AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034971.t1 MTR_1g062160 100.000 200 0 0 1 200 4 203 4.98e-152 419
MS.gene034971.t1 MTR_7g102790 78.607 201 40 2 1 199 4 203 1.28e-106 305
MS.gene034971.t1 MTR_5g007230 55.612 196 79 4 4 199 21 208 2.51e-72 218
MS.gene034971.t1 MTR_5g030130 54.680 203 79 4 4 199 35 231 7.17e-72 218
MS.gene034971.t1 MTR_8g066820 55.340 206 73 5 4 199 33 229 4.31e-70 213
MS.gene034971.t1 MTR_4g078170 53.465 202 81 4 4 199 15 209 4.99e-70 212
MS.gene034971.t1 MTR_5g030130 66.667 129 42 1 4 132 35 162 4.57e-59 184
MS.gene034971.t1 MTR_2g084495 38.136 236 100 7 1 198 2 229 9.77e-46 151
MS.gene034971.t1 MTR_2g060500 49.650 143 62 4 1 134 8 149 1.81e-40 135
MS.gene034971.t1 MTR_2g060540 51.079 139 58 4 1 130 8 145 4.08e-40 134
MS.gene034971.t1 MTR_2g084510 37.398 246 101 7 1 198 1 241 6.40e-40 136
MS.gene034971.t1 MTR_2g084525 46.951 164 74 6 1 155 1 160 4.97e-38 131
MS.gene034971.t1 MTR_2g055210 42.308 130 72 3 2 131 100 226 2.31e-33 122
MS.gene034971.t1 MTR_4g094680 32.877 219 119 6 4 198 22 236 3.90e-30 111
MS.gene034971.t1 MTR_4g116300 42.188 128 72 2 4 131 6 131 1.94e-29 109
MS.gene034971.t1 MTR_2g036170 31.250 224 118 6 4 199 37 252 5.97e-28 105
MS.gene034971.t1 MTR_8g105930 36.054 147 70 6 6 131 15 158 6.22e-20 84.7
MS.gene034971.t1 MTR_5g077740 29.744 195 106 6 4 198 23 186 2.78e-19 81.6
MS.gene034971.t1 MTR_8g097310 32.075 159 96 3 43 198 4 153 5.15e-19 80.1
MS.gene034971.t1 MTR_2g083710 48.333 60 29 2 1 59 4 62 6.20e-14 64.3
MS.gene034971.t1 MTR_1g032880 39.535 86 47 3 51 132 27 111 1.40e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034971.t1 AT1G32700 53.769 199 86 3 4 199 12 207 3.07e-71 215
MS.gene034971.t1 AT2G27930 54.327 208 66 3 1 199 1 188 6.41e-68 206
MS.gene034971.t1 AT2G27930 54.327 208 66 3 1 199 1 188 6.41e-68 206
MS.gene034971.t1 AT1G76590 46.957 230 85 4 4 198 18 245 3.97e-65 201
MS.gene034971.t1 AT1G21000 45.923 233 86 6 4 198 13 243 1.62e-64 199
MS.gene034971.t1 AT1G21000 45.923 233 86 6 4 198 16 246 2.07e-64 199
MS.gene034971.t1 AT4G17900 51.471 204 81 7 4 199 20 213 2.96e-64 197
MS.gene034971.t1 AT4G17900 51.471 204 81 7 4 199 34 227 3.90e-64 198
MS.gene034971.t1 AT1G43000 45.540 213 99 5 1 198 13 223 1.40e-59 186
MS.gene034971.t1 AT1G43000 45.540 213 99 5 1 198 6 216 1.53e-59 186
