AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene012303

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012303.t1 MTR_4g126900 92.273 220 13 2 1 220 1 216 1.51e-138 387
MS.gene012303.t1 MTR_8g095670 83.495 103 13 2 1 103 83 181 6.57e-45 148
MS.gene012303.t1 MTR_5g013010 53.741 147 58 2 61 207 112 248 1.99e-41 142
MS.gene012303.t1 MTR_5g014890 63.077 130 36 4 80 207 115 234 1.54e-40 139
MS.gene012303.t1 MTR_4g100550 54.422 147 56 3 80 218 102 245 3.64e-40 139
MS.gene012303.t1 MTR_8g006705 63.248 117 40 1 91 207 145 258 4.90e-39 136
MS.gene012303.t1 MTR_7g093430 47.239 163 67 3 50 207 123 271 2.21e-37 132
MS.gene012303.t1 MTR_1g054285 47.853 163 65 4 50 207 118 265 3.22e-37 132
MS.gene012303.t1 MTR_4g097600 60.684 117 42 2 91 207 126 238 7.66e-37 130
MS.gene012303.t1 MTR_2g038625 43.478 207 95 5 11 215 15 201 2.19e-36 127
MS.gene012303.t1 MTR_2g038580 43.478 207 95 5 11 215 15 201 2.19e-36 127
MS.gene012303.t1 MTR_2g061030 53.623 138 49 3 79 204 187 321 7.18e-36 129
MS.gene012303.t1 MTR_1g017090 60.345 116 44 2 91 206 129 242 3.32e-35 126
MS.gene012303.t1 MTR_4g084750 50.400 125 58 2 86 207 59 182 9.23e-32 115
MS.gene012303.t1 MTR_3g103590 51.587 126 48 3 86 207 139 255 4.70e-28 108
MS.gene012303.t1 MTR_5g013010 55.422 83 30 1 61 143 112 187 3.12e-21 87.8
MS.gene012303.t1 MTR_7g010020 48.864 88 45 0 91 178 79 166 3.36e-19 84.0
MS.gene012303.t1 MTR_3g080100 47.368 95 43 1 92 179 20 114 4.33e-19 82.4
MS.gene012303.t1 MTR_3g080100 47.368 95 43 1 92 179 59 153 5.60e-19 82.8
MS.gene012303.t1 MTR_8g469430 48.936 94 41 1 92 178 89 182 8.77e-19 82.8
MS.gene012303.t1 MTR_5g038280 46.809 94 43 1 92 178 87 180 2.30e-18 82.4
MS.gene012303.t1 MTR_7g103340 42.453 106 61 0 73 178 44 149 2.37e-18 80.9
MS.gene012303.t1 MTR_6g007647 48.387 93 41 1 92 177 33 125 6.17e-18 80.1
MS.gene012303.t1 MTR_6g007647 48.387 93 41 1 92 177 67 159 7.95e-18 80.1
MS.gene012303.t1 MTR_6g011610 47.872 94 42 1 92 178 96 189 1.58e-17 79.3
MS.gene012303.t1 MTR_8g468210 46.591 88 47 0 92 179 77 164 2.14e-17 79.0
MS.gene012303.t1 MTR_6g011610 47.872 94 42 1 92 178 77 170 2.26e-17 78.6
MS.gene012303.t1 MTR_8g089895 37.500 136 71 2 91 219 53 181 2.28e-17 79.3
MS.gene012303.t1 MTR_5g039000 45.455 88 48 0 92 179 77 164 8.56e-17 77.4
