AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062079

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062079.t1 MTR_2g045020 78.075 187 28 2 10 196 1 174 8.54e-94 271
MS.gene062079.t1 MTR_3g437790 64.848 165 54 4 35 197 12 174 1.04e-60 187
MS.gene062079.t1 MTR_8g022970 50.867 173 78 5 29 197 8 177 4.84e-46 150
MS.gene062079.t1 MTR_3g109930 49.367 158 75 4 41 197 7 160 1.19e-40 136
MS.gene062079.t1 MTR_7g028448 33.824 136 76 3 56 190 31 153 4.48e-17 75.5
MS.gene062079.t1 MTR_4g036915 33.824 136 76 3 56 190 31 153 4.48e-17 75.5
MS.gene062079.t1 MTR_2g105290 36.420 162 91 6 36 190 5 161 5.83e-17 75.1
MS.gene062079.t1 MTR_8g086290 34.810 158 94 6 36 190 10 161 5.85e-14 67.4
MS.gene062079.t1 MTR_2g030740 34.320 169 90 7 29 187 2 159 1.46e-13 67.4
MS.gene062079.t1 MTR_5g053390 30.864 162 105 6 29 187 2 159 2.67e-13 66.6
MS.gene062079.t1 MTR_8g043650 35.404 161 80 8 37 184 7 156 3.88e-13 66.2
MS.gene062079.t1 MTR_1g106070 34.177 158 92 7 37 187 7 159 8.42e-13 64.3
MS.gene062079.t1 MTR_3g052920 35.366 164 82 8 37 187 7 159 1.12e-12 64.7
MS.gene062079.t1 MTR_1g105910 33.133 166 90 7 29 184 2 156 1.71e-12 64.3
MS.gene062079.t1 MTR_1g012570 30.120 166 101 7 29 187 2 159 2.82e-12 63.5
MS.gene062079.t1 MTR_3g030770 31.737 167 97 6 29 187 2 159 4.22e-11 60.5
MS.gene062079.t1 MTR_3g080940 27.607 163 97 6 38 190 11 162 4.62e-11 60.1
MS.gene062079.t1 MTR_1g105920 31.953 169 94 7 29 187 2 159 5.94e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062079.t1 AT2G24840 28.289 152 105 4 38 187 65 214 1.73e-13 67.4
MS.gene062079.t1 AT5G60440 32.075 159 92 7 38 187 9 160 5.08e-13 66.6

