AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035321

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035321.t1 MTR_4g119550 65.054 186 62 1 4 186 205 390 1.68e-84 254
MS.gene035321.t1 MTR_2g437960 51.562 192 90 1 1 189 208 399 1.83e-63 201
MS.gene035321.t1 MTR_2g437960 51.562 192 90 1 1 189 208 399 3.00e-63 201
MS.gene035321.t1 MTR_2g438010 50.259 193 93 1 2 191 226 418 5.55e-63 201
MS.gene035321.t1 MTR_2g437090 52.632 171 78 1 22 189 1 171 2.13e-62 191
MS.gene035321.t1 MTR_2g437240 52.880 191 87 1 1 188 220 410 2.23e-62 199
MS.gene035321.t1 MTR_2g437990 49.479 192 94 1 3 191 206 397 8.48e-61 195
MS.gene035321.t1 MTR_2g437940 50.515 194 93 1 1 191 176 369 1.41e-60 193
MS.gene035321.t1 MTR_2g436440 51.064 188 89 1 1 185 198 385 3.96e-60 192
MS.gene035321.t1 MTR_2g076320 50.521 192 92 1 3 191 207 398 8.69e-60 192
MS.gene035321.t1 MTR_2g437030 49.738 191 93 1 1 188 278 468 1.63e-59 192
MS.gene035321.t1 MTR_2g437180 51.042 192 89 2 1 189 204 393 4.13e-59 190
MS.gene035321.t1 MTR_2g437130 50.000 190 92 1 3 189 195 384 8.90e-59 189
MS.gene035321.t1 MTR_2g437080 50.000 188 91 1 1 185 192 379 3.47e-58 187
MS.gene035321.t1 MTR_2g437150 49.479 192 94 1 1 189 212 403 1.32e-57 186
MS.gene035321.t1 MTR_2g437060 49.468 188 92 1 1 185 207 394 1.77e-57 186
MS.gene035321.t1 MTR_2g437040 48.925 186 92 1 6 188 197 382 1.90e-57 185
MS.gene035321.t1 MTR_2g437170 48.958 192 95 1 1 189 212 403 2.35e-57 186
MS.gene035321.t1 MTR_2g437020 54.706 170 73 2 19 185 211 379 5.88e-57 184
MS.gene035321.t1 MTR_2g437200 51.955 179 83 1 1 176 220 398 1.01e-56 184
MS.gene035321.t1 MTR_2g438020 51.042 192 90 2 1 189 259 449 1.18e-56 186
MS.gene035321.t1 MTR_2g436400 48.634 183 91 1 1 180 199 381 2.93e-56 182
MS.gene035321.t1 MTR_2g437120 50.785 191 90 2 1 188 206 395 5.47e-56 182
MS.gene035321.t1 MTR_2g437160 49.735 189 92 1 4 189 220 408 1.70e-55 181
MS.gene035321.t1 MTR_2g437160 49.457 184 90 1 9 189 134 317 3.93e-55 177
MS.gene035321.t1 MTR_2g437100 51.397 179 84 1 1 176 217 395 1.31e-54 178
MS.gene035321.t1 MTR_2g436460 47.778 180 90 2 4 179 200 379 7.35e-53 173
MS.gene035321.t1 MTR_2g437260 46.584 161 83 1 24 181 211 371 6.60e-47 158
MS.gene035321.t1 MTR_2g019840 44.681 188 97 4 4 186 196 381 2.90e-44 151
MS.gene035321.t1 MTR_2g019810 51.299 154 70 3 26 176 208 359 1.46e-43 149
MS.gene035321.t1 MTR_4g119580 43.503 177 97 1 1 174 194 370 4.15e-43 148
MS.gene035321.t1 MTR_4g120380 41.477 176 100 1 1 173 194 369 5.43e-41 142
MS.gene035321.t1 MTR_4g120380 41.401 157 89 1 1 154 194 350 3.76e-35 128
MS.gene035321.t1 MTR_4g119570 37.931 174 78 1 1 174 86 229 7.29e-33 117
MS.gene035321.t1 MTR_3g450500 32.955 176 113 2 6 176 197 372 1.91e-26 103
