AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073348

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073348.t1 MTR_4g126900 93.151 219 12 2 1 219 1 216 4.94e-140 390
MS.gene073348.t1 MTR_8g095670 85.294 102 12 2 1 102 83 181 5.36e-46 150
MS.gene073348.t1 MTR_5g013010 53.741 147 58 2 60 206 112 248 6.52e-41 141
MS.gene073348.t1 MTR_5g014890 63.077 130 36 4 79 206 115 234 3.64e-40 139
MS.gene073348.t1 MTR_4g100550 55.000 140 54 2 79 212 102 238 1.04e-39 137
MS.gene073348.t1 MTR_8g006705 63.248 117 40 1 90 206 145 258 1.63e-38 135
MS.gene073348.t1 MTR_2g038625 44.175 206 94 5 11 214 15 201 1.56e-37 130
MS.gene073348.t1 MTR_2g038580 44.175 206 94 5 11 214 15 201 1.56e-37 130
MS.gene073348.t1 MTR_7g093430 48.428 159 59 3 55 206 129 271 7.30e-37 130
MS.gene073348.t1 MTR_1g054285 46.951 164 66 3 50 206 116 265 1.55e-36 130
MS.gene073348.t1 MTR_4g097600 60.684 117 42 2 90 206 126 238 2.94e-36 128
MS.gene073348.t1 MTR_2g061030 54.348 138 48 3 78 203 187 321 5.70e-36 129
MS.gene073348.t1 MTR_1g017090 60.345 116 44 2 90 205 129 242 3.70e-35 126
MS.gene073348.t1 MTR_4g084750 49.206 126 58 3 85 206 59 182 3.27e-30 110
MS.gene073348.t1 MTR_3g103590 51.587 126 48 3 85 206 139 255 1.01e-27 107
MS.gene073348.t1 MTR_5g013010 55.422 83 30 1 60 142 112 187 4.78e-21 87.4
MS.gene073348.t1 MTR_7g010020 48.864 88 45 0 90 177 79 166 4.19e-19 83.6
MS.gene073348.t1 MTR_3g080100 47.872 94 42 1 91 177 20 113 6.15e-19 82.0
MS.gene073348.t1 MTR_3g080100 47.872 94 42 1 91 177 59 152 9.52e-19 82.4
MS.gene073348.t1 MTR_8g469430 48.936 94 41 1 91 177 89 182 1.25e-18 82.4
MS.gene073348.t1 MTR_5g038280 46.809 94 43 1 91 177 87 180 3.82e-18 81.6
MS.gene073348.t1 MTR_7g103340 42.453 106 61 0 72 177 44 149 4.30e-18 80.1
MS.gene073348.t1 MTR_6g007647 48.387 93 41 1 91 176 33 125 7.63e-18 79.7
MS.gene073348.t1 MTR_6g007647 48.387 93 41 1 91 176 67 159 1.09e-17 79.7
MS.gene073348.t1 MTR_6g011610 47.872 94 42 1 91 177 96 189 2.64e-17 78.6
MS.gene073348.t1 MTR_8g468210 47.126 87 46 0 91 177 77 163 3.17e-17 78.6
MS.gene073348.t1 MTR_6g011610 47.872 94 42 1 91 177 77 170 3.92e-17 77.8
MS.gene073348.t1 MTR_8g089895 38.636 132 67 2 90 214 53 177 3.94e-17 78.6
MS.gene073348.t1 MTR_5g039000 45.977 87 47 0 91 177 77 163 1.56e-16 76.6
MS.gene073348.t1 MTR_1g061660 43.956 91 51 0 87 177 55 145 7.57e-16 73.9