Find 30 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGGACTTTAAGAATTCTT+TGG 0.239126 2.3:-45277250 MS.gene062079:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.3:+45277400 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2.3:+45277298 None:intergenic
TGATGTTGAATGTAACAAAC+TGG 0.415899 2.3:-45277779 MS.gene062079:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.3:+45277401 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2.3:+45277525 None:intergenic
GTGATGTCAATTTCCATGAT+TGG 0.461626 2.3:-45277311 MS.gene062079:CDS
GAATTCTTTGGAGAGTTTCA+AGG 0.479356 2.3:-45277238 MS.gene062079:CDS
AATTCTTTGGAGAGTTTCAA+GGG 0.490979 2.3:-45277237 MS.gene062079:CDS
ACGATGAATGACAGCATCAC+AGG 0.499770 2.3:+45277491 None:intergenic
ATCCTCGGCCATCATATGTC+CGG 0.508496 2.3:+45277461 None:intergenic
GACATATGATGGCCGAGGAT+GGG 0.528388 2.3:-45277458 MS.gene062079:CDS
GCTTCTGAGATAAAGAATGC+TGG 0.529757 2.3:-45277708 MS.gene062079:CDS
ATGAAATTGCTGAAACCCTA+AGG 0.533334 2.3:-45277416 MS.gene062079:CDS
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2.3:-45277615 MS.gene062079:CDS
TGTCTGAAAAGAACACTGCT+AGG 0.558447 2.3:-45277731 MS.gene062079:CDS
TCTTGTCCGGCGATTTGACG+AGG 0.561634 2.3:+45277538 None:intergenic
GGACATATGATGGCCGAGGA+TGG 0.572212 2.3:-45277459 MS.gene062079:CDS
GGCACTCCTCGTCAAATCGC+CGG 0.575658 2.3:-45277544 MS.gene062079:CDS
GACCGGACATATGATGGCCG+AGG 0.586444 2.3:-45277463 MS.gene062079:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2.3:-45277213 MS.gene062079:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2.3:+45277492 None:intergenic
TATGAATTTAGCATCTCTTG+AGG 0.622708 2.3:-45277268 MS.gene062079:CDS
GTCTGAAAAGAACACTGCTA+GGG 0.626438 2.3:-45277730 MS.gene062079:CDS
ATGTCAATTTCCATGATTGG+TGG 0.630551 2.3:-45277308 MS.gene062079:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2.3:-45277519 MS.gene062079:CDS
GAACAAAACTGAACAACACA+CGG 0.651271 2.3:-45277686 MS.gene062079:CDS
GATGTTGAATGTAACAAACT+GGG 0.728152 2.3:-45277778 MS.gene062079:CDS
GAAAGCTGTCAAAGTCACCG+AGG 0.773790 2.3:-45277343 MS.gene062079:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2.3:+45277493 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAGAAGAAAAACTGAA+CGG - chr2.3:45277341-45277360 MS.gene062079:CDS 25.0%
! AATTCTATGCCAATCAAAAA+CGG - chr2.3:45277418-45277437 MS.gene062079:CDS 25.0%
TAGAATTATTCCACCAATCA+TGG + chr2.3:45277688-45277707 None:intergenic 30.0%
TATGAATTTAGCATCTCTTG+AGG - chr2.3:45277715-45277734 MS.gene062079:CDS 30.0%
TCAAGAAAAACTTGAAGAAG+AGG - chr2.3:45277607-45277626 MS.gene062079:CDS 30.0%
! AATTCTTTGGAGAGTTTCAA+GGG - chr2.3:45277746-45277765 MS.gene062079:CDS 30.0%
! TGAGGACTTTAAGAATTCTT+TGG - chr2.3:45277733-45277752 MS.gene062079:CDS 30.0%
AAGAACAAGTTCTATGCATG+TGG - chr2.3:45277464-45277483 MS.gene062079:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG - chr2.3:45277567-45277586 MS.gene062079:CDS 35.0%
ATGTCAATTTCCATGATTGG+TGG - chr2.3:45277675-45277694 MS.gene062079:CDS 35.0%
GAACAAAACTGAACAACACA+CGG - chr2.3:45277297-45277316 MS.gene062079:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG - chr2.3:45277672-45277691 MS.gene062079:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.3:45277585-45277604 None:intergenic 35.0%
! GAATTCTTTGGAGAGTTTCA+AGG - chr2.3:45277745-45277764 MS.gene062079:CDS 35.0%
GTCTGAAAAGAACACTGCTA+GGG - chr2.3:45277253-45277272 MS.gene062079:CDS 40.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.3:45277586-45277605 None:intergenic 40.0%
TGTCTGAAAAGAACACTGCT+AGG - chr2.3:45277252-45277271 MS.gene062079:CDS 40.0%
! CTTCTTCTTTTTCCCATCCT+CGG + chr2.3:45277540-45277559 None:intergenic 40.0%
! GCATAGAACTTGTTCTTGTC+CGG + chr2.3:45277461-45277480 None:intergenic 40.0%
! GTCATTCATCGTTTTCTGAC+CGG - chr2.3:45277503-45277522 MS.gene062079:CDS 40.0%
! TTTTCTGACCGGACATATGA+TGG - chr2.3:45277514-45277533 MS.gene062079:CDS 40.0%
!! GCTTCTGAGATAAAGAATGC+TGG - chr2.3:45277275-45277294 MS.gene062079:CDS 40.0%
AATTTACGTGCAGCAAGCGA+AGG - chr2.3:45277770-45277789 MS.gene062079:CDS 45.0%
ACGATGAATGACAGCATCAC+AGG + chr2.3:45277495-45277514 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG + chr2.3:45277494-45277513 None:intergenic 45.0%
GAGTTCTCAAGACGCAAACT+CGG - chr2.3:45277368-45277387 MS.gene062079:CDS 45.0%
GATGAATGACAGCATCACAG+GGG + chr2.3:45277493-45277512 None:intergenic 45.0%
! GACATCACTCTTTTGTGCCT+CGG + chr2.3:45277660-45277679 None:intergenic 45.0%
ATCCTCGGCCATCATATGTC+CGG + chr2.3:45277525-45277544 None:intergenic 50.0%
GAAAGCTGTCAAAGTCACCG+AGG - chr2.3:45277640-45277659 MS.gene062079:CDS 50.0%
GACATATGATGGCCGAGGAT+GGG - chr2.3:45277525-45277544 MS.gene062079:CDS 50.0%
!!! CGAGGAGTGCCGTTTTTGAT+TGG + chr2.3:45277430-45277449 None:intergenic 50.0%
GGACATATGATGGCCGAGGA+TGG - chr2.3:45277524-45277543 MS.gene062079:CDS 55.0%
TCTTGTCCGGCGATTTGACG+AGG + chr2.3:45277448-45277467 None:intergenic 55.0%
GACCGGACATATGATGGCCG+AGG - chr2.3:45277520-45277539 MS.gene062079:CDS 60.0%
GGCACTCCTCGTCAAATCGC+CGG - chr2.3:45277439-45277458 MS.gene062079:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 45277206 45277799 45277206 ID=MS.gene062079
chr2.3 mRNA 45277206 45277799 45277206 ID=MS.gene062079.t1;Parent=MS.gene062079
chr2.3 exon 45277206 45277799 45277206 ID=MS.gene062079.t1.exon1;Parent=MS.gene062079.t1
chr2.3 CDS 45277206 45277799 45277206 ID=cds.MS.gene062079.t1;Parent=MS.gene062079.t1
Gene Sequence

>MS.gene062079

ATGTTGAATGTAACAAACTGGGACAACATGAATAAGAATTGTGAACTGTCTGAAAAGAACACTGCTAGGGCTTCTGAGATAAAGAATGCTGGAACAAAACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGTTCTGAGTTCTCAAGACGCAAACTCGGAATATTCAACAAAGCAATAGAGCTGTCAATTCTATGCCAATCAAAAACGGCACTCCTCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTGACCGGACATATGATGGCCGAGGATGGGAAAAAGAAGAAGCAAGATGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGATGATAATTTGAAAGCTGTCAAAGTCACCGAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAGGACTTTAAGAATTCTTTGGAGAGTTTCAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>MS.gene062079.t1

MLNVTNWDNMNKNCELSEKNTARASEIKNAGTKLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTALLVKSPDKNKFYACGYPCDAVIHRFLTGHMMAEDGKKKKQDDEIAETLRLQYEALQEKLEEEDDNLKAVKVTEAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK