 45 170 34 161 2.49e-40 135
MS.gene011104.t1 AT5G15830 50.000 144 67 3 47 190 40 178 9.06e-37 126
MS.gene011104.t1 AT2G04038 62.105 95 36 0 64 158 55 149 3.25e-35 122
MS.gene011104.t1 AT1G68880 51.250 80 39 0 81 160 45 124 2.42e-23 90.5
MS.gene011104.t1 AT1G75390 46.809 94 45 1 63 151 16 109 7.45e-17 74.7
MS.gene011104.t1 AT5G60830 47.500 80 42 0 81 160 69 148 8.23e-17 75.5
MS.gene011104.t1 AT2G18160 47.222 72 38 0 80 151 28 99 1.42e-15 71.2
MS.gene011104.t1 AT1G75390 45.055 91 46 1 61 147 15 105 1.78e-15 69.7
MS.gene011104.t1 AT3G62420 38.614 101 58 1 79 175 21 121 1.81e-14 67.8
MS.gene011104.t1 AT4G34590 43.243 74 42 0 78 151 22 95 3.08e-12 62.0
MS.gene011104.t1 AT4G37730 45.238 84 46 0 75 158 189 272 9.72e-12 62.8

Find 31 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCAAAAGTTTCTTCTTTA+AGG 0.049723 8.3:-73736408 None:intergenic
AGATTATTTATATGATAATT+TGG 0.173759 8.3:-73736076 None:intergenic
TTCTCAATCATGAACTTTAG+AGG 0.310979 8.3:-73736533 None:intergenic
TTCTGTGGCAAGACAAAGTT+TGG 0.311505 8.3:-73736046 None:intergenic
ATGGTAGCTGACATGCAAAT+TGG 0.415880 8.3:+73736439 MS.gene011104:CDS
AGACAAAGTTTGGTTGAACT+TGG 0.417616 8.3:-73736036 None:intergenic
TTTGCATGTCAGCTACCATT+TGG 0.441661 8.3:-73736435 None:intergenic
GCTGATGGGTAATGGAAGTT+TGG 0.447856 8.3:-73736112 None:intergenic
ACATAAATCTTCCATGCTGC+AGG 0.469344 8.3:-73736473 None:intergenic
ACGATGGTGGAGCAAATTCA+TGG 0.483705 8.3:-73736138 None:intergenic
GAGAATCAGCTAGGAGATCA+AGG 0.496394 8.3:+73736254 MS.gene011104:CDS
CATGGCCTGCTGATGGGTAA+TGG 0.501858 8.3:-73736120 None:intergenic
TGAACTTGGAATGAATTCTC+AGG 0.503018 8.3:-73736022 None:intergenic
TTAACTCCTCTGATCTCTCT+AGG 0.517612 8.3:-73735986 None:intergenic
CATGGTTGAGTTTGTCAACA+AGG 0.524031 8.3:-73736345 None:intergenic
CTCTGTTTGATATCATTCGC+CGG 0.528366 8.3:-73736234 None:intergenic
CAAATTCATGGCCTGCTGAT+GGG 0.533266 8.3:-73736126 None:intergenic
AACTTCCATTACCCATCAGC+AGG 0.542481 8.3:+73736115 MS.gene011104:CDS
TAATTTGGAATTTCATTCTG+TGG 0.545612 8.3:-73736061 None:intergenic
CAGCTAGGAGATCAAGGATG+AGG 0.553553 8.3:+73736260 MS.gene011104:CDS
GCAAATTCATGGCCTGCTGA+TGG 0.554547 8.3:-73736127 None:intergenic
TTGTGTTGAGATGTGTTGCA+TGG 0.567617 8.3:-73736502 None:intergenic
TCTGATCTCTCTAGGAACCA+TGG 0.617254 8.3:-73735978 None:intergenic
AGTTTAACATCATCGACGAA+AGG 0.620965 8.3:+73736206 MS.gene011104:CDS
TATCAAACAGAGAATCAGCT+AGG 0.629542 8.3:+73736245 MS.gene011104:CDS
TCATCGACGAAAGGAAGCAC+CGG 0.644213 8.3:+73736215 MS.gene011104:CDS
ACTTGGAATGAATTCTCAGG+AGG 0.648127 8.3:-73736019 None:intergenic
TTGCTGCTTAAACACGATGG+TGG 0.650100 8.3:-73736151 None:intergenic
ATGGTTCCTAGAGAGATCAG+AGG 0.663186 8.3:+73735980 MS.gene011104:CDS
TGTCATGTGACTCAGACGCA+TGG 0.679884 8.3:-73736363 None:intergenic
GAGTTGCTGCTTAAACACGA+TGG 0.774209 8.3:-73736154 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTATTTATATGATAATT+TGG - chr8.3:73736079-73736098 None:intergenic 10.0%
!!! TATCATATAAATAATCTTTT+AGG + chr8.3:73736082-73736101 MS.gene011104:CDS 10.0%
! GATCAAAAGTTTCTTCTTTA+AGG - chr8.3:73736411-73736430 None:intergenic 25.0%
!! TAATTTGGAATTTCATTCTG+TGG - chr8.3:73736064-73736083 None:intergenic 25.0%
AAAAACACTTGGATGAACTT+TGG + chr8.3:73736287-73736306 MS.gene011104:CDS 30.0%
AGACAAAGTTTGGTTGAACT+TGG - chr8.3:73736039-73736058 None:intergenic 35.0%
AGTTTAACATCATCGACGAA+AGG + chr8.3:73736206-73736225 MS.gene011104:CDS 35.0%
GATGAGGAAACAAAAACACT+TGG + chr8.3:73736276-73736295 MS.gene011104:CDS 35.0%
TATCAAACAGAGAATCAGCT+AGG + chr8.3:73736245-73736264 MS.gene011104:CDS 35.0%
TGAACTTGGAATGAATTCTC+AGG - chr8.3:73736025-73736044 None:intergenic 35.0%
! AACTTTTGATCTTCGCCAAA+TGG + chr8.3:73736420-73736439 MS.gene011104:CDS 35.0%
ACATAAATCTTCCATGCTGC+AGG - chr8.3:73736476-73736495 None:intergenic 40.0%
ACTTGGAATGAATTCTCAGG+AGG - chr8.3:73736022-73736041 None:intergenic 40.0%
ATGGTAGCTGACATGCAAAT+TGG + chr8.3:73736439-73736458 MS.gene011104:CDS 40.0%
CATGGTTGAGTTTGTCAACA+AGG - chr8.3:73736348-73736367 None:intergenic 40.0%
CTCTGTTTGATATCATTCGC+CGG - chr8.3:73736237-73736256 None:intergenic 40.0%
TTAACTCCTCTGATCTCTCT+AGG - chr8.3:73735989-73736008 None:intergenic 40.0%
TTCTGTGGCAAGACAAAGTT+TGG - chr8.3:73736049-73736068 None:intergenic 40.0%
TTGTGTTGAGATGTGTTGCA+TGG - chr8.3:73736505-73736524 None:intergenic 40.0%
TTTGCATGTCAGCTACCATT+TGG - chr8.3:73736438-73736457 None:intergenic 40.0%
! TAACTCTTTTACCTGCAGCA+TGG + chr8.3:73736462-73736481 MS.gene011104:CDS 40.0%
AACTTCCATTACCCATCAGC+AGG + chr8.3:73736115-73736134 MS.gene011104:CDS 45.0%
ATGGTTCCTAGAGAGATCAG+AGG + chr8.3:73735980-73735999 MS.gene011104:CDS 45.0%
CAAATTCATGGCCTGCTGAT+GGG - chr8.3:73736129-73736148 None:intergenic 45.0%
GAGAATCAGCTAGGAGATCA+AGG + chr8.3:73736254-73736273 MS.gene011104:CDS 45.0%
! GAGTTGCTGCTTAAACACGA+TGG - chr8.3:73736157-73736176 None:intergenic 45.0%
! TTGCTGCTTAAACACGATGG+TGG - chr8.3:73736154-73736173 None:intergenic 45.0%
!! ACGATGGTGGAGCAAATTCA+TGG - chr8.3:73736141-73736160 None:intergenic 45.0%
!! GCTGATGGGTAATGGAAGTT+TGG - chr8.3:73736115-73736134 None:intergenic 45.0%
CAGCTAGGAGATCAAGGATG+AGG + chr8.3:73736260-73736279 MS.gene011104:CDS 50.0%
GCAAATTCATGGCCTGCTGA+TGG - chr8.3:73736130-73736149 None:intergenic 50.0%
TGTCATGTGACTCAGACGCA+TGG - chr8.3:73736366-73736385 None:intergenic 50.0%
! TCATCGACGAAAGGAAGCAC+CGG + chr8.3:73736215-73736234 MS.gene011104:CDS 50.0%
! CATGGCCTGCTGATGGGTAA+TGG - chr8.3:73736123-73736142 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 73735980 73736552 73735980 ID=MS.gene011104
chr8.3 mRNA 73735980 73736552 73735980 ID=MS.gene011104.t1;Parent=MS.gene011104
chr8.3 exon 73735980 73736552 73735980 ID=MS.gene011104.t1.exon1;Parent=MS.gene011104.t1
chr8.3 CDS 73735980 73736552 73735980 ID=cds.MS.gene011104.t1;Parent=MS.gene011104.t1
Gene Sequence

