AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85771

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85771.t1 MTR_1g049100 89.899 198 17 2 1 196 1 197 2.76e-109 311
MS.gene85771.t1 MTR_5g036480 67.511 237 36 4 1 196 1 237 6.06e-89 261
MS.gene85771.t1 MTR_4g106590 59.669 181 66 3 3 179 21 198 9.40e-63 194
MS.gene85771.t1 MTR_3g078613 61.006 159 56 2 7 162 22 177 1.31e-60 187
MS.gene85771.t1 MTR_3g078613 60.625 160 56 3 7 162 22 178 7.98e-59 183
MS.gene85771.t1 MTR_7g490310 51.813 193 78 3 7 184 8 200 2.20e-56 178
MS.gene85771.t1 MTR_8g038620 59.155 142 53 2 7 143 8 149 7.97e-51 162
MS.gene85771.t1 MTR_3g093860 58.696 138 50 3 4 138 14 147 1.01e-49 158
MS.gene85771.t1 MTR_3g015490 52.903 155 61 3 7 152 3 154 8.39e-46 149
MS.gene85771.t1 MTR_3g088630 50.676 148 57 3 6 138 20 166 8.62e-43 143
MS.gene85771.t1 MTR_6g007460 41.622 185 52 4 7 138 10 191 2.63e-35 123
MS.gene85771.t1 MTR_4g061360 35.075 134 75 2 8 141 89 210 1.82e-17 80.1
MS.gene85771.t1 MTR_3g092780 29.932 147 88 2 8 151 56 190 5.36e-17 78.6
MS.gene85771.t1 MTR_3g092780 29.932 147 88 2 8 151 56 190 6.16e-17 78.6
MS.gene85771.t1 MTR_3g092780 29.730 148 88 2 8 151 56 191 9.80e-17 77.8
MS.gene85771.t1 MTR_3g092780 29.730 148 88 2 8 151 56 191 1.09e-16 77.8
MS.gene85771.t1 MTR_7g118260 31.757 148 87 3 14 161 22 155 6.08e-16 75.5
MS.gene85771.t1 MTR_4g051330 52.239 67 29 1 89 152 77 143 5.83e-15 69.3
MS.gene85771.t1 MTR_7g118260 32.308 130 74 3 14 143 22 137 2.14e-14 71.2
MS.gene85771.t1 MTR_8g024260 30.882 136 82 1 8 143 36 159 5.09e-14 70.1
MS.gene85771.t1 MTR_1g067110 28.788 132 82 1 10 141 87 206 2.23e-13 68.2
MS.gene85771.t1 MTR_1g067110 28.788 132 82 1 10 141 87 206 2.66e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85771.t1 AT1G59940 59.406 202 61 5 4 188 29 226 1.82e-71 216
MS.gene85771.t1 AT1G59940 59.406 202 61 5 4 188 121 318 5.68e-70 216
MS.gene85771.t1 AT1G10470 70.199 151 40 3 6 155 18 164 1.75e-69 212
MS.gene85771.t1 AT1G10470 70.199 151 40 3 6 155 32 178 3.66e-69 211
MS.gene85771.t1 AT3G48100 65.563 151 50 1 8 158 25 173 1.16e-63 195
MS.gene85771.t1 AT5G62920 72.656 128 32 1 8 135 25 149 3.45e-61 189
MS.gene85771.t1 AT1G74890 71.318 129 34 1 7 135 17 142 3.43e-59 184
MS.gene85771.t1 AT1G19050 65.441 136 44 1 7 142 23 155 2.41e-58 182
MS.gene85771.t1 AT2G40670 59.259 135 55 0 4 138 25 159 1.32e-54 171
MS.gene85771.t1 AT3G57040 58.993 139 50 2 7 138 8 146 1.87e-53 171
