AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073575

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073575.t1 MTR_1g049100 89.899 198 17 2 1 196 1 197 1.74e-109 311
MS.gene073575.t1 MTR_5g036480 67.932 237 35 4 1 196 1 237 2.90e-90 264
MS.gene073575.t1 MTR_4g106590 59.669 181 66 3 3 179 21 198 8.61e-63 194
MS.gene073575.t1 MTR_3g078613 61.006 159 56 2 7 162 22 177 1.15e-60 188
MS.gene073575.t1 MTR_3g078613 60.625 160 56 3 7 162 22 178 7.55e-59 183
MS.gene073575.t1 MTR_7g490310 51.813 193 78 3 7 184 8 200 1.25e-56 179
MS.gene073575.t1 MTR_8g038620 59.155 142 53 2 7 143 8 149 7.89e-51 162
MS.gene073575.t1 MTR_3g093860 58.696 138 50 3 4 138 14 147 1.26e-49 158
MS.gene073575.t1 MTR_3g015490 52.903 155 61 3 7 152 3 154 6.83e-46 149
MS.gene073575.t1 MTR_3g088630 50.676 148 57 3 6 138 20 166 8.34e-43 143
MS.gene073575.t1 MTR_6g007460 39.320 206 63 5 7 159 10 206 1.26e-35 124
MS.gene073575.t1 MTR_4g061360 35.075 134 75 2 8 141 89 210 1.70e-17 80.1
MS.gene073575.t1 MTR_3g092780 29.932 147 88 2 8 151 56 190 5.73e-17 78.6
MS.gene073575.t1 MTR_3g092780 29.932 147 88 2 8 151 56 190 6.65e-17 78.6
MS.gene073575.t1 MTR_3g092780 29.730 148 88 2 8 151 56 191 1.08e-16 77.8
MS.gene073575.t1 MTR_3g092780 29.730 148 88 2 8 151 56 191 1.17e-16 77.8
MS.gene073575.t1 MTR_4g051330 52.239 67 29 1 89 152 77 143 6.75e-15 69.3
MS.gene073575.t1 MTR_7g118260 32.308 130 74 3 14 143 22 137 1.89e-14 71.2
MS.gene073575.t1 MTR_8g024260 30.882 136 82 1 8 143 36 159 5.09e-14 70.1
MS.gene073575.t1 MTR_1g067110 28.788 132 82 1 10 141 87 206 1.88e-13 68.6
MS.gene073575.t1 MTR_1g067110 28.788 132 82 1 10 141 87 206 2.24e-13 68.2
MS.gene073575.t1 MTR_7g118260 29.870 154 96 2 8 161 14 155 9.95e-13 66.2
MS.gene073575.t1 MTR_4g131570 27.778 162 101 4 8 168 21 167 3.33e-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.gene073575.t1 AT1G59940 59.901 202 60 5 4 188 29 226 5.84e-73 220
MS.gene073575.t1 AT1G59940 59.901 202 60 5 4 188 121 318 1.65e-71 219
MS.gene073575.t1 AT1G10470 55.752 226 57 6 6 192 18 239 3.37e-70 214
MS.gene073575.t1 AT1G10470 55.752 226 57 6 6 192 32 253 8.79e-70 213
MS.gene073575.t1 AT3G48100 65.563 151 50 1 8 158 25 173 8.73e-64 195
MS.gene073575.t1 AT5G62920 72.656 128 32 1 8 135 25 149 3.06e-61 189
MS.gene073575.t1 AT1G74890 71.318 129 34 1 7 135 17 142 3.82e-59 184
MS.gene073575.t1 AT1G19050 60.784 153 53 2 7 155 23 172 2.26e-58 182