MS.gene035321.t1 MTR_4g007490 32.911 158 103 1 20 174 211 368 3.40e-22 92.4
MS.gene035321.t1 MTR_2g436380 46.269 67 36 0 22 88 1 67 6.50e-14 68.6
MS.gene035321.t1 MTR_2g019830 54.688 64 28 1 116 179 140 202 7.37e-14 67.4
MS.gene035321.t1 MTR_4g119615 54.000 50 23 0 118 167 26 75 6.23e-12 59.7
MS.gene035321.t1 MTR_8g080990 27.848 158 111 1 16 170 211 368 1.60e-11 62.4
MS.gene035321.t1 MTR_8g081000 27.160 162 115 1 16 174 224 385 3.04e-11 61.6
MS.gene035321.t1 MTR_8g081000 27.160 162 115 1 16 174 224 385 3.14e-11 61.6
MS.gene035321.t1 MTR_8g081000 24.859 177 128 2 3 174 209 385 3.85e-11 61.2
MS.gene035321.t1 MTR_3g085240 42.857 91 32 2 81 168 176 249 4.43e-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.gene035321.t1 AT5G07900 33.775 151 96 2 27 173 249 399 2.56e-24 98.6
MS.gene035321.t1 AT1G21150 29.730 148 94 4 33 173 206 350 3.57e-13 67.0
MS.gene035321.t1 AT1G21150 29.730 148 94 4 33 173 242 386 4.79e-13 67.0
MS.gene035321.t1 AT1G21150 29.730 148 94 4 33 173 306 450 5.89e-13 66.6

Find 36 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTATGTTGTTTCGTATT+TGG 0.132694 8.3:+7404658 MS.gene035321:CDS
ACGAAACAACATAGCAATTT+TGG 0.140017 8.3:-7404652 None:intergenic
ATTCTTCAAATTGCTCTTTC+GGG 0.177196 8.3:+7404745 MS.gene035321:CDS
AATTCTTCAAATTGCTCTTT+CGG 0.217634 8.3:+7404744 MS.gene035321:CDS
TCACCTAGGTTTGGATTCTT+TGG 0.241549 8.3:+7404941 MS.gene035321:CDS
AGACCAACCCCATTTCTTAA+AGG 0.278227 8.3:-7404826 None:intergenic
TAGTAGGCCATTTGCTATTT+CGG 0.280128 8.3:+7405070 MS.gene035321:CDS
AAGTTGAAACCTTTAAGAAA+TGG 0.349354 8.3:+7404817 MS.gene035321:CDS
AGTTGAAACCTTTAAGAAAT+GGG 0.355687 8.3:+7404818 MS.gene035321:CDS
TGTTGAGGAATTGAAGCAAT+TGG 0.357320 8.3:+7404716 MS.gene035321:CDS
TTGGGTTCATCACCTAGGTT+TGG 0.373459 8.3:+7404932 MS.gene035321:CDS
CTGCAGTTTCTTACGTCAAA+AGG 0.400200 8.3:+7405023 MS.gene035321:CDS
ATTCCTCAACAGTATGCAAC+AGG 0.441134 8.3:-7404704 None:intergenic
GTTGAGGAATTGAAGCAATT+GGG 0.442381 8.3:+7404717 MS.gene035321:CDS
GTTGGAAGAAGAATATATCT+TGG 0.458359 8.3:-7404682 None:intergenic
AATAGCAAATGGCCTACTAA+TGG 0.468558 8.3:-7405066 None:intergenic
AAAAGAAGGCTGCCATTAGT+AGG 0.477983 8.3:+7405054 MS.gene035321:CDS
AACTGCAGAACTGAAGCCCT+TGG 0.495873 8.3:-7405008 None:intergenic
TTGGAAGAAGAATATATCTT+GGG 0.497045 8.3:-7404681 None:intergenic
AGCTCCTCCGAAATAGCAAA+TGG 0.511246 8.3:-7405077 None:intergenic
CAACCTGTTGCATACTGTTG+AGG 0.536585 8.3:+7404701 MS.gene035321:CDS
TTCTTCAAATTGCTCTTTCG+GGG 0.552276 8.3:+7404746 MS.gene035321:CDS
GTTGAAACCTTTAAGAAATG+GGG 0.553181 8.3:+7404819 MS.gene035321:CDS
CGACAAGAGGATTATTCCAA+GGG 0.558587 8.3:+7404992 MS.gene035321:CDS
CTCAACAGTATGCAACAGGT+TGG 0.574346 8.3:-7404700 None:intergenic
AAACCTTTAAGAAATGGGGT+TGG 0.575676 8.3:+7404823 MS.gene035321:CDS