MS.gene073348.t1 MTR_3g086790 40.385 104 53 2 81 177 52 153 3.51e-15 73.2
MS.gene073348.t1 MTR_4g107650 45.161 93 44 1 91 176 95 187 1.66e-14 71.6
MS.gene073348.t1 MTR_8g026960 38.235 102 63 0 75 176 18 119 6.53e-13 66.2
MS.gene073348.t1 MTR_3g092150 39.785 93 49 1 94 179 41 133 1.15e-12 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073348.t1 AT4G37790 40.323 248 95 8 1 206 1 237 1.79e-40 139
MS.gene073348.t1 AT3G60390 58.779 131 50 3 77 206 147 274 3.09e-40 140
MS.gene073348.t1 AT5G06710 52.555 137 47 2 77 206 176 301 4.87e-38 135
MS.gene073348.t1 AT4G16780 57.143 126 50 2 80 205 119 240 1.19e-37 132
MS.gene073348.t1 AT2G44910 58.120 117 46 1 90 206 162 275 2.56e-35 127
MS.gene073348.t1 AT2G22800 42.439 205 84 5 1 177 1 199 3.60e-35 125
MS.gene073348.t1 AT5G47370 49.296 142 69 1 77 218 116 254 6.42e-35 125
MS.gene073348.t1 AT4G17460 53.175 126 56 1 90 215 134 256 4.88e-34 123
MS.gene073348.t1 AT1G70920 42.958 142 68 2 66 206 14 143 7.35e-28 104
MS.gene073348.t1 AT1G70920 42.958 142 68 2 66 206 44 173 9.17e-28 105
MS.gene073348.t1 AT2G01430 46.667 135 61 2 77 206 120 248 1.10e-27 106
MS.gene073348.t1 AT5G06710 59.155 71 29 0 72 142 171 241 1.24e-21 90.5
MS.gene073348.t1 AT1G26960 40.336 119 70 1 60 177 39 157 1.46e-18 81.6
MS.gene073348.t1 AT1G69780 49.425 87 44 0 91 177 85 171 2.82e-17 79.0
MS.gene073348.t1 AT3G01470 48.387 93 41 2 91 176 68 160 7.14e-17 77.4
MS.gene073348.t1 AT3G01220 50.633 79 39 0 91 169 87 165 9.94e-17 77.4
MS.gene073348.t1 AT2G01430 48.864 88 38 2 77 159 120 205 1.20e-16 75.9
MS.gene073348.t1 AT5G15150 48.936 94 41 1 91 177 115 208 2.34e-16 76.6
MS.gene073348.t1 AT2G46680 43.158 95 50 1 82 176 27 117 6.83e-16 74.7
MS.gene073348.t1 AT2G46680 43.158 95 50 1 82 176 27 117 6.86e-16 74.7
MS.gene073348.t1 AT5G65310 43.617 94 46 1 91 177 72 165 2.17e-15 73.9
MS.gene073348.t1 AT5G65310 43.617 94 46 1 91 177 54 147 2.27e-15 73.6
MS.gene073348.t1 AT5G03790 43.617 94 53 0 84 177 70 163 3.35e-15 72.4
MS.gene073348.t1 AT2G22430 44.681 94 45 1 91 177 62 155 6.83e-15 72.4
MS.gene073348.t1 AT4G40060 45.556 90 45 1 91 176 59 148 9.31e-15 72.0
MS.gene073348.t1 AT5G03790 44.444 90 50 0 84 173 70 159 3.40e-14 68.9
MS.gene073348.t1 AT3G61890 40.964 83 49 0 94 176 33 115 2.33e-13 67.4
MS.gene073348.t1 AT2G36610 39.286 112 60 2 74 177 54 165 7.32e-13 65.1