MS.gene034971.t1 AT2G27930 61.290 155 51 1 1 146 1 155 8.25e-59 182
MS.gene034971.t1 AT2G27930 61.290 155 51 1 1 146 1 155 8.25e-59 182
MS.gene034971.t1 AT5G46710 48.744 199 97 4 4 198 12 209 1.97e-57 180
MS.gene034971.t1 AT5G46710 48.744 199 97 4 4 198 28 225 2.90e-57 180
MS.gene034971.t1 AT1G32700 52.632 171 75 3 32 199 1 168 1.20e-55 174
MS.gene034971.t1 AT5G46710 58.140 129 52 2 4 131 28 155 3.64e-49 157
MS.gene034971.t1 AT2G27930 52.318 151 43 3 58 199 61 191 9.14e-42 139
MS.gene034971.t1 AT2G27930 52.318 151 43 3 58 199 61 191 9.14e-42 139
MS.gene034971.t1 AT1G31040 34.802 227 113 8 4 198 19 242 4.31e-35 124
MS.gene034971.t1 AT3G60670 39.490 157 86 4 4 153 7 161 8.27e-31 113
MS.gene034971.t1 AT2G12646 43.750 128 70 2 4 131 6 131 1.91e-29 110
MS.gene034971.t1 AT2G12646 43.750 128 70 2 4 131 6 131 1.91e-29 110
MS.gene034971.t1 AT2G12646 43.077 130 72 2 2 131 1 128 1.99e-29 109
MS.gene034971.t1 AT2G01818 30.516 213 124 7 6 198 13 221 8.43e-23 91.7

Find 43 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAGTTCGTTTCTGTTCTT+TGG 0.184177 1.3:+44694377 MS.gene034971:CDS
AGAAGTGGTTTGAGCCATTT+AGG 0.224568 1.3:-44693854 None:intergenic
AGAAACGAACTTGGTCTAAA+AGG 0.306972 1.3:-44694368 None:intergenic
ATTCCTCATAGGGCTCCTTT+TGG 0.317747 1.3:+44694987 MS.gene034971:CDS
ACACAATGTTGGTTCCTAAA+TGG 0.324494 1.3:+44693840 None:intergenic
CAAGGATCATCAAGTCATTC+AGG 0.333682 1.3:+44693997 MS.gene034971:CDS
TTTCTTCTCCTTGCGTTTGA+AGG 0.347275 1.3:-44694960 None:intergenic
CAAGTTCGTTTCTGTTCTTT+GGG 0.351554 1.3:+44694378 MS.gene034971:CDS
CTTGTAGGAATAAAGAGAAA+TGG 0.373461 1.3:+44694804 MS.gene034971:CDS
TTTCTGTTCTTTGGGATGTA+AGG 0.374729 1.3:+44694386 MS.gene034971:CDS
CAGAAAATGTTGGACATTAG+TGG 0.376562 1.3:+44694237 MS.gene034971:CDS
GGAGGTGTTGGAGGAGTTGC+TGG 0.378339 1.3:-44694939 None:intergenic
GAGAGGCCTCAACCAAAATC+TGG 0.407501 1.3:+44694306 MS.gene034971:CDS
GAAGAAAAGGGATTCCTCAT+AGG 0.407985 1.3:+44694976 MS.gene034971:CDS
CAATGATTGAATTAGCTTGT+AGG 0.416656 1.3:+44694789 MS.gene034971:intron
TTGTAGGAATAAAGAGAAAT+GGG 0.420634 1.3:+44694805 MS.gene034971:CDS
TCAAACGCAAGGAGAAGAAA+AGG 0.442491 1.3:+44694963 MS.gene034971:CDS
CCTTACATTTGTGAGATTTG+TGG 0.451494 1.3:+44694339 MS.gene034971:CDS
CTTGCGTTTGAAGGAGGTGT+TGG 0.453994 1.3:-44694951 None:intergenic