MS.gene85771.t1 AT3G57040 58.993 139 50 2 7 138 8 146 1.87e-53 171
MS.gene85771.t1 AT3G56380 61.194 134 48 2 6 138 18 148 2.28e-53 167
MS.gene85771.t1 AT2G41310 59.441 143 52 2 1 138 3 144 4.94e-53 169
MS.gene85771.t1 AT2G40670 58.824 136 55 1 4 138 25 160 8.22e-53 167
MS.gene85771.t1 AT3G56380 60.741 135 48 3 6 138 18 149 1.55e-51 163
MS.gene85771.t1 AT1G10470 56.044 91 30 6 70 155 17 102 1.68e-23 92.4
MS.gene85771.t1 AT5G24470 30.216 139 83 3 8 146 52 176 2.20e-15 73.9
MS.gene85771.t1 AT2G46790 31.343 134 80 2 8 141 37 158 2.31e-15 73.9
MS.gene85771.t1 AT2G46790 31.343 134 80 2 8 141 37 158 2.79e-15 73.6
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.88e-14 71.2
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.88e-14 71.2
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 1.88e-14 71.2
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 3.07e-14 70.9
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 3.16e-14 70.5
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 3.16e-14 70.5
MS.gene85771.t1 AT5G60100 34.848 132 74 2 10 141 66 185 3.16e-14 70.5
MS.gene85771.t1 AT2G07440 60.000 50 20 0 89 138 9 58 1.98e-13 64.7
MS.gene85771.t1 AT5G02810 28.358 134 84 1 8 141 78 199 1.03e-12 66.2

Find 39 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGTGATTACATGCTTCTTC+TGG 0.290924 1.2:+32678458 None:intergenic
ATTGAAAATATTCAGATGTT+TGG 0.307010 1.2:-32678594 MS.gene85771:intron
AACTCATAACCAGTCATTTC+TGG 0.328147 1.2:+32679473 None:intergenic
TTTGTTGCCTTAGCCTTTGA+AGG 0.366124 1.2:-32679525 MS.gene85771:intron
CTCAAAATTTCTGCTTGTAA+AGG 0.386939 1.2:-32679931 MS.gene85771:intron
TTCTGAAGAGGTTCATGTAT+TGG 0.402386 1.2:-32679998 MS.gene85771:CDS
TACTGGAATTTCCTTAAAAG+TGG 0.438337 1.2:+32679316 None:intergenic
TTAGTTACTGCTGTGGATAG+TGG 0.438893 1.2:-32679704 MS.gene85771:intron
TTCACATCACATAACTTCAC+TGG 0.475573 1.2:+32678542 None:intergenic
ATAACAGTACCTGTCTATGC+GGG 0.487586 1.2:+32679265 None:intergenic
TCAGAAGACATAATCACTAC+TGG 0.489512 1.2:+32679299 None:intergenic
ATGTGAAGGTGATGATGAAA+TGG 0.496627 1.2:+32678421 None:intergenic
ATATTCTGCCCCGCATAGAC+AGG 0.510615 1.2:-32679274 MS.gene85771:intron
ATATTCAGATGTTTGGAAGA+AGG 0.511460 1.2:-32678587 MS.gene85771:intron
TATTGCATGCCAGAAATGAC+TGG 0.520879 1.2:-32679482 MS.gene85771:CDS
TGCTTGATTCTTCAATCAGA+CGG 0.521707 1.2:-32678370 MS.gene85771:CDS
TTGATCGGAAAGTTATTGAA+AGG 0.524082 1.2:-32679957 MS.gene85771:CDS