MS.gene012303.t1 MTR_1g061660 43.011 93 53 0 88 180 55 147 2.96e-16 75.1
MS.gene012303.t1 MTR_3g086790 40.385 104 53 2 82 178 52 153 2.18e-15 73.6
MS.gene012303.t1 MTR_4g107650 45.161 93 44 1 92 177 95 187 1.08e-14 72.0
MS.gene012303.t1 MTR_8g026960 39.048 105 57 1 96 193 38 142 2.90e-13 67.0
MS.gene012303.t1 MTR_3g092150 42.857 84 48 0 95 178 41 124 2.35e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012303.t1 AT4G37790 40.244 246 99 6 1 207 1 237 3.48e-41 141
MS.gene012303.t1 AT3G60390 58.015 131 51 2 78 207 147 274 2.25e-40 140
MS.gene012303.t1 AT4G16780 57.143 126 50 2 81 206 119 240 3.87e-38 134
MS.gene012303.t1 AT5G06710 52.593 135 50 2 78 207 176 301 6.76e-38 134
MS.gene012303.t1 AT2G22800 39.316 234 105 6 1 207 1 224 1.47e-36 129
MS.gene012303.t1 AT2G44910 58.120 117 46 1 91 207 162 275 1.27e-35 128
MS.gene012303.t1 AT5G47370 49.296 142 69 1 78 219 116 254 2.39e-35 126
MS.gene012303.t1 AT4G17460 42.941 170 78 3 47 216 106 256 2.66e-34 124
MS.gene012303.t1 AT2G01430 46.667 135 61 2 78 207 120 248 1.34e-28 108
MS.gene012303.t1 AT1G70920 42.958 142 68 2 67 207 44 173 2.52e-28 106
MS.gene012303.t1 AT1G70920 42.958 142 68 2 67 207 14 143 2.71e-28 105
MS.gene012303.t1 AT5G06710 59.155 71 29 0 73 143 171 241 9.04e-22 90.9
MS.gene012303.t1 AT1G26960 40.000 120 71 1 61 179 39 158 8.57e-19 82.4
MS.gene012303.t1 AT1G69780 48.864 88 45 0 92 179 85 172 1.25e-17 79.7
MS.gene012303.t1 AT3G01470 48.387 93 41 2 92 177 68 160 5.02e-17 77.8
MS.gene012303.t1 AT3G01220 47.312 93 45 1 92 180 87 179 6.66e-17 77.8
MS.gene012303.t1 AT2G01430 48.864 88 38 2 78 160 120 205 7.37e-17 76.3
MS.gene012303.t1 AT5G15150 48.936 94 41 1 92 178 115 208 1.54e-16 77.0
MS.gene012303.t1 AT2G46680 43.158 95 50 1 83 177 27 117 5.17e-16 74.7
MS.gene012303.t1 AT2G46680 43.158 95 50 1 83 177 27 117 5.42e-16 74.7
MS.gene012303.t1 AT5G65310 43.158 95 47 1 92 179 72 166 1.22e-15 74.7
MS.gene012303.t1 AT5G65310 43.158 95 47 1 92 179 54 148 1.45e-15 74.3
MS.gene012303.t1 AT5G03790 42.708 96 55 0 85 180 70 165 1.84e-15 73.2
MS.gene012303.t1 AT4G40060 44.086 93 48 1 92 180 59 151 4.56e-15 72.8
MS.gene012303.t1 AT2G22430 44.211 95 46 1 92 179 62 156 5.78e-15 72.8
MS.gene012303.t1 AT5G03790 44.444 90 50 0 85 174 70 159 3.43e-14 68.9
MS.gene012303.t1 AT3G61890 40.964 83 49 0 95 177 33 115 2.13e-13 67.4