CCAAAGAACAGAAACGAACT+TGG 0.484387 1.3:-44694377 None:intergenic
CCACAAATCTCACAAATGTA+AGG 0.486176 1.3:-44694339 None:intergenic
TAAAATGACTAGGGTCCAAA+AGG 0.492758 1.3:-44695002 None:intergenic
GCGTTTGAAGGAGGTGTTGG+AGG 0.501278 1.3:-44694948 None:intergenic
CTTCTCCTTGCGTTTGAAGG+AGG 0.504177 1.3:-44694957 None:intergenic
GAGGTATCAACAATGGAAGA+AGG 0.508623 1.3:+44694861 MS.gene034971:CDS
GGCTGAAATTCAGAAAATGT+TGG 0.529817 1.3:+44694227 MS.gene034971:CDS
ATTTGTGAGATTTGTGGAAG+AGG 0.530195 1.3:+44694345 MS.gene034971:CDS
AAGAAAAGGGATTCCTCATA+GGG 0.544259 1.3:+44694977 MS.gene034971:CDS
CAAACGCAAGGAGAAGAAAA+GGG 0.546728 1.3:+44694964 MS.gene034971:CDS
AGAACGACAATAGAAGCAAA+AGG 0.552138 1.3:-44693966 None:intergenic
GGATTCACGCCGACGCTGCA+AGG 0.558870 1.3:+44693903 MS.gene034971:CDS
AGGTATCAACAATGGAAGAA+GGG 0.569523 1.3:+44694862 MS.gene034971:CDS
GGTCCAAAAGGAGCCCTATG+AGG 0.587771 1.3:-44694990 None:intergenic
TTTAGATGCAAATAACAATG+AGG 0.589036 1.3:+44694842 MS.gene034971:CDS
CTTCATATCATGATGTAGTG+AGG 0.591334 1.3:+44694202 MS.gene034971:CDS
TAACAATGAGGTATCAACAA+TGG 0.597297 1.3:+44694854 MS.gene034971:CDS
TTCATATCATGATGTAGTGA+GGG 0.599632 1.3:+44694203 MS.gene034971:CDS
TTGTCGTTCTTCAAAACACA+AGG 0.606276 1.3:+44693979 MS.gene034971:CDS
ACATTCACTCCTTGCAGCGT+CGG 0.607724 1.3:-44693912 None:intergenic
CAACACCTCCTTCAAACGCA+AGG 0.609547 1.3:+44694952 MS.gene034971:CDS
TTGCGTGAAGGCTCACAACA+AGG 0.621390 1.3:+44694909 MS.gene034971:CDS
CAAGAAGAAGAATTGCGTGA+AGG 0.666815 1.3:+44694897 MS.gene034971:CDS
ATATCATGATGTAGTGAGGG+TGG 0.676670 1.3:+44694206 MS.gene034971:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAAAAATATATACTTT+AGG - chr1.3:44694158-44694177 None:intergenic 10.0%
!! ATAATTATTGAATAGTAGAT+AGG + chr1.3:44694683-44694702 MS.gene034971:intron 15.0%
!!! AGTATATATTTTTTTGTTGT+TGG + chr1.3:44694160-44694179 MS.gene034971:intron 15.0%
!!! TTATGCACATTTTTTATAAT+GGG + chr1.3:44694048-44694067 MS.gene034971:intron 15.0%
!! TATATGAAGCATATAACTAT+AGG + chr1.3:44694579-44694598 MS.gene034971:intron 20.0%
!!! CTTATGCACATTTTTTATAA+TGG + chr1.3:44694047-44694066 MS.gene034971:intron 20.0%
!!! TATGCACATTTTTTATAATG+GGG + chr1.3:44694049-44694068 MS.gene034971:intron 20.0%
! ATACACATGATGATTAATGA+TGG - chr1.3:44694562-44694581 None:intergenic 25.0%