>MS.gene011104

ATGGTTCCTAGAGAGATCAGAGGAGTTAATTATCTAACTCCTCCTGAGAATTCATTCCAAGTTCAACCAAACTTTGTCTTGCCACAGAATGAAATTCCAAATTATCATATAAATAATCTTTTAGGCAGCTTACCAAACTTCCATTACCCATCAGCAGGCCATGAATTTGCTCCACCATCGTGTTTAAGCAGCAACTCGACTACTTCTGATGAAGCAGATGAACTTCAGTTTAACATCATCGACGAAAGGAAGCACCGGCGAATGATATCAAACAGAGAATCAGCTAGGAGATCAAGGATGAGGAAACAAAAACACTTGGATGAACTTTGGTCACAAGTGATGAAACTCAGAACTGAAAATCACAACCTTGTTGACAAACTCAACCATGCGTCTGAGTCACATGACAAAGTTGTTCAAGAGAATGCACGCCTTAAAGAAGAAACTTTTGATCTTCGCCAAATGGTAGCTGACATGCAAATTGGTAACTCTTTTACCTGCAGCATGGAAGATTTATGTGAAATTCCATGCAACACATCTCAACACAAAGATGATTCCTCTAAAGTTCATGATTGA
Protein sequence

>MS.gene011104.t1

MVPREIRGVNYLTPPENSFQVQPNFVLPQNEIPNYHINNLLGSLPNFHYPSAGHEFAPPSCLSSNSTTSDEADELQFNIIDERKHRRMISNRESARRSRMRKQKHLDELWSQVMKLRTENHNLVDKLNHASESHDKVVQENARLKEETFDLRQMVADMQIGNSFTCSMEDLCEIPCNTSQHKDDSSKVHD