MS.gene073575.t1 AT2G40670 59.259 135 55 0 4 138 25 159 1.18e-54 171
MS.gene073575.t1 AT3G57040 58.993 139 50 2 7 138 8 146 2.22e-53 171
MS.gene073575.t1 AT3G57040 58.993 139 50 2 7 138 8 146 2.22e-53 171
MS.gene073575.t1 AT3G56380 61.194 134 48 2 6 138 18 148 2.36e-53 167
MS.gene073575.t1 AT2G41310 59.441 143 52 2 1 138 3 144 5.10e-53 169
MS.gene073575.t1 AT2G40670 58.824 136 55 1 4 138 25 160 7.95e-53 167
MS.gene073575.t1 AT3G56380 60.741 135 48 3 6 138 18 149 1.73e-51 163
MS.gene073575.t1 AT1G10470 56.044 91 30 6 70 155 17 102 1.52e-23 92.8
MS.gene073575.t1 AT2G46790 31.343 134 80 2 8 141 37 158 2.20e-15 73.9
MS.gene073575.t1 AT5G24470 30.216 139 83 3 8 146 52 176 2.38e-15 73.9
MS.gene073575.t1 AT2G46790 31.343 134 80 2 8 141 37 158 2.44e-15 73.9
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.61e-14 71.2
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.61e-14 71.2
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.61e-14 71.2
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 2.71e-14 70.9
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 2.73e-14 70.9
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 2.73e-14 70.9
MS.gene073575.t1 AT5G60100 34.848 132 74 2 10 141 66 185 2.73e-14 70.9
MS.gene073575.t1 AT2G07440 60.000 50 20 0 89 138 9 58 1.56e-13 65.1
MS.gene073575.t1 AT5G02810 28.358 134 84 1 8 141 78 199 9.46e-13 66.6

Find 38 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTGATTACATGCTTCTTC+TGG 0.272524 1.1:+34030876 None:intergenic
ATTGAAAATATTCAGATGTT+TGG 0.307010 1.1:-34031012 MS.gene073575:intron
AACTCATAACCAGTCATTTC+TGG 0.328147 1.1:+34031904 None:intergenic
TTTGTTGCCTTAGCCTTTGA+AGG 0.366124 1.1:-34031956 MS.gene073575:intron
CTCAAAATTTCTGCTTGTAA+AGG 0.386939 1.1:-34032362 MS.gene073575:intron
TTCTGAAGAGGTTCATGTAT+TGG 0.402386 1.1:-34032429 MS.gene073575:CDS
TACTGGAATTTCCTTAAAAG+TGG 0.438337 1.1:+34031747 None:intergenic
TTAGTTACTGCTGTGGATAG+TGG 0.438893 1.1:-34032135 MS.gene073575:intron
TTCACATCACATAACTTCAC+TGG 0.475573 1.1:+34030960 None:intergenic
ATAACAGTACCTGTCTATGC+GGG 0.487586 1.1:+34031696 None:intergenic
TCAGAAGACATAATCACTAC+TGG 0.489512 1.1:+34031730 None:intergenic
ATGTGAAGGTGATGATGAAA+TGG 0.496627 1.1:+34030839 None:intergenic
ATATTCTGCCCCGCATAGAC+AGG 0.510615 1.1:-34031705 MS.gene073575:intron
ATATTCAGATGTTTGGAAGA+AGG 0.511460 1.1:-34031005 MS.gene073575:intron
TATTGCATGCCAGAAATGAC+TGG 0.520879 1.1:-34031913 MS.gene073575:CDS