! ATACTAATTAATTGTTGTGC+TGG + chr1.3:44694766-44694785 MS.gene034971:intron 25.0%
! GTGCATAAGAAAAATAATTG+AGG - chr1.3:44694036-44694055 None:intergenic 25.0%
! TGATGGAAGGAATATAATTA+TGG - chr1.3:44694545-44694564 None:intergenic 25.0%
! TTGTAGGAATAAAGAGAAAT+GGG + chr1.3:44694805-44694824 MS.gene034971:CDS 25.0%
! TTTAGATGCAAATAACAATG+AGG + chr1.3:44694842-44694861 MS.gene034971:CDS 25.0%
!! TTTAAAATTATGGTGTGAAG+AGG - chr1.3:44694484-44694503 None:intergenic 25.0%
AAGTCATTCAGGTAAATTAG+AGG + chr1.3:44694008-44694027 MS.gene034971:intron 30.0%
AGTCATTCAGGTAAATTAGA+GGG + chr1.3:44694009-44694028 MS.gene034971:intron 30.0%
ATGAGCTTTCCAAATAATGT+AGG - chr1.3:44694518-44694537 None:intergenic 30.0%
CTTGTAGGAATAAAGAGAAA+TGG + chr1.3:44694804-44694823 MS.gene034971:CDS 30.0%
TTCATATCATGATGTAGTGA+GGG + chr1.3:44694203-44694222 MS.gene034971:CDS 30.0%
TTGAATAGTAGATAGGAACA+TGG + chr1.3:44694690-44694709 MS.gene034971:intron 30.0%
! ACATGATGATTAATGATGGA+AGG - chr1.3:44694558-44694577 None:intergenic 30.0%
! TAACAATGAGGTATCAACAA+TGG + chr1.3:44694854-44694873 MS.gene034971:CDS 30.0%
!! CAATGATTGAATTAGCTTGT+AGG + chr1.3:44694789-44694808 MS.gene034971:intron 30.0%
!!! CACATTTTTTATAATGGGGT+TGG + chr1.3:44694053-44694072 MS.gene034971:intron 30.0%
!!! GGTGGGTGTTTTTAAAATTA+TGG - chr1.3:44694494-44694513 None:intergenic 30.0%
AAAAATGGTGTGCTAAGAAG+TGG - chr1.3:44693872-44693891 None:intergenic 35.0%
AAGAAAAGGGATTCCTCATA+GGG + chr1.3:44694977-44694996 MS.gene034971:CDS 35.0%
AGAAACGAACTTGGTCTAAA+AGG - chr1.3:44694371-44694390 None:intergenic 35.0%
AGAACGACAATAGAAGCAAA+AGG - chr1.3:44693969-44693988 None:intergenic 35.0%
AGCTTTCCAAATAATGTAGG+TGG - chr1.3:44694515-44694534 None:intergenic 35.0%
AGGTATCAACAATGGAAGAA+GGG + chr1.3:44694862-44694881 MS.gene034971:CDS 35.0%
ATTTGTGAGATTTGTGGAAG+AGG + chr1.3:44694345-44694364 MS.gene034971:CDS 35.0%
CAAGTTCGTTTCTGTTCTTT+GGG + chr1.3:44694378-44694397 MS.gene034971:CDS 35.0%
CAGAAAATGTTGGACATTAG+TGG + chr1.3:44694237-44694256 MS.gene034971:CDS 35.0%
CCACAAATCTCACAAATGTA+AGG - chr1.3:44694342-44694361 None:intergenic 35.0%
CCTTACATTTGTGAGATTTG+TGG + chr1.3:44694339-44694358 MS.gene034971:CDS 35.0%
CTTCATATCATGATGTAGTG+AGG + chr1.3:44694202-44694221 MS.gene034971:CDS 35.0%
GGCTGAAATTCAGAAAATGT+TGG + chr1.3:44694227-44694246 MS.gene034971:CDS 35.0%