TGACAACCCAAATAGTCATT+CGG 0.532453 1.2:+32678331 None:intergenic
ATAACAAGATCCACCTTCAA+AGG 0.539532 1.2:+32679512 None:intergenic
GTTGCCTTAGCCTTTGAAGG+TGG 0.539999 1.2:-32679522 MS.gene85771:intron
TACATGACAACAAGGGAGGT+TGG 0.562595 1.2:-32678506 MS.gene85771:CDS
AGCACACTGGATGCAGACAA+TGG 0.577593 1.2:+32678389 None:intergenic
ACAACAAGGGAGGTTGGAGT+AGG 0.598300 1.2:-32678500 MS.gene85771:CDS
ATGTTTGGAAGAAGGTGCAA+AGG 0.598645 1.2:-32678579 MS.gene85771:CDS
AGAGAGAAGTCTGAATCTGA+TGG 0.604808 1.2:-32679644 MS.gene85771:CDS
GTGAACTTTAGTTACTGCTG+TGG 0.606977 1.2:-32679711 MS.gene85771:intron
GATGGAGACAAATTCTGAAG+AGG 0.610289 1.2:-32680010 MS.gene85771:CDS
TTGATGATAGTCTCATTGAT+CGG 0.612021 1.2:-32679972 MS.gene85771:CDS
TGAAGGGTTACATGACAACA+AGG 0.633631 1.2:-32678514 MS.gene85771:CDS
GATTGAAGAATCAAGCACAC+TGG 0.636985 1.2:+32678376 None:intergenic
ATGTGATGTGAAACGACTGA+AGG 0.663812 1.2:-32678531 MS.gene85771:CDS
TGTGATGTGAAACGACTGAA+GGG 0.670059 1.2:-32678530 MS.gene85771:CDS
TATAACAGTACCTGTCTATG+CGG 0.670864 1.2:+32679264 None:intergenic
AATGGAGATGATGAATGTGA+AGG 0.695750 1.2:+32678407 None:intergenic
TAACAGTACCTGTCTATGCG+GGG 0.697429 1.2:+32679266 None:intergenic
GGTGATGATGAAATGGACGG+TGG 0.704627 1.2:+32678428 None:intergenic
GGGTTACATGACAACAAGGG+AGG 0.715675 1.2:-32678510 MS.gene85771:CDS
GAAGGTGATGATGAAATGGA+CGG 0.719690 1.2:+32678425 None:intergenic
GAAGGGTTACATGACAACAA+GGG 0.758159 1.2:-32678513 MS.gene85771:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACAATTTTAAAAAAATAGT+TGG + chr1.2:32679681-32679700 None:intergenic 10.0%
!! TTTAAGGGATTATTATTATT+AGG - chr1.2:32679129-32679148 MS.gene85771:intron 15.0%
!!! TATAGTAATGATTTTTTCAA+TGG + chr1.2:32678946-32678965 None:intergenic 15.0%
!! ATTGAAAATATTCAGATGTT+TGG - chr1.2:32679761-32679780 MS.gene85771:intron 20.0%
!!! CCAATGATTATACTTTTTAA+TGG - chr1.2:32679322-32679341 MS.gene85771:CDS 20.0%
!!! CCATTAAAAAGTATAATCAT+TGG + chr1.2:32679325-32679344 None:intergenic 20.0%
!!! TATTTTTAGACCAAAGAAAA+AGG - chr1.2:32679444-32679463 MS.gene85771:intron 20.0%
! TGAGTTGCTCAAAAAAATTA+AGG - chr1.2:32678899-32678918 MS.gene85771:intron 25.0%
!! GTTATTGTTATTAGTTACCA+CGG - chr1.2:32679698-32679717 MS.gene85771:CDS 25.0%
!! TTATTGTTATTAGTTACCAC+GGG - chr1.2:32679699-32679718 MS.gene85771:CDS 25.0%
!! TTGTGTCATTGAAAACATTA+AGG + chr1.2:32679384-32679403 None:intergenic 25.0%