TTGATCGGAAAGTTATTGAA+AGG 0.524082 1.1:-34032388 MS.gene073575:CDS
ATAACAAGATCCACCTTCAA+AGG 0.539532 1.1:+34031943 None:intergenic
GTTGCCTTAGCCTTTGAAGG+TGG 0.539999 1.1:-34031953 MS.gene073575:intron
TGCTTGATTCTCCAATCAGA+CGG 0.554606 1.1:-34030788 MS.gene073575:CDS
TACATGACAACAAGGGAGGT+TGG 0.562595 1.1:-34030924 MS.gene073575:CDS
ACAACAAGGGAGGTTGGAGT+AGG 0.598300 1.1:-34030918 MS.gene073575:CDS
ATGTTTGGAAGAAGGTGCAA+AGG 0.598645 1.1:-34030997 MS.gene073575:CDS
AGAGAGAAGTCTGAATCTGA+TGG 0.604808 1.1:-34032075 MS.gene073575:CDS
GTGAACTTTAGTTACTGCTG+TGG 0.606977 1.1:-34032142 MS.gene073575:intron
TTGATGATAGTCTCATTGAT+CGG 0.612021 1.1:-34032403 MS.gene073575:CDS
GATGGAGACAAATTCTGAAG+AGG 0.614838 1.1:-34032441 MS.gene073575:CDS
AGCACACTGGATGCAGACAA+CGG 0.623915 1.1:+34030807 None:intergenic
TGAAGGGTTACATGACAACA+AGG 0.633631 1.1:-34030932 MS.gene073575:CDS
GATTGGAGAATCAAGCACAC+TGG 0.650465 1.1:+34030794 None:intergenic
ATGTGATGTGAAACGACTGA+AGG 0.663812 1.1:-34030949 MS.gene073575:CDS
TGTGATGTGAAACGACTGAA+GGG 0.670059 1.1:-34030948 MS.gene073575:CDS
TATAACAGTACCTGTCTATG+CGG 0.670864 1.1:+34031695 None:intergenic
TAACAGTACCTGTCTATGCG+GGG 0.697429 1.1:+34031697 None:intergenic
GGTGATGATGAAATGGACGG+TGG 0.704627 1.1:+34030846 None:intergenic
GGGTTACATGACAACAAGGG+AGG 0.715675 1.1:-34030928 MS.gene073575:CDS
AACGGAGATGATGAATGTGA+AGG 0.717795 1.1:+34030825 None:intergenic
GAAGGTGATGATGAAATGGA+CGG 0.719690 1.1:+34030843 None:intergenic
GAAGGGTTACATGACAACAA+GGG 0.758159 1.1:-34030931 MS.gene073575:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAAGGGATTATTATTATT+AGG - chr1.1:34031546-34031565 MS.gene073575:intron 15.0%
!!! AACAATTTTTGAAAAATAGT+TGG + chr1.1:34032112-34032131 None:intergenic 15.0%
!!! TATAGTAATGATTTTTTCAA+TGG + chr1.1:34031364-34031383 None:intergenic 15.0%
!! ATTGAAAATATTCAGATGTT+TGG - chr1.1:34032192-34032211 MS.gene073575:intron 20.0%
!!! ACGAAATAGATGTTTTTAAA+GGG - chr1.1:34031674-34031693 MS.gene073575:intron 20.0%
!!! ATTTAAGTGTCTTTTTTCTT+TGG + chr1.1:34031830-34031849 None:intergenic 20.0%
!!! TACGAAATAGATGTTTTTAA+AGG - chr1.1:34031673-34031692 MS.gene073575:intron 20.0%
! TGAGTTGCTCAAAAAAATTA+AGG - chr1.1:34031317-34031336 MS.gene073575:intron 25.0%
!! GTCATTAAAAAGTATAACCA+TGG + chr1.1:34031742-34031761 None:intergenic 25.0%
!! TTTTCAATTGTAACAAACCA+TGG - chr1.1:34031722-34031741 MS.gene073575:CDS 25.0%