MS.gene073348.t1 AT4G36740 40.625 96 57 0 82 177 47 142 4.57e-12 63.5
MS.gene073348.t1 AT4G36740 40.625 96 57 0 82 177 46 141 4.99e-12 63.2
MS.gene073348.t1 AT2G18550 38.679 106 63 1 72 177 44 147 5.87e-12 63.2
MS.gene073348.t1 AT5G53980 43.333 90 49 2 89 177 9 97 8.60e-12 61.6
MS.gene073348.t1 AT5G66700 45.833 72 39 0 91 162 71 142 2.49e-11 61.6

Find 36 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAGGTGAAAGATTCAATT+TGG 0.267895 8.3:+4042357 MS.gene073348:CDS
ACGTTCATAGGTTCTCCTTT+TGG 0.352374 8.3:-4042316 None:intergenic
TTGAGGTTTGGTTTCAGAAC+AGG 0.362659 8.3:+4042884 MS.gene073348:CDS
GTCTTGTCTTTAACCTCAAT+TGG 0.365222 8.3:-4042858 None:intergenic
TTGTTGTTGTGTACGTTCAT+AGG 0.371543 8.3:-4042328 None:intergenic
TTATGTCTCGGTCTTGGAAT+AGG 0.375581 8.3:+4042214 MS.gene073348:CDS
TCTACGATCGTTGTTGTTGT+TGG 0.376794 8.3:-4042431 None:intergenic
ACAGGTTTATGTCTCGGTCT+TGG 0.398879 8.3:+4042208 MS.gene073348:CDS
AAGATTAAAGAAGGAATTGC+AGG 0.404223 8.3:+4043241 MS.gene073348:CDS
AGACAAGACAAATTGAGGTT+TGG 0.409339 8.3:+4042872 MS.gene073348:CDS
TTGCAGGAACTCAAATTTGT+TGG 0.422420 8.3:+4043257 MS.gene073348:CDS
TAGCACTTGCTGACCAATTG+AGG 0.458161 8.3:+4042845 MS.gene073348:CDS
GCATTCTTCATCACTTTCCA+TGG 0.470187 8.3:-4042182 None:intergenic
GTTAAAGACAAGACAAATTG+AGG 0.472426 8.3:+4042867 MS.gene073348:CDS
ATACCGGATTAAGAGTGTTA+TGG 0.475608 8.3:-4042510 None:intergenic
AGTGATGAAGAATGCAATAC+AGG 0.485322 8.3:+4042190 MS.gene073348:CDS
GCTCCATAACACTCTTAATC+CGG 0.495490 8.3:+4042507 MS.gene073348:CDS
AAGAGTGTTATGGAGCTTGA+AGG 0.507942 8.3:-4042500 None:intergenic
TGCAATACAGGTTTATGTCT+CGG 0.509331 8.3:+4042202 MS.gene073348:CDS
TGATCTTCATTATGCTTCAA+CGG 0.512123 8.3:-4043362 None:intergenic
TTGGACAAAGCTCAAAAGCT+AGG 0.524782 8.3:-4042297 None:intergenic
GACTAAGCTGAAGCAGATAG+AGG 0.526640 8.3:+4043166 MS.gene073348:CDS
TGAGAACAAAAGATTAAAGA+AGG 0.527592 8.3:+4043232 MS.gene073348:CDS
TCAAAACAAGGTGCCATCAC+AGG 0.535661 8.3:-4042274 None:intergenic
CTTGAAGGTGCTCTCAAGCA+TGG 0.539476 8.3:-4042485 None:intergenic
ATTAGTGAATAAACCTGTGA+TGG 0.545697 8.3:+4042261 MS.gene073348:CDS
GATAAACGTTGAGGGCATAA+CGG 0.556727 8.3:-4043287 None:intergenic
GGTTTCAGAACAGGAGAGCA+AGG 0.572572 8.3:+4042893 MS.gene073348:CDS
TCTTGGAATAGGTGCAACAA+AGG 0.625237 8.3:+4042225 MS.gene073348:CDS