TTCCAAATAATGTAGGTGGT+GGG - chr1.3:44694511-44694530 None:intergenic 35.0%
TTGTCGTTCTTCAAAACACA+AGG + chr1.3:44693979-44693998 MS.gene034971:CDS 35.0%
TTTCCAAATAATGTAGGTGG+TGG - chr1.3:44694512-44694531 None:intergenic 35.0%
!! TTTCTGTTCTTTGGGATGTA+AGG + chr1.3:44694386-44694405 MS.gene034971:CDS 35.0%
!!! GAGTTTTGTTTCTGAATGAG+AGG + chr1.3:44694289-44694308 MS.gene034971:CDS 35.0%
AGAAGTGGTTTGAGCCATTT+AGG - chr1.3:44693857-44693876 None:intergenic 40.0%
ATATCATGATGTAGTGAGGG+TGG + chr1.3:44694206-44694225 MS.gene034971:CDS 40.0%
ATCCGACACTCGTTGAAAAA+TGG - chr1.3:44693887-44693906 None:intergenic 40.0%
CAAACGCAAGGAGAAGAAAA+GGG + chr1.3:44694964-44694983 MS.gene034971:CDS 40.0%
CAAGAAGAAGAATTGCGTGA+AGG + chr1.3:44694897-44694916 MS.gene034971:CDS 40.0%
CAAGGATCATCAAGTCATTC+AGG + chr1.3:44693997-44694016 MS.gene034971:CDS 40.0%
CCAAAGAACAGAAACGAACT+TGG - chr1.3:44694380-44694399 None:intergenic 40.0%
CCAAGTTCGTTTCTGTTCTT+TGG + chr1.3:44694377-44694396 MS.gene034971:CDS 40.0%
GAAGAAAAGGGATTCCTCAT+AGG + chr1.3:44694976-44694995 MS.gene034971:CDS 40.0%
TCAAACGCAAGGAGAAGAAA+AGG + chr1.3:44694963-44694982 MS.gene034971:CDS 40.0%
TTTCTTCTCCTTGCGTTTGA+AGG - chr1.3:44694963-44694982 None:intergenic 40.0%
! GAGGTATCAACAATGGAAGA+AGG + chr1.3:44694861-44694880 MS.gene034971:CDS 40.0%
!! CACCATTTTTCAACGAGTGT+CGG + chr1.3:44693882-44693901 MS.gene034971:CDS 40.0%
!! GGAACTGCTTTTCCAGATTT+TGG - chr1.3:44694321-44694340 None:intergenic 40.0%
!!! GCTTTTCCAGATTTTGGTTG+AGG - chr1.3:44694315-44694334 None:intergenic 40.0%
CACCCACCACCTACATTATT+TGG + chr1.3:44694506-44694525 MS.gene034971:intron 45.0%
! ATTCCTCATAGGGCTCCTTT+TGG + chr1.3:44694987-44695006 MS.gene034971:CDS 45.0%
ACATTCACTCCTTGCAGCGT+CGG - chr1.3:44693915-44693934 None:intergenic 50.0%
CAACACCTCCTTCAAACGCA+AGG + chr1.3:44694952-44694971 MS.gene034971:CDS 50.0%
CTTCTCCTTGCGTTTGAAGG+AGG - chr1.3:44694960-44694979 None:intergenic 50.0%
GAGAGGCCTCAACCAAAATC+TGG + chr1.3:44694306-44694325 MS.gene034971:CDS 50.0%
TTGCGTGAAGGCTCACAACA+AGG + chr1.3:44694909-44694928 MS.gene034971:CDS 50.0%
! CTTGCGTTTGAAGGAGGTGT+TGG - chr1.3:44694954-44694973 None:intergenic 50.0%
GGTCCAAAAGGAGCCCTATG+AGG - chr1.3:44694993-44695012 None:intergenic 55.0%
!! GCGTTTGAAGGAGGTGTTGG+AGG - chr1.3:44694951-44694970 None:intergenic 55.0%