!!! ACGAAATAGATGTTTTTTGA+GGG - chr1.2:32679257-32679276 MS.gene85771:intron 25.0%
!!! GTGTTGATGATTTTTGTTTT+TGG - chr1.2:32678622-32678641 MS.gene85771:intron 25.0%
!!! TACGAAATAGATGTTTTTTG+AGG - chr1.2:32679256-32679275 MS.gene85771:intron 25.0%
!!! TTTTAAGTGTCCTTTTTCTT+TGG + chr1.2:32679457-32679476 None:intergenic 25.0%
ATATTCAGATGTTTGGAAGA+AGG - chr1.2:32679768-32679787 MS.gene85771:intron 30.0%
CCTGCTTCAAAATGAAATTT+CGG + chr1.2:32679013-32679032 None:intergenic 30.0%
CTCAAAATTTCTGCTTGTAA+AGG - chr1.2:32678424-32678443 MS.gene85771:CDS 30.0%
TACTGGAATTTCCTTAAAAG+TGG + chr1.2:32679042-32679061 None:intergenic 30.0%
TTGATCGGAAAGTTATTGAA+AGG - chr1.2:32678398-32678417 MS.gene85771:CDS 30.0%
! TTGATGATAGTCTCATTGAT+CGG - chr1.2:32678383-32678402 MS.gene85771:CDS 30.0%
!!! CGAAATAGATGTTTTTTGAG+GGG - chr1.2:32679258-32679277 MS.gene85771:intron 30.0%
AACTCATAACCAGTCATTTC+TGG + chr1.2:32678885-32678904 None:intergenic 35.0%
AATGGAGATGATGAATGTGA+AGG + chr1.2:32679951-32679970 None:intergenic 35.0%
ATAACAAGATCCACCTTCAA+AGG + chr1.2:32678846-32678865 None:intergenic 35.0%
GTAAAGGTGAGTTTGTGATT+TGG - chr1.2:32678440-32678459 MS.gene85771:CDS 35.0%
TATAACAGTACCTGTCTATG+CGG + chr1.2:32679094-32679113 None:intergenic 35.0%
TCAGAAGACATAATCACTAC+TGG + chr1.2:32679059-32679078 None:intergenic 35.0%
TGCTTGATTCTTCAATCAGA+CGG - chr1.2:32679985-32680004 MS.gene85771:CDS 35.0%
TTCACATCACATAACTTCAC+TGG + chr1.2:32679816-32679835 None:intergenic 35.0%
! ATGTGAAGGTGATGATGAAA+TGG + chr1.2:32679937-32679956 None:intergenic 35.0%
! TCTGATGGTTCTATTGTATG+TGG - chr1.2:32678726-32678745 MS.gene85771:intron 35.0%
! TTCTGAAGAGGTTCATGTAT+TGG - chr1.2:32678357-32678376 MS.gene85771:CDS 35.0%
!!! AATCAGAGCACTGCAATTTT+TGG - chr1.2:32678674-32678693 MS.gene85771:intron 35.0%
!!! ATCAGAGCACTGCAATTTTT+GGG - chr1.2:32678675-32678694 MS.gene85771:intron 35.0%
!!! CCGAAATTTCATTTTGAAGC+AGG - chr1.2:32679010-32679029 MS.gene85771:intron 35.0%
AACTTCATCACAATTTCCCG+TGG + chr1.2:32679718-32679737 None:intergenic 40.0%
AGAGAGAAGTCTGAATCTGA+TGG - chr1.2:32678711-32678730 MS.gene85771:intron 40.0%
ATAACAGTACCTGTCTATGC+GGG + chr1.2:32679093-32679112 None:intergenic 40.0%
ATGTGATGTGAAACGACTGA+AGG - chr1.2:32679824-32679843 MS.gene85771:intron 40.0%
GAAGGGTTACATGACAACAA+GGG - chr1.2:32679842-32679861 MS.gene85771:intron 40.0%
GAGTGATTACATGCTTCTTC+TGG + chr1.2:32679900-32679919 None:intergenic 40.0%