TTCAACGGAGTCTCGACAAG+AGG 0.589874 8.3:+7404979 MS.gene035321:CDS
GTGGACGACAACATACAACT+AGG 0.595092 8.3:-7404882 None:intergenic
TCGACAAGAGGATTATTCCA+AGG 0.595557 8.3:+7404991 MS.gene035321:CDS
TAGGCCATTTGCTATTTCGG+AGG 0.618869 8.3:+7405073 MS.gene035321:CDS
AAGTTTGAACAAAACAAGGT+GGG 0.631687 8.3:+7404788 MS.gene035321:CDS
TGGACGACAACATACAACTA+GGG 0.637259 8.3:-7404881 None:intergenic
GAAGTTTGAACAAAACAAGG+TGG 0.641228 8.3:+7404787 MS.gene035321:CDS
AGAGAAGTTTGAACAAAACA+AGG 0.656841 8.3:+7404784 MS.gene035321:CDS
GGTCCAAAGAATCCAAACCT+AGG 0.665901 8.3:-7404944 None:intergenic
AGATTAAGAAGTTACACACC+AGG 0.688361 8.3:-7405206 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCTTGTAATAATTTTTCAA+CGG + chr8.3:7404964-7404983 MS.gene035321:CDS 20.0%
! AAAAGGTCTTAGAAAAAAGA+AGG + chr8.3:7405040-7405059 MS.gene035321:CDS 25.0%
! AATTCTTCAAATTGCTCTTT+CGG + chr8.3:7404744-7404763 MS.gene035321:CDS 25.0%
! TCCGTTGAAAAATTATTACA+AGG - chr8.3:7404968-7404987 None:intergenic 25.0%
! TTGGAAGAAGAATATATCTT+GGG - chr8.3:7404684-7404703 None:intergenic 25.0%
!! AAGTTGAAACCTTTAAGAAA+TGG + chr8.3:7404817-7404836 MS.gene035321:CDS 25.0%
!! AGTTGAAACCTTTAAGAAAT+GGG + chr8.3:7404818-7404837 MS.gene035321:CDS 25.0%
AAGTTTGAACAAAACAAGGT+GGG + chr8.3:7404788-7404807 MS.gene035321:CDS 30.0%
AGAGAAGTTTGAACAAAACA+AGG + chr8.3:7404784-7404803 MS.gene035321:CDS 30.0%
ATTCTTCAAATTGCTCTTTC+GGG + chr8.3:7404745-7404764 MS.gene035321:CDS 30.0%
GTTGGAAGAAGAATATATCT+TGG - chr8.3:7404685-7404704 None:intergenic 30.0%
! ACGAAACAACATAGCAATTT+TGG - chr8.3:7404655-7404674 None:intergenic 30.0%
! CAGGTTTGTGAAATGTTTTA+AGG + chr8.3:7405109-7405128 MS.gene035321:CDS 30.0%
! GTTGAAACCTTTAAGAAATG+GGG + chr8.3:7404819-7404838 MS.gene035321:CDS 30.0%
!! TTGCTATGTTGTTTCGTATT+TGG + chr8.3:7404658-7404677 MS.gene035321:CDS 30.0%
!!! GTTTGTGAAATGTTTTAAGG+AGG + chr8.3:7405112-7405131 MS.gene035321:CDS 30.0%
AATAGCAAATGGCCTACTAA+TGG - chr8.3:7405069-7405088 None:intergenic 35.0%
GAAGTTTGAACAAAACAAGG+TGG + chr8.3:7404787-7404806 MS.gene035321:CDS 35.0%
GTTGAGGAATTGAAGCAATT+GGG + chr8.3:7404717-7404736 MS.gene035321:CDS 35.0%
TGTTGAGGAATTGAAGCAAT+TGG + chr8.3:7404716-7404735 MS.gene035321:CDS 35.0%
TTCTTCAAATTGCTCTTTCG+GGG + chr8.3:7404746-7404765 MS.gene035321:CDS 35.0%
! AAACCTTTAAGAAATGGGGT+TGG + chr8.3:7404823-7404842 MS.gene035321:CDS 35.0%
!! TAGTAGGCCATTTGCTATTT+CGG + chr8.3:7405070-7405089 MS.gene035321:CDS 35.0%
AAAAGAAGGCTGCCATTAGT+AGG + chr8.3:7405054-7405073 MS.gene035321:CDS 40.0%
AGACCAACCCCATTTCTTAA+AGG - chr8.3:7404829-7404848 None:intergenic 40.0%
AGTGAGAAAAAGTCTTTGCC+TGG + chr8.3:7405188-7405207 MS.gene035321:CDS 40.0%
ATTCCTCAACAGTATGCAAC+AGG - chr8.3:7404707-7404726 None:intergenic 40.0%