MS.gene012303.t1 AT2G36610 36.496 137 74 3 75 203 54 185 2.58e-13 66.2
MS.gene012303.t1 AT4G36740 40.625 96 57 0 83 178 47 142 5.52e-12 63.2
MS.gene012303.t1 AT5G53980 43.333 90 49 2 90 178 9 97 5.69e-12 62.0
MS.gene012303.t1 AT2G18550 38.679 106 63 1 73 178 44 147 5.92e-12 63.2
MS.gene012303.t1 AT4G36740 40.625 96 57 0 83 178 46 141 6.02e-12 63.2
MS.gene012303.t1 AT5G66700 45.833 72 39 0 92 163 71 142 2.36e-11 61.6
MS.gene012303.t1 AT1G27045 41.935 93 47 1 92 177 68 160 7.24e-11 60.5
MS.gene012303.t1 AT1G27045 41.489 94 48 1 92 178 68 161 9.15e-11 60.1

Find 34 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAGGTGAAAGATTCAATT+TGG 0.267895 8.4:+7996658 MS.gene012303:CDS
ACGTTCATAGGTTCTCCTTT+TGG 0.352374 8.4:-7996614 None:intergenic
TTGAGGTTTGGTTTCAGAAC+AGG 0.362659 8.4:+7997233 MS.gene012303:CDS
GTCTTGTCTTTAACCTCAAT+TGG 0.365222 8.4:-7997207 None:intergenic
TTGTTGTTGTGTACGTTCAT+AGG 0.371543 8.4:-7996626 None:intergenic
TCTACGATCGTTGTTGTTGT+TGG 0.376794 8.4:-7996732 None:intergenic
AAGATTAAAGAAGGAATTGC+AGG 0.404223 8.4:+7997595 MS.gene012303:CDS
AGACAAGACAAATTGAGGTT+TGG 0.409339 8.4:+7997221 MS.gene012303:CDS
ACAGGTTTATGTCTAGGTCT+TGG 0.420666 8.4:+7996506 MS.gene012303:CDS
TTATGTCTAGGTCTTGGAAT+AGG 0.424289 8.4:+7996512 MS.gene012303:CDS
TTGCAGGAACTCAAAGTTGT+TGG 0.456628 8.4:+7997611 MS.gene012303:CDS
TAGCACTTGCTGACCAATTG+AGG 0.458161 8.4:+7997194 MS.gene012303:CDS
GCATTCTTCATCACTTTCCA+TGG 0.470187 8.4:-7996480 None:intergenic
GTTAAAGACAAGACAAATTG+AGG 0.472426 8.4:+7997216 MS.gene012303:CDS
ATACCGGATTAAGAGTGTTA+TGG 0.475608 8.4:-7996811 None:intergenic
AGTGATGAAGAATGCAATAC+AGG 0.485322 8.4:+7996488 MS.gene012303:CDS
GCTCCATAACACTCTTAATC+CGG 0.495490 8.4:+7996808 MS.gene012303:CDS
AAGAGTGTTATGGAGCTTGA+AGG 0.507942 8.4:-7996801 None:intergenic
TTGGACAAAGCTCAAAAGCT+AGG 0.524782 8.4:-7996595 None:intergenic
GACTAAGCTGAAGCAGATAG+AGG 0.526640 8.4:+7997520 MS.gene012303:CDS
TGAGAACAAAAGATTAAAGA+AGG 0.527592 8.4:+7997586 MS.gene012303:CDS
TGATCTTCATTATGCTTCAA+CGG 0.529611 8.4:-7997716 None:intergenic
TGCAATACAGGTTTATGTCT+AGG 0.537810 8.4:+7996500 MS.gene012303:CDS
CTTGAAGGTGCTCTCAAGCA+TGG 0.539476 8.4:-7996786 None:intergenic
GATGAACGTTGAGGGCATAA+CGG 0.572104 8.4:-7997641 None:intergenic
GGTTTCAGAACAGGAGAGCA+AGG 0.572572 8.4:+7997242 MS.gene012303:CDS