ACAGTACTATGAGTCACCAC+TGG 0.648715 8.3:-4043317 None:intergenic
TAAGCTGAAGCAGATAGAGG+TGG 0.656332 8.3:+4043169 MS.gene073348:CDS
AAAGAAACTGAGGCTAACAA+AGG 0.656758 8.3:+4042453 MS.gene073348:CDS
TCAAAAGCTAGGTCAAAACA+AGG 0.669862 8.3:-4042286 None:intergenic
GAAGCATAATGAAGATCACA+AGG 0.690141 8.3:+4043367 MS.gene073348:CDS
ACGTTTATCATCAAAACCAG+TGG 0.690620 8.3:+4043301 MS.gene073348:CDS
ACGATCGTAGAAAGAAACTG+AGG 0.720750 8.3:+4042443 MS.gene073348:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATTATTATTATTTTTAA+TGG + chr8.3:4042690-4042709 MS.gene073348:intron 0.0%
!! TACAACAATTTATAAACTAA+TGG - chr8.3:4043128-4043147 None:intergenic 15.0%
!! TGTATTTATTTATATAACAC+AGG + chr8.3:4043144-4043163 MS.gene073348:intron 15.0%
!!! TACATATTATAGAGAATTTT+TGG - chr8.3:4042553-4042572 None:intergenic 15.0%
!! ATTTGTTCTTCATATTATCT+GGG + chr8.3:4042988-4043007 MS.gene073348:intron 20.0%
!!! AATTTGTTCTTCATATTATC+TGG + chr8.3:4042987-4043006 MS.gene073348:intron 20.0%
!!! ACGTTACATTTTGATAATAT+TGG - chr8.3:4042390-4042409 None:intergenic 20.0%
!!! ATTAGTTTTTCTATATGACA+AGG + chr8.3:4042767-4042786 MS.gene073348:intron 20.0%
!!! TTAGTTTTTCTATATGACAA+GGG + chr8.3:4042768-4042787 MS.gene073348:intron 20.0%
! TGAGAACAAAAGATTAAAGA+AGG + chr8.3:4043232-4043251 MS.gene073348:CDS 25.0%
! TGTCATATTGTGTATGTATA+AGG + chr8.3:4042595-4042614 MS.gene073348:intron 25.0%
!! TTTTGGTATGAATGAATGAA+TGG - chr8.3:4042536-4042555 None:intergenic 25.0%
!!! TTTTGGTTTCATATATATGC+AGG + chr8.3:4042813-4042832 MS.gene073348:intron 25.0%
AAGATTAAAGAAGGAATTGC+AGG + chr8.3:4043241-4043260 MS.gene073348:CDS 30.0%
ATGAATGAATGAATGGATAC+CGG - chr8.3:4042529-4042548 None:intergenic 30.0%
ATTAGTGAATAAACCTGTGA+TGG + chr8.3:4042261-4042280 MS.gene073348:CDS 30.0%
CAAAGGTGAAAGATTCAATT+TGG + chr8.3:4042357-4042376 MS.gene073348:CDS 30.0%
GTTAAAGACAAGACAAATTG+AGG + chr8.3:4042867-4042886 MS.gene073348:CDS 30.0%
TGATCTTCATTATGCTTCAA+CGG - chr8.3:4043365-4043384 None:intergenic 30.0%
! CTATATGTTGATATCGATTG+CGG + chr8.3:4043070-4043089 MS.gene073348:intron 30.0%
!! GTTTTGATGATAAACGTTGA+GGG - chr8.3:4043298-4043317 None:intergenic 30.0%
AAAGAAACTGAGGCTAACAA+AGG + chr8.3:4042453-4042472 MS.gene073348:CDS 35.0%
ACGTTTATCATCAAAACCAG+TGG + chr8.3:4043301-4043320 MS.gene073348:CDS 35.0%