!!! CGAAATAGATGTTTTTAAAG+GGG - chr1.1:34031675-34031694 MS.gene073575:intron 25.0%
!!! GTGTTGATGATTTTTGTTTT+TGG - chr1.1:34031040-34031059 MS.gene073575:intron 25.0%
ATATTCAGATGTTTGGAAGA+AGG - chr1.1:34032199-34032218 MS.gene073575:intron 30.0%
CCTGCTTCAAAATGAAATTT+CGG + chr1.1:34031431-34031450 None:intergenic 30.0%
CTCAAAATTTCTGCTTGTAA+AGG - chr1.1:34030842-34030861 MS.gene073575:CDS 30.0%
TACTGGAATTTCCTTAAAAG+TGG + chr1.1:34031460-34031479 None:intergenic 30.0%
TTGATCGGAAAGTTATTGAA+AGG - chr1.1:34030816-34030835 MS.gene073575:CDS 30.0%
! ATCATTTTAAACCGTCTGAT+TGG + chr1.1:34032430-34032449 None:intergenic 30.0%
! TTATTGTTATTAGTTACCGC+TGG - chr1.1:34032130-34032149 MS.gene073575:CDS 30.0%
! TTGATGATAGTCTCATTGAT+CGG - chr1.1:34030801-34030820 MS.gene073575:CDS 30.0%
AACTCATAACCAGTCATTTC+TGG + chr1.1:34031303-34031322 None:intergenic 35.0%
AACTTCATCTCAATTTCCAG+CGG + chr1.1:34032149-34032168 None:intergenic 35.0%
ATAACAAGATCCACCTTCAA+AGG + chr1.1:34031264-34031283 None:intergenic 35.0%
GATTGATTACATGCTTCTTC+TGG + chr1.1:34032331-34032350 None:intergenic 35.0%
GTAAAGGTGAGTTTGTGATT+TGG - chr1.1:34030858-34030877 MS.gene073575:CDS 35.0%
TATAACAGTACCTGTCTATG+CGG + chr1.1:34031512-34031531 None:intergenic 35.0%
TCAGAAGACATAATCACTAC+TGG + chr1.1:34031477-34031496 None:intergenic 35.0%
TTCACATCACATAACTTCAC+TGG + chr1.1:34032247-34032266 None:intergenic 35.0%
! ATGTGAAGGTGATGATGAAA+TGG + chr1.1:34032368-34032387 None:intergenic 35.0%
! TCTGATGGTTCTATTGTATG+TGG - chr1.1:34031144-34031163 MS.gene073575:intron 35.0%
! TTCTGAAGAGGTTCATGTAT+TGG - chr1.1:34030775-34030794 MS.gene073575:CDS 35.0%
!!! AATCAGAGCACTGCAATTTT+TGG - chr1.1:34031092-34031111 MS.gene073575:intron 35.0%
!!! ATCAGAGCACTGCAATTTTT+GGG - chr1.1:34031093-34031112 MS.gene073575:intron 35.0%
!!! CCGAAATTTCATTTTGAAGC+AGG - chr1.1:34031428-34031447 MS.gene073575:intron 35.0%
AACGGAGATGATGAATGTGA+AGG + chr1.1:34032382-34032401 None:intergenic 40.0%
AGAGAGAAGTCTGAATCTGA+TGG - chr1.1:34031129-34031148 MS.gene073575:intron 40.0%
ATAACAGTACCTGTCTATGC+GGG + chr1.1:34031511-34031530 None:intergenic 40.0%
ATGTGATGTGAAACGACTGA+AGG - chr1.1:34032255-34032274 MS.gene073575:intron 40.0%
GAAGGGTTACATGACAACAA+GGG - chr1.1:34032273-34032292 MS.gene073575:intron 40.0%
GTGAACTTTAGTTACTGCTG+TGG - chr1.1:34031062-34031081 MS.gene073575:intron 40.0%
TATTGCATGCCAGAAATGAC+TGG - chr1.1:34031291-34031310 MS.gene073575:intron 40.0%