GATTGAAGAATCAAGCACAC+TGG + chr1.2:32679982-32680001 None:intergenic 40.0%
GTGAACTTTAGTTACTGCTG+TGG - chr1.2:32678644-32678663 MS.gene85771:intron 40.0%
TATTGCATGCCAGAAATGAC+TGG - chr1.2:32678873-32678892 MS.gene85771:intron 40.0%
TGAAGGGTTACATGACAACA+AGG - chr1.2:32679841-32679860 MS.gene85771:intron 40.0%
TGTGATGTGAAACGACTGAA+GGG - chr1.2:32679825-32679844 MS.gene85771:intron 40.0%
TTAGTTACTGCTGTGGATAG+TGG - chr1.2:32678651-32678670 MS.gene85771:intron 40.0%
! ATGTTTGGAAGAAGGTGCAA+AGG - chr1.2:32679776-32679795 MS.gene85771:intron 40.0%
! GAAGGTGATGATGAAATGGA+CGG + chr1.2:32679933-32679952 None:intergenic 40.0%
! TTTGTTGCCTTAGCCTTTGA+AGG - chr1.2:32678830-32678849 MS.gene85771:intron 40.0%
!!! TCAGAGCACTGCAATTTTTG+GGG - chr1.2:32678676-32678695 MS.gene85771:intron 40.0%
AGATCCACCTTCAAAGGCTA+AGG + chr1.2:32678840-32678859 None:intergenic 45.0%
TAACAGTACCTGTCTATGCG+GGG + chr1.2:32679092-32679111 None:intergenic 45.0%
TACATGACAACAAGGGAGGT+TGG - chr1.2:32679849-32679868 MS.gene85771:intron 45.0%
!! GCAGGAATCGTCCACTTTTA+AGG - chr1.2:32679028-32679047 MS.gene85771:intron 45.0%
!!! AGCACTGCAATTTTTGGGGT+TGG - chr1.2:32678680-32678699 MS.gene85771:intron 45.0%
!! TAATTTATACTTATATATAA+TGG + chr1.2:32679490-32679509 None:intergenic 5.0%
!!! ATTTTTTTTAAACTTTTTTA+AGG - chr1.2:32679113-32679132 MS.gene85771:intron 5.0%
!!! TTTTTTTTAAACTTTTTTAA+GGG - chr1.2:32679114-32679133 MS.gene85771:intron 5.0%
ACAACAAGGGAGGTTGGAGT+AGG - chr1.2:32679855-32679874 MS.gene85771:intron 50.0%
AGCACACTGGATGCAGACAA+TGG + chr1.2:32679969-32679988 None:intergenic 50.0%
ATATTCTGCCCCGCATAGAC+AGG - chr1.2:32679081-32679100 MS.gene85771:intron 50.0%
GGGTTACATGACAACAAGGG+AGG - chr1.2:32679845-32679864 MS.gene85771:intron 50.0%
! GGTGATGATGAAATGGACGG+TGG + chr1.2:32679930-32679949 None:intergenic 50.0%
! GTTGCCTTAGCCTTTGAAGG+TGG - chr1.2:32678833-32678852 MS.gene85771:intron 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 32678346 32680031 32678346 ID=MS.gene85771
chr1.2 mRNA 32678346 32680031 32678346 ID=MS.gene85771.t1;Parent=MS.gene85771
chr1.2 exon 32679932 32680031 32679932 ID=MS.gene85771.t1.exon1;Parent=MS.gene85771.t1
chr1.2 CDS 32679932 32680031 32679932 ID=cds.MS.gene85771.t1;Parent=MS.gene85771.t1
chr1.2 exon 32679637 32679722 32679637 ID=MS.gene85771.t1.exon2;Parent=MS.gene85771.t1
chr1.2 CDS 32679637 32679722 32679637 ID=cds.MS.gene85771.t1;Parent=MS.gene85771.t1