AGACAAGACAAATTGAGGTT+TGG + chr8.3:4042872-4042891 MS.gene073348:CDS 35.0%
AGTGATGAAGAATGCAATAC+AGG + chr8.3:4042190-4042209 MS.gene073348:CDS 35.0%
GAAGCATAATGAAGATCACA+AGG + chr8.3:4043367-4043386 MS.gene073348:CDS 35.0%
GTAGAAATGAGTTTATGCGT+TGG + chr8.3:4042790-4042809 MS.gene073348:intron 35.0%
GTCTTGTCTTTAACCTCAAT+TGG - chr8.3:4042861-4042880 None:intergenic 35.0%
TCAAAAGCTAGGTCAAAACA+AGG - chr8.3:4042289-4042308 None:intergenic 35.0%
TGCAATACAGGTTTATGTCT+CGG + chr8.3:4042202-4042221 MS.gene073348:CDS 35.0%
TTGCAGGAACTCAAATTTGT+TGG + chr8.3:4043257-4043276 MS.gene073348:CDS 35.0%
! TTGTTGTTGTGTACGTTCAT+AGG - chr8.3:4042331-4042350 None:intergenic 35.0%
!! ATACCGGATTAAGAGTGTTA+TGG - chr8.3:4042513-4042532 None:intergenic 35.0%
!! GGTTTTGATGATAAACGTTG+AGG - chr8.3:4043299-4043318 None:intergenic 35.0%
!!! ATGAGTTTATGCGTTGGTTT+TGG + chr8.3:4042796-4042815 MS.gene073348:intron 35.0%
ACGATCGTAGAAAGAAACTG+AGG + chr8.3:4042443-4042462 MS.gene073348:CDS 40.0%
CACAACAACAACAACAGCAA+AGG + chr8.3:4042340-4042359 MS.gene073348:CDS 40.0%
GCTCCATAACACTCTTAATC+CGG + chr8.3:4042507-4042526 MS.gene073348:CDS 40.0%
TCTTGGAATAGGTGCAACAA+AGG + chr8.3:4042225-4042244 MS.gene073348:CDS 40.0%
TTATGTCTCGGTCTTGGAAT+AGG + chr8.3:4042214-4042233 MS.gene073348:CDS 40.0%
TTGGACAAAGCTCAAAAGCT+AGG - chr8.3:4042300-4042319 None:intergenic 40.0%
! ACGTTCATAGGTTCTCCTTT+TGG - chr8.3:4042319-4042338 None:intergenic 40.0%
! GATAAACGTTGAGGGCATAA+CGG - chr8.3:4043290-4043309 None:intergenic 40.0%
! TCTACGATCGTTGTTGTTGT+TGG - chr8.3:4042434-4042453 None:intergenic 40.0%
! TTGAGGTTTGGTTTCAGAAC+AGG + chr8.3:4042884-4042903 MS.gene073348:CDS 40.0%
!! AAGAGTGTTATGGAGCTTGA+AGG - chr8.3:4042503-4042522 None:intergenic 40.0%
!! GCTTTTGAGCTTTGTCCAAA+AGG + chr8.3:4042301-4042320 MS.gene073348:CDS 40.0%
ACAGGTTTATGTCTCGGTCT+TGG + chr8.3:4042208-4042227 MS.gene073348:CDS 45.0%
ACAGTACTATGAGTCACCAC+TGG - chr8.3:4043320-4043339 None:intergenic 45.0%
GACTAAGCTGAAGCAGATAG+AGG + chr8.3:4043166-4043185 MS.gene073348:CDS 45.0%
TAAGCTGAAGCAGATAGAGG+TGG + chr8.3:4043169-4043188 MS.gene073348:CDS 45.0%
! TAGCACTTGCTGACCAATTG+AGG + chr8.3:4042845-4042864 MS.gene073348:CDS 45.0%
! TCAAAACAAGGTGCCATCAC+AGG - chr8.3:4042277-4042296 None:intergenic 45.0%
!! AATAAATACTAAAATTAAAT+AGG - chr8.3:4043034-4043053 None:intergenic 5.0%