ATTAGTGAATAAATCTGTGA+TGG 0.573054 8.4:+7996559 MS.gene012303:CDS
TCTTGGAATAGGTGCAACAA+AGG 0.613459 8.4:+7996523 MS.gene012303:CDS
ACAGTACTATGAGTCACCAC+TGG 0.648715 8.4:-7997671 None:intergenic
TAAGCTGAAGCAGATAGAGG+TGG 0.656332 8.4:+7997523 MS.gene012303:CDS
AAAGAAACTGAGGCTAACAA+AGG 0.656758 8.4:+7996754 MS.gene012303:CDS
TCAAAAGCTAGGTCAAAACA+AGG 0.669862 8.4:-7996584 None:intergenic
ACGTTCATCATCAAAACCAG+TGG 0.688173 8.4:+7997655 MS.gene012303:CDS
ACGATCGTAGAAAGAAACTG+AGG 0.720750 8.4:+7996744 MS.gene012303:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATTATTATTATTTTTAA+TGG + chr8.4:7997039-7997058 MS.gene012303:intron 0.0%
!! ACAATTTATTTATAAGCTAA+TGG - chr8.4:7997478-7997497 None:intergenic 15.0%
!! TGTATTTATTTATATAACAC+AGG + chr8.4:7997498-7997517 MS.gene012303:intron 15.0%
!!! AATTTTTCTTCATATTATCT+GGG + chr8.4:7997336-7997355 MS.gene012303:intron 15.0%
!!! TAATTTTTCTTCATATTATC+TGG + chr8.4:7997335-7997354 MS.gene012303:intron 15.0%
!!! TACATATTATAGAGAATTTT+TGG - chr8.4:7996854-7996873 None:intergenic 15.0%
!!! ACGTTACATTTTGATAATAT+TGG - chr8.4:7996691-7996710 None:intergenic 20.0%
! ATTAGTGAATAAATCTGTGA+TGG + chr8.4:7996559-7996578 MS.gene012303:CDS 25.0%
! TGAGAACAAAAGATTAAAGA+AGG + chr8.4:7997586-7997605 MS.gene012303:CDS 25.0%
! TGTCATATTGTGTATGTATA+AGG + chr8.4:7996896-7996915 MS.gene012303:intron 25.0%
!! TTTTGGTATGAATGAATGAA+TGG - chr8.4:7996837-7996856 None:intergenic 25.0%
!!! ATTAGTTTTTCTAGATGACA+AGG + chr8.4:7997116-7997135 MS.gene012303:intron 25.0%
!!! TTAGTTTTTCTAGATGACAA+GGG + chr8.4:7997117-7997136 MS.gene012303:intron 25.0%
!!! TTTTGGTTTCATATATATGC+AGG + chr8.4:7997162-7997181 MS.gene012303:intron 25.0%
AAGATTAAAGAAGGAATTGC+AGG + chr8.4:7997595-7997614 MS.gene012303:CDS 30.0%
ATGAATGAATGAATGGATAC+CGG - chr8.4:7996830-7996849 None:intergenic 30.0%
CAAAGGTGAAAGATTCAATT+TGG + chr8.4:7996658-7996677 MS.gene012303:CDS 30.0%
GTTAAAGACAAGACAAATTG+AGG + chr8.4:7997216-7997235 MS.gene012303:CDS 30.0%
TGATCTTCATTATGCTTCAA+CGG - chr8.4:7997719-7997738 None:intergenic 30.0%
! CTATATGTTGATATCGATTG+CGG + chr8.4:7997420-7997439 MS.gene012303:intron 30.0%
AAAGAAACTGAGGCTAACAA+AGG + chr8.4:7996754-7996773 MS.gene012303:CDS 35.0%
AACAACAACAACAACAGCAA+AGG + chr8.4:7996641-7996660 MS.gene012303:CDS 35.0%