TGAAGGGTTACATGACAACA+AGG - chr1.1:34032272-34032291 MS.gene073575:intron 40.0%
TGCTTGATTCTCCAATCAGA+CGG - chr1.1:34032416-34032435 MS.gene073575:CDS 40.0%
TGTGATGTGAAACGACTGAA+GGG - chr1.1:34032256-34032275 MS.gene073575:intron 40.0%
TTAGTTACTGCTGTGGATAG+TGG - chr1.1:34031069-34031088 MS.gene073575:intron 40.0%
! ATGTTTGGAAGAAGGTGCAA+AGG - chr1.1:34032207-34032226 MS.gene073575:intron 40.0%
! GAAGGTGATGATGAAATGGA+CGG + chr1.1:34032364-34032383 None:intergenic 40.0%
! TTTGTTGCCTTAGCCTTTGA+AGG - chr1.1:34031248-34031267 MS.gene073575:intron 40.0%
!!! TCAGAGCACTGCAATTTTTG+GGG - chr1.1:34031094-34031113 MS.gene073575:intron 40.0%
AGATCCACCTTCAAAGGCTA+AGG + chr1.1:34031258-34031277 None:intergenic 45.0%
GATTGGAGAATCAAGCACAC+TGG + chr1.1:34032413-34032432 None:intergenic 45.0%
TAACAGTACCTGTCTATGCG+GGG + chr1.1:34031510-34031529 None:intergenic 45.0%
TACATGACAACAAGGGAGGT+TGG - chr1.1:34032280-34032299 MS.gene073575:intron 45.0%
!! GCAGGAATCGTCCACTTTTA+AGG - chr1.1:34031446-34031465 MS.gene073575:intron 45.0%
!!! AGCACTGCAATTTTTGGGGT+TGG - chr1.1:34031098-34031117 MS.gene073575:intron 45.0%
!! TAATTTATACTTATATATAA+TGG + chr1.1:34031864-34031883 None:intergenic 5.0%
!!! ATTTTTTTAAACTTTTTTAA+GGG - chr1.1:34031531-34031550 MS.gene073575:intron 5.0%
!!! TATTTTTTTAAACTTTTTTA+AGG - chr1.1:34031530-34031549 MS.gene073575:intron 5.0%
ACAACAAGGGAGGTTGGAGT+AGG - chr1.1:34032286-34032305 MS.gene073575:intron 50.0%
AGCACACTGGATGCAGACAA+CGG + chr1.1:34032400-34032419 None:intergenic 50.0%
ATATTCTGCCCCGCATAGAC+AGG - chr1.1:34031499-34031518 MS.gene073575:intron 50.0%
GGGTTACATGACAACAAGGG+AGG - chr1.1:34032276-34032295 MS.gene073575:intron 50.0%
! GGTGATGATGAAATGGACGG+TGG + chr1.1:34032361-34032380 None:intergenic 50.0%
! GTTGCCTTAGCCTTTGAAGG+TGG - chr1.1:34031251-34031270 MS.gene073575:intron 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 34030764 34032462 34030764 ID=MS.gene073575
chr1.1 mRNA 34030764 34032462 34030764 ID=MS.gene073575.t1;Parent=MS.gene073575
chr1.1 exon 34032363 34032462 34032363 ID=MS.gene073575.t1.exon1;Parent=MS.gene073575.t1
chr1.1 CDS 34032363 34032462 34032363 ID=cds.MS.gene073575.t1;Parent=MS.gene073575.t1
chr1.1 exon 34032068 34032153 34032068 ID=MS.gene073575.t1.exon2;Parent=MS.gene073575.t1
chr1.1 CDS 34032068 34032153 34032068 ID=cds.MS.gene073575.t1;Parent=MS.gene073575.t1
chr1.1 exon 34031888 34031965 34031888 ID=MS.gene073575.t1.exon3;Parent=MS.gene073575.t1