GGTTTCAGAACAGGAGAGCA+AGG + chr8.3:4042893-4042912 MS.gene073348:CDS 50.0%
!! CTTGAAGGTGCTCTCAAGCA+TGG - chr8.3:4042488-4042507 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 4042184 4043400 4042184 ID=MS.gene073348
chr8.3 mRNA 4042184 4043400 4042184 ID=MS.gene073348.t1;Parent=MS.gene073348
chr8.3 exon 4042184 4042528 4042184 ID=MS.gene073348.t1.exon1;Parent=MS.gene073348.t1
chr8.3 CDS 4042184 4042528 4042184 ID=cds.MS.gene073348.t1;Parent=MS.gene073348.t1
chr8.3 exon 4042835 4042914 4042835 ID=MS.gene073348.t1.exon2;Parent=MS.gene073348.t1
chr8.3 CDS 4042835 4042914 4042835 ID=cds.MS.gene073348.t1;Parent=MS.gene073348.t1
chr8.3 exon 4043166 4043400 4043166 ID=MS.gene073348.t1.exon3;Parent=MS.gene073348.t1
chr8.3 CDS 4043166 4043400 4043166 ID=cds.MS.gene073348.t1;Parent=MS.gene073348.t1
Gene Sequence

>MS.gene073348

ATGGAAAGTGATGAAGAATGCAATACAGGTTTATGTCTCGGTCTTGGAATAGGTGCAACAAAGGTGAAGAAGCAGAAATTAGTGAATAAACCTGTGATGGCACCTTGTTTTGACCTAGCTTTTGAGCTTTGTCCAAAAGGAGAACCTATGAACGTACACAACAACAACAACAGCAAAGGTGAAAGATTCAATTTGGAGAGACACCAATATTATCAAAATGTAACGTGTAGCACTGATTCTGATAACACCAACAACAACAACGATCGTAGAAAGAAACTGAGGCTAACAAAGGAGCAATCATCCATGCTTGAGAGCACCTTCAAGCTCCATAACACTCTTAATCCGGTATCCATTCATTCATTCATACCAAAAATTCTCTATAATATGTATTAGCATATATGTAACATAATCTGTCATATTGTGTATGTATAAGGTTGTAGAACTTTAATAGACTGAATTATATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTTTTAATGGCAAATTGAAAAACAAATTATTGTCTATTTACTATTTCTTTTTTGTTCAACTATAATTAGTTTTTCTATATGACAAGGGTAGAAATGAGTTTATGCGTTGGTTTTGGTTTCATATATATGCAGGTTCAGAAAATAGCACTTGCTGACCAATTGAGGTTAAAGACAAGACAAATTGAGGTTTGGTTTCAGAACAGGAGAGCAAGGTACGTTAATTAATTTATGTGTTCAGATATTTCATTGATCTTATAACTATGTTGTTACTTTTGTCTAGCATTAATTTGTTCTTCATATTATCTGGGTTTCGTAACTGAATATATCACCTATTTAATTTTAGTATTTATTTATGTTGTTGACTAAGCTATATGTTGATATCGATTGCGGAATAGTACGTAGTAGTATTATATATTTAATTTCCATTAGTTTATAAATTGTTGTATTTATTTATATAACACAGGACTAAGCTGAAGCAGATAGAGGTGGATTATGAGTTGTTGAAAAAACATTGTCAAAATCTAAGTGATGAGAACAAAAGATTAAAGAAGGAATTGCAGGAACTCAAATTTGTTGGACAATTTCCGTTATGCCCTCAACGTTTATCATCAAAACCAGTGGTGACTCATAGTACTGTGTGCTCTTCTTGTGAGCAGAAACCGTTGAAGCATAATGAAGATCACAAGGATAATTTATAA
Protein sequence

>MS.gene073348.t1

MESDEECNTGLCLGLGIGATKVKKQKLVNKPVMAPCFDLAFELCPKGEPMNVHNNNNSKGERFNLERHQYYQNVTCSTDSDNTNNNNDRRKKLRLTKEQSSMLESTFKLHNTLNPVQKIALADQLRLKTRQIEVWFQNRRARTKLKQIEVDYELLKKHCQNLSDENKRLKKELQELKFVGQFPLCPQRLSSKPVVTHSTVCSSCEQKPLKHNEDHKDNL