AGACAAGACAAATTGAGGTT+TGG + chr8.4:7997221-7997240 MS.gene012303:CDS 35.0%
AGTGATGAAGAATGCAATAC+AGG + chr8.4:7996488-7996507 MS.gene012303:CDS 35.0%
GTAGAAATGAGTTTATGCGT+TGG + chr8.4:7997139-7997158 MS.gene012303:intron 35.0%
GTCTTGTCTTTAACCTCAAT+TGG - chr8.4:7997210-7997229 None:intergenic 35.0%
TCAAAAGCTAGGTCAAAACA+AGG - chr8.4:7996587-7996606 None:intergenic 35.0%
TGCAATACAGGTTTATGTCT+AGG + chr8.4:7996500-7996519 MS.gene012303:CDS 35.0%
TTATGTCTAGGTCTTGGAAT+AGG + chr8.4:7996512-7996531 MS.gene012303:CDS 35.0%
! TTGTTGTTGTGTACGTTCAT+AGG - chr8.4:7996629-7996648 None:intergenic 35.0%
!! ATACCGGATTAAGAGTGTTA+TGG - chr8.4:7996814-7996833 None:intergenic 35.0%
!!! ATGAGTTTATGCGTTGGTTT+TGG + chr8.4:7997145-7997164 MS.gene012303:intron 35.0%
!!! GTTTTGATGATGAACGTTGA+GGG - chr8.4:7997652-7997671 None:intergenic 35.0%
ACAGGTTTATGTCTAGGTCT+TGG + chr8.4:7996506-7996525 MS.gene012303:CDS 40.0%
ACGATCGTAGAAAGAAACTG+AGG + chr8.4:7996744-7996763 MS.gene012303:CDS 40.0%
ACGTTCATCATCAAAACCAG+TGG + chr8.4:7997655-7997674 MS.gene012303:CDS 40.0%
GCTCCATAACACTCTTAATC+CGG + chr8.4:7996808-7996827 MS.gene012303:CDS 40.0%
TCTTGGAATAGGTGCAACAA+AGG + chr8.4:7996523-7996542 MS.gene012303:CDS 40.0%
TTGCAGGAACTCAAAGTTGT+TGG + chr8.4:7997611-7997630 MS.gene012303:CDS 40.0%
TTGGACAAAGCTCAAAAGCT+AGG - chr8.4:7996598-7996617 None:intergenic 40.0%
! ACGTTCATAGGTTCTCCTTT+TGG - chr8.4:7996617-7996636 None:intergenic 40.0%
! TCTACGATCGTTGTTGTTGT+TGG - chr8.4:7996735-7996754 None:intergenic 40.0%
! TTGAGGTTTGGTTTCAGAAC+AGG + chr8.4:7997233-7997252 MS.gene012303:CDS 40.0%
!! AAGAGTGTTATGGAGCTTGA+AGG - chr8.4:7996804-7996823 None:intergenic 40.0%
!! GCTTTTGAGCTTTGTCCAAA+AGG + chr8.4:7996599-7996618 MS.gene012303:CDS 40.0%
!!! GGTTTTGATGATGAACGTTG+AGG - chr8.4:7997653-7997672 None:intergenic 40.0%
ACAGTACTATGAGTCACCAC+TGG - chr8.4:7997674-7997693 None:intergenic 45.0%
GACTAAGCTGAAGCAGATAG+AGG + chr8.4:7997520-7997539 MS.gene012303:CDS 45.0%
TAAGCTGAAGCAGATAGAGG+TGG + chr8.4:7997523-7997542 MS.gene012303:CDS 45.0%
! GATGAACGTTGAGGGCATAA+CGG - chr8.4:7997644-7997663 None:intergenic 45.0%
! TAGCACTTGCTGACCAATTG+AGG + chr8.4:7997194-7997213 MS.gene012303:CDS 45.0%
!! AATAAATACTAAAATTAAAT+AGG - chr8.4:7997384-7997403 None:intergenic 5.0%
GGTTTCAGAACAGGAGAGCA+AGG + chr8.4:7997242-7997261 MS.gene012303:CDS 50.0%