!! GGAGGTGTTGGAGGAGTTGC+TGG - chr1.3:44694942-44694961 None:intergenic 60.0%
GGATTCACGCCGACGCTGCA+AGG + chr1.3:44693903-44693922 MS.gene034971:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 44693845 44695016 44693845 ID=MS.gene034971
chr1.3 mRNA 44693845 44695016 44693845 ID=MS.gene034971.t1;Parent=MS.gene034971
chr1.3 exon 44693845 44694018 44693845 ID=MS.gene034971.t1.exon1;Parent=MS.gene034971.t1
chr1.3 CDS 44693845 44694018 44693845 ID=cds.MS.gene034971.t1;Parent=MS.gene034971.t1
chr1.3 exon 44694192 44694407 44694192 ID=MS.gene034971.t1.exon2;Parent=MS.gene034971.t1
chr1.3 CDS 44694192 44694407 44694192 ID=cds.MS.gene034971.t1;Parent=MS.gene034971.t1
chr1.3 exon 44694804 44695016 44694804 ID=MS.gene034971.t1.exon3;Parent=MS.gene034971.t1
chr1.3 CDS 44694804 44695016 44694804 ID=cds.MS.gene034971.t1;Parent=MS.gene034971.t1
Gene Sequence

>MS.gene034971

ATGTTGGTTCCTAAATGGCTCAAACCACTTCTTAGCACACCATTTTTCAACGAGTGTCGGATTCACGCCGACGCTGCAAGGAGTGAATGTAACATGTTTTGCTTAGATTGCAATGTTGATGCCTTTTGCTTCTATTGTCGTTCTTCAAAACACAAGGATCATCAAGTCATTCAGGTAAATTAGAGGGTCCTCAATTATTTTTCTTATGCACATTTTTTATAATGGGGTTGGTTAAATTTTGTGATTTTTTAATATGTTTATAATGATTGAAATTCAGCACTCTTATTATATGATCTTCATTTTTCTTTATCCTAAAGTATATATTTTTTTGTTGTTGGTTTAATTAGATAAGACGATCTTCATATCATGATGTAGTGAGGGTGGCTGAAATTCAGAAAATGTTGGACATTAGTGGAGTACAAACATATGTGATCAATAGTGCTAGAGTTTTGTTTCTGAATGAGAGGCCTCAACCAAAATCTGGAAAAGCAGTTCCTTACATTTGTGAGATTTGTGGAAGAGGCCTTTTAGACCAAGTTCGTTTCTGTTCTTTGGGATGTAAGGTGAGATTTTGTTTCATAAACATTTTTCATAGCATCAAAATGTACATATAATTCACAAATCAAATAGCTTAGTCCTCTTCACACCATAATTTTAAAAACACCCACCACCTACATTATTTGGAAAGCTCATCACACCATAATTATATTCCTTCCATCATTAATCATCATGTGTATATGAAGCATATAACTATAGGCGCACATTGACATTTCATCACATTTATAAAAATAATCATATTATTATCTAGTTAATATTATTGATATATTTTTTTATAAAGATAATTATTGAATAGTAGATAGGAACATGGTATAATAATGTGTATAAAATAATAATGAATCAATATATGATTTGTTTAATTTGATACTAATTAATTGTTGTGCTGGCAATGATTGAATTAGCTTGTAGGAATAAAGAGAAATGGGAATGCAAGCTTTGTTTTAGATGCAAATAACAATGAGGTATCAACAATGGAAGAAGGGATGTCAAGACAACAAGAAGAAGAATTGCGTGAAGGCTCACAACAAGGCATGTATCCAGCAACTCCTCCAACACCTCCTTCAAACGCAAGGAGAAGAAAAGGGATTCCTCATAGGGCTCCTTTTGGACCCTAG
Protein sequence

>MS.gene034971.t1

MLVPKWLKPLLSTPFFNECRIHADAARSECNMFCLDCNVDAFCFYCRSSKHKDHQVIQIRRSSYHDVVRVAEIQKMLDISGVQTYVINSARVLFLNERPQPKSGKAVPYICEICGRGLLDQVRFCSLGCKLVGIKRNGNASFVLDANNNEVSTMEEGMSRQQEEELREGSQQGMYPATPPTPPSNARRRKGIPHRAPFGP