chr1.2 exon 32679457 32679534 32679457 ID=MS.gene85771.t1.exon3;Parent=MS.gene85771.t1
chr1.2 CDS 32679457 32679534 32679457 ID=cds.MS.gene85771.t1;Parent=MS.gene85771.t1
chr1.2 exon 32679275 32679345 32679275 ID=MS.gene85771.t1.exon4;Parent=MS.gene85771.t1
chr1.2 CDS 32679275 32679345 32679275 ID=cds.MS.gene85771.t1;Parent=MS.gene85771.t1
chr1.2 exon 32678346 32678601 32678346 ID=MS.gene85771.t1.exon5;Parent=MS.gene85771.t1
chr1.2 CDS 32678346 32678601 32678346 ID=cds.MS.gene85771.t1;Parent=MS.gene85771.t1
Gene Sequence

>MS.gene85771

ATGGAGACAAATTCTGAAGAGGTTCATGTATTGGCTGTTGATGATAGTCTCATTGATCGGAAAGTTATTGAAAGGTTGCTCAAAATTTCTGCTTGTAAAGGTGAGTTTGTGATTTGGTAAAACAAAAATAAAATTAATAAAATGTTTTTTCATTTGTGAAGATTTTTGAAGATATTCTCATTTGTGAAGATTTTTGTTTAACAAATATAAGTGAAATGAAAAAGAAGTAGAATTTTTTTTAGTGTTATTTTTTTTAATTTCTTTTTAAATTTTAATGTGTTGATGATTTTTGTTTTTGGTGAACTTTAGTTACTGCTGTGGATAGTGGAATCAGAGCACTGCAATTTTTGGGGTTGGATGAGCAGAGAGAGAAGTCTGAATCTGATGGTTCTATTGTATGTGGCAATTATTTTATTTTATTTATTTTATAGTTTTTATTCTTTTAATATAATGTTAATTAATTTACTGATTTTATTATTTTATTTTTGTTGCCTTAGCCTTTGAAGGTGGATCTTGTTATTACAGATTATTGCATGCCAGAAATGACTGGTTATGAGTTGCTCAAAAAAATTAAGGTTCAAATTCATTATCACAATTCCATTGAAAAAATCATTACTATAATTTATTTTTCACTCTTTTGATTATATTGTTAGTGAAGTTTGATCCGAAATTTCATTTTGAAGCAGGAATCGTCCACTTTTAAGGAAATTCCAGTAGTGATTATGTCTTCTGAAAATATTCTGCCCCGCATAGACAGGTACTGTTATATTTTTTTTAAACTTTTTTAAGGGATTATTATTATTAGGTAATTTTGACTTTTTATTTTATTTTACTAACACATCTAAATTATGAACATTGTATTTTGTGAAATTTTGATTTTGATAAAAATAATTTTGATTGAAATAATAAGTACGAAATAGATGTTTTTTGAGGGGAAGTTTGAAATAGATGTTTGTGAGTTTTAAATTCTAACAAACCAATGATTATACTTTTTAATGGCACTGATAATATAAAAATAACAGATGTAATATGAATCCTTAATGTTTTCAATGACACAAATAATATAATTTTTTTTATAAGCAATAGTTTATTTAAAAGTATTTTTAGACCAAAGAAAAAGGACACTTAAAAAAATATATCACCATTATATATAAGTATAAATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTCTGTTCAATAAATCATTATTGTTATCTTCAAAAAAATAAATCATTATTGTTAATTTGTTGCATACATAACTTTTAACACAGTAAACCAACTATTTTTTTAAAATTGTTATTGTTATTAGTTACCACGGGAAATTGTGATGAAGTTGAAAAAATGAGTGATTTGTAAATATTGAAAATATTCAGATGTTTGGAAGAAGGTGCAAAGGATTTTATAATAAAGCCAGTGAAGTTATGTGATGTGAAACGACTGAAGGGTTACATGACAACAAGGGAGGTTGGAGTAGGAATCAACAATAAACAGAAGCCAGAAGAAGCATGTAATCACTCATCATCACCACCGTCCATTTCATCATCACCTTCACATTCATCATCTCCATTGTCTGCATCCAGTGTGCTTGATTCTTCAATCAGACGGTTTAAAATGATTGACACCGAATGA
Protein sequence

>MS.gene85771.t1

METNSEEVHVLAVDDSLIDRKVIERLLKISACKVTAVDSGIRALQFLGLDEQREKSESDGSIPLKVDLVITDYCMPEMTGYELLKKIKESSTFKEIPVVIMSSENILPRIDRCLEEGAKDFIIKPVKLCDVKRLKGYMTTREVGVGINNKQKPEEACNHSSSPPSISSSPSHSSSPLSASSVLDSSIRRFKMIDTE