!! CTTGAAGGTGCTCTCAAGCA+TGG - chr8.4:7996789-7996808 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 7996482 7997754 7996482 ID=MS.gene012303
chr8.4 mRNA 7996482 7997754 7996482 ID=MS.gene012303.t1;Parent=MS.gene012303
chr8.4 exon 7996482 7996829 7996482 ID=MS.gene012303.t1.exon1;Parent=MS.gene012303.t1
chr8.4 CDS 7996482 7996829 7996482 ID=cds.MS.gene012303.t1;Parent=MS.gene012303.t1
chr8.4 exon 7997184 7997263 7997184 ID=MS.gene012303.t1.exon2;Parent=MS.gene012303.t1
chr8.4 CDS 7997184 7997263 7997184 ID=cds.MS.gene012303.t1;Parent=MS.gene012303.t1
chr8.4 exon 7997520 7997754 7997520 ID=MS.gene012303.t1.exon3;Parent=MS.gene012303.t1
chr8.4 CDS 7997520 7997754 7997520 ID=cds.MS.gene012303.t1;Parent=MS.gene012303.t1
Gene Sequence

>MS.gene012303

ATGGAAAGTGATGAAGAATGCAATACAGGTTTATGTCTAGGTCTTGGAATAGGTGCAACAAAGGTGAAGAAGCAGAAATTAGTGAATAAATCTGTGATGGCACCTTGTTTTGACCTAGCTTTTGAGCTTTGTCCAAAAGGAGAACCTATGAACGTACACAACAACAACAACAACAGCAAAGGTGAAAGATTCAATTTGGAGAGACACCAATATTATCAAAATGTAACGTGTAGCACTGATTCTGATAACACCAACAACAACAACGATCGTAGAAAGAAACTGAGGCTAACAAAGGAGCAATCATCCATGCTTGAGAGCACCTTCAAGCTCCATAACACTCTTAATCCGGTATCCATTCATTCATTCATACCAAAAATTCTCTATAATATGTATTAGCATATATGTAACATAATCTGTCATATTGTGTATGTATAAGGTTGTAGAACTTTAATAAACTGAATTATATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTTTTAATGGCAAATTGAAAAACAAATTATTGTCTATTTACTATTTCTTTTTTGTTCAACTATAATTAGTTTTTCTAGATGACAAGGGTAGAAATGAGTTTATGCGTTGGTTTTGGTTTCATATATATGCAGGTTCAGAAAATAGCACTTGCTGACCAATTGAGGTTAAAGACAAGACAAATTGAGGTTTGGTTTCAGAACAGGAGAGCAAGGTACGTTAATTAATTTATGTGTTCAGATATTTCATTGATCTTATAACTATGTTGTTACTTTTGTCTAGCATTAATTTTTCTTCATATTATCTGGGTTTCGTAACTGAATATATATCACCTATTTAATTTTAGTATTTATTTATGTTGTTGACTAAGCTATATGTTGATATCGATTGCGGAATAGTACGTAGTAGTATTATATATTTAATTTCCATTAGCTTATAAATAAATTGTTGTATTTATTTATATAACACAGGACTAAGCTGAAGCAGATAGAGGTGGATTATGAGTTGTTGAAAAAACATTGTCAAAATCTAAGTGATGAGAACAAAAGATTAAAGAAGGAATTGCAGGAACTCAAAGTTGTTGGACAATTTCCGTTATGCCCTCAACGTTCATCATCAAAACCAGTGGTGACTCATAGTACTGTGTGCTCTTCTTGTGAGCAGAAACCGTTGAAGCATAATGAAGATCACAGTAATAATTTATAA
Protein sequence

>MS.gene012303.t1

MESDEECNTGLCLGLGIGATKVKKQKLVNKSVMAPCFDLAFELCPKGEPMNVHNNNNNSKGERFNLERHQYYQNVTCSTDSDNTNNNNDRRKKLRLTKEQSSMLESTFKLHNTLNPVQKIALADQLRLKTRQIEVWFQNRRARTKLKQIEVDYELLKKHCQNLSDENKRLKKELQELKVVGQFPLCPQRSSSKPVVTHSTVCSSCEQKPLKHNEDHSNNL