CGACAAGAGGATTATTCCAA+GGG + chr8.3:7404992-7405011 MS.gene035321:CDS 40.0%
CTGCAGTTTCTTACGTCAAA+AGG + chr8.3:7405023-7405042 MS.gene035321:CDS 40.0%
TCACCTAGGTTTGGATTCTT+TGG + chr8.3:7404941-7404960 MS.gene035321:CDS 40.0%
TCGACAAGAGGATTATTCCA+AGG + chr8.3:7404991-7405010 MS.gene035321:CDS 40.0%
TGGACGACAACATACAACTA+GGG - chr8.3:7404884-7404903 None:intergenic 40.0%
! CGATGCACTCATGTGTTTTT+GGG + chr8.3:7404914-7404933 MS.gene035321:CDS 40.0%
! TCGATGCACTCATGTGTTTT+TGG + chr8.3:7404913-7404932 MS.gene035321:CDS 40.0%
!! TATTTCGGAGGAGCTGTTTT+TGG + chr8.3:7405085-7405104 MS.gene035321:CDS 40.0%
!!! GAGTGCATCGATTTTATGAG+TGG - chr8.3:7404904-7404923 None:intergenic 40.0%
!!! TGTTTTTGGGTTCATCACCT+AGG + chr8.3:7404927-7404946 MS.gene035321:CDS 40.0%
AGCTCCTCCGAAATAGCAAA+TGG - chr8.3:7405080-7405099 None:intergenic 45.0%
CAACCTGTTGCATACTGTTG+AGG + chr8.3:7404701-7404720 MS.gene035321:CDS 45.0%
CTCAACAGTATGCAACAGGT+TGG - chr8.3:7404703-7404722 None:intergenic 45.0%
GGTCCAAAGAATCCAAACCT+AGG - chr8.3:7404947-7404966 None:intergenic 45.0%
GTGGACGACAACATACAACT+AGG - chr8.3:7404885-7404904 None:intergenic 45.0%
TTGGGTTCATCACCTAGGTT+TGG + chr8.3:7404932-7404951 MS.gene035321:CDS 45.0%
!! TAGGCCATTTGCTATTTCGG+AGG + chr8.3:7405073-7405092 MS.gene035321:CDS 45.0%
AACTGCAGAACTGAAGCCCT+TGG - chr8.3:7405011-7405030 None:intergenic 50.0%
TTCAACGGAGTCTCGACAAG+AGG + chr8.3:7404979-7404998 MS.gene035321:CDS 50.0%
!!! CGGAGGAGCTGTTTTTGGAC+AGG + chr8.3:7405090-7405109 MS.gene035321:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 7404642 7405217 7404642 ID=MS.gene035321
chr8.3 mRNA 7404642 7405217 7404642 ID=MS.gene035321.t1;Parent=MS.gene035321
chr8.3 exon 7404642 7405217 7404642 ID=MS.gene035321.t1.exon1;Parent=MS.gene035321.t1
chr8.3 CDS 7404642 7405217 7404642 ID=cds.MS.gene035321.t1;Parent=MS.gene035321.t1
Gene Sequence

>MS.gene035321

ATGAACAATTCCAAAATTGCTATGTTGTTTCGTATTTGGCCCAAGATATATTCTTCTTCCAACCTGTTGCATACTGTTGAGGAATTGAAGCAATTGGGTTTCAATTCTTCAAATTGCTCTTTCGGGGTTGCATTGCTTGCTAAGAGAAGTTTGAACAAAACAAGGTGGGATCATAAAGTTGAAACCTTTAAGAAATGGGGTTGGTCTGATGAACATATTTTTCATTCTTTTAAGAAGCACCCTAGTTGTATGTTGTCGTCCACTCATAAAATCGATGCACTCATGTGTTTTTGGGTTCATCACCTAGGTTTGGATTCTTTGGACCTTGTAATAATTTTTCAACGGAGTCTCGACAAGAGGATTATTCCAAGGGCTTCAGTTCTGCAGTTTCTTACGTCAAAAGGTCTTAGAAAAAAGAAGGCTGCCATTAGTAGGCCATTTGCTATTTCGGAGGAGCTGTTTTTGGACAGGTTTGTGAAATGTTTTAAGGAGGATTCATCTCATCTGTTGAAGCTGTATGAAGAAAAAATGAATCTTGCAGATAACAGTGAGAAAAAGTCTTTGCCTGGTGTGTAA
Protein sequence

>MS.gene035321.t1

MNNSKIAMLFRIWPKIYSSSNLLHTVEELKQLGFNSSNCSFGVALLAKRSLNKTRWDHKVETFKKWGWSDEHIFHSFKKHPSCMLSSTHKIDALMCFWVHHLGLDSLDLVIIFQRSLDKRIIPRASVLQFLTSKGLRKKKAAISRPFAISEELFLDRFVKCFKEDSSHLLKLYEEKMNLADNSEKKSLPGV