chr1.1 CDS 34031888 34031965 34031888 ID=cds.MS.gene073575.t1;Parent=MS.gene073575.t1
chr1.1 exon 34031706 34031776 34031706 ID=MS.gene073575.t1.exon4;Parent=MS.gene073575.t1
chr1.1 CDS 34031706 34031776 34031706 ID=cds.MS.gene073575.t1;Parent=MS.gene073575.t1
chr1.1 exon 34030764 34031019 34030764 ID=MS.gene073575.t1.exon5;Parent=MS.gene073575.t1
chr1.1 CDS 34030764 34031019 34030764 ID=cds.MS.gene073575.t1;Parent=MS.gene073575.t1
Gene Sequence

>MS.gene073575

ATGGAGACAAATTCTGAAGAGGTTCATGTATTGGCTGTTGATGATAGTCTCATTGATCGGAAAGTTATTGAAAGGTTGCTCAAAATTTCTGCTTGTAAAGGTGAGTTTGTGATTTGGTAAAACAAAAATAAAATTAATAAAATGTTTTTTCATTTGTGAAGATTTTTGAAGATATTCTCATTTGTGAAGATTTTTGTTTAACAAATATAAGTGAAATGAAAAAGAAGTAGAATTTTTTTTAGTGTTATTTTTTTTAATTTCTTTTTAAATTTTAATGTGTTGATGATTTTTGTTTTTGGTGAACTTTAGTTACTGCTGTGGATAGTGGAATCAGAGCACTGCAATTTTTGGGGTTGGATGAGCAGAGAGAGAAGTCTGAATCTGATGGTTCTATTGTATGTGGCAATTATTTTATTTTATTTATTTTATAGTTTTTATTCTTTTAATATAATGTTAATTAATTTACTGATTTTATTATTTTATTTTTGTTGCCTTAGCCTTTGAAGGTGGATCTTGTTATTACAGATTATTGCATGCCAGAAATGACTGGTTATGAGTTGCTCAAAAAAATTAAGGTTCAAATTCATTATCACAATTCCATTGAAAAAATCATTACTATAATTTATTTTTCACTCTTTTGATTATATTGTTAGTGAAGTTTGATCCGAAATTTCATTTTGAAGCAGGAATCGTCCACTTTTAAGGAAATTCCAGTAGTGATTATGTCTTCTGAAAATATTCTGCCCCGCATAGACAGGTACTGTTATATTTTTTTAAACTTTTTTAAGGGATTATTATTATTAGGTAATTTTGACTTTTTATTTTATTTTACTAACACATCTAAATTATGAACATTGTATTTTGTGAAATTTTGATTTTGATAAAAATAATTTTGATTGAAATAATAAGTACGAAATAGATGTTTTTAAAGGGGAAGAATGAAATAGATGTTTGTGAGTTTTCAATTGTAACAAACCATGGTTATACTTTTTAATGACATGTTTTCAATGAAACAAATAATATAATATTTTTATAAACAAGTTTATTTAAAAGTATTTTTTGACCAAAGAAAAAAGACACTTAAATTTTTTTTATCACCATTATATATAAGTATAAATTATTATTATTATTTTTATTATTATTATTATTATTATTATTTTTATTATTATTATTATTATTTTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATGTTCAATAAATCATTATTGTTATCTTCAAAAAAATAAATCATTATTGTTAATTTGTTGCATACATAACTTTTAACACAGTAAACCAACTATTTTTCAAAAATTGTTATTGTTATTAGTTACCGCTGGAAATTGAGATGAAGTTGAAAAAATGAGTGATTTGTAAATATTGAAAATATTCAGATGTTTGGAAGAAGGTGCAAAGGATTTTATAATAAAGCCAGTGAAGTTATGTGATGTGAAACGACTGAAGGGTTACATGACAACAAGGGAGGTTGGAGTAGGAATCAACAACAAACAGAAGCCAGAAGAAGCATGTAATCAATCATCATCACCACCGTCCATTTCATCATCACCTTCACATTCATCATCTCCGTTGTCTGCATCCAGTGTGCTTGATTCTCCAATCAGACGGTTTAAAATGATTGACACTGAATGA
Protein sequence

>MS.gene073575.t1

METNSEEVHVLAVDDSLIDRKVIERLLKISACKVTAVDSGIRALQFLGLDEQREKSESDGSIPLKVDLVITDYCMPEMTGYELLKKIKESSTFKEIPVVIMSSENILPRIDRCLEEGAKDFIIKPVKLCDVKRLKGYMTTREVGVGINNKQKPEEACNQSSSPPSISSSPSHSSSPLSASSVLDSPIRRFKMIDTE