AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene94239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94239.t1 MTR_5g082780 78.879 232 36 2 25 244 1 231 3.26e-126 358
MS.gene94239.t1 MTR_1g064570 42.073 328 133 10 1 277 79 400 1.13e-73 231
MS.gene94239.t1 MTR_5g082770 56.757 222 81 6 1 212 74 290 3.27e-71 221
MS.gene94239.t1 MTR_5g038260 45.548 292 127 9 15 277 95 383 5.61e-68 216
MS.gene94239.t1 MTR_5g038230 45.907 281 112 9 15 275 93 353 5.51e-64 204
MS.gene94239.t1 MTR_1g108740 42.435 271 124 8 15 275 96 344 7.20e-57 186
MS.gene94239.t1 MTR_7g077660 42.958 284 122 13 16 277 103 368 1.40e-54 181
MS.gene94239.t1 MTR_7g077620 41.118 304 128 14 2 275 88 370 1.24e-49 168
MS.gene94239.t1 MTR_7g077650 40.070 287 129 14 16 277 104 372 3.79e-47 161
MS.gene94239.t1 MTR_7g076110 39.041 292 139 14 13 277 34 313 2.11e-43 150
MS.gene94239.t1 MTR_7g076100 43.515 239 105 10 61 277 70 300 1.06e-41 145
MS.gene94239.t1 MTR_1g016150 40.777 103 45 4 2 99 88 179 1.78e-13 68.6
MS.gene94239.t1 MTR_1g016150 41.584 101 53 3 125 224 141 236 2.04e-13 68.6
MS.gene94239.t1 MTR_3g114990 26.667 330 174 18 1 273 90 408 9.25e-13 68.2
MS.gene94239.t1 MTR_6g023955 44.706 85 44 2 50 134 64 145 8.60e-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

Find 57 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTAATCCCATTGGAAATT+TGG 0.111032 5.4:+65482007 None:intergenic
GAGCTGGCTTCATTCCTTTA+TGG 0.175035 5.4:-65482506 MS.gene94239:CDS
TAAGAATTTGGCAATTTAAA+TGG 0.183830 5.4:+65482814 None:intergenic
AGCAGGACCCACAACCTTTC+TGG 0.187221 5.4:-65482036 MS.gene94239:CDS
TAATCATTTGGTCTTGTTAT+AGG 0.187600 5.4:+65482616 None:intergenic
TTTATGGATGTTATGTTCTA+TGG 0.218295 5.4:-65482490 MS.gene94239:CDS
TAAATATGGTAATAAGAATT+TGG 0.257178 5.4:+65482802 None:intergenic
AATCATTTGGTCTTGTTATA+GGG 0.294407 5.4:+65482617 None:intergenic
GGCTAAATCCACAATAAATA+TGG 0.298457 5.4:+65482788 None:intergenic
ATAGGAGCAACATTCTTAAA+AGG 0.302714 5.4:+65482715 None:intergenic
AACAAGACCAAATGATTATA+TGG 0.314220 5.4:-65482611 MS.gene94239:CDS
TTCACGGTCCATTTCATATA+GGG 0.322905 5.4:-65482120 MS.gene94239:CDS
CAAATTTCCAATGGGATTAG+TGG 0.338785 5.4:-65482006 None:intergenic
TCGAGGGTTGGAAGACTAAT+AGG 0.340960 5.4:+65482697 None:intergenic
GCTATGTCCTGAATTGGATT+TGG 0.346401 5.4:+65482397 None:intergenic
TGAAAAGCTATGTCCTGAAT+TGG 0.358033 5.4:+65482391 None:intergenic
ATTCACGGTCCATTTCATAT+AGG 0.364892 5.4:-65482121 MS.gene94239:CDS
GATAACTCCAAATCCAATTC+AGG 0.366133 5.4:-65482404 MS.gene94239:CDS
GCCACAACCATATAATCATT+TGG 0.389176 5.4:+65482604 None:intergenic
GCATCAGGTTCATACTTCTC+TGG 0.392853 5.4:-65482172 MS.gene94239:CDS
ACTGATTCAATTTCTGCATC+AGG 0.401480 5.4:-65482187 MS.gene94239:CDS
GCAGGACCCACAACCTTTCT+GGG 0.410798 5.4:-65482035 MS.gene94239:CDS
AAAAGGATGCAATAGTGTTA+TGG 0.423581 5.4:+65482732 None:intergenic
GATTCAATTTATTACATTCA+CGG 0.424146 5.4:-65482136 MS.gene94239:CDS
TTATATATCCCTATATGAAA+TGG 0.424795 5.4:+65482112 None:intergenic
TTGGAATTCGATGTTGAGAC+TGG 0.428338 5.4:-65482271 MS.gene94239:CDS
TTATCTTGTGAAGTCATTAG+AGG 0.436221 5.4:-65482353 MS.gene94239:CDS
GCAATTCACACTAACATTGA+TGG 0.439424 5.4:-65482583 MS.gene94239:CDS
ATAGAACATAACATCCATAA+AGG 0.458967 5.4:+65482492 None:intergenic
GGTCCTGCTTGTTGAAGAAA+TGG 0.463160 5.4:+65482050 None:intergenic
GGTAAAACCCAGAAAGGTTG+TGG 0.463897 5.4:+65482028 None:intergenic
ATGCTAAAGCTTGAGAGTCT+TGG 0.465110 5.4:-65482235 MS.gene94239:CDS
CTTATGTATGGTTCTCGAGC+TGG 0.466024 5.4:-65482522 MS.gene94239:CDS
ATTGTGGATTTAGCCATGGT+TGG 0.471805 5.4:-65482780 MS.gene94239:CDS
TCTTATTACCATATTTATTG+TGG 0.472815 5.4:-65482796 MS.gene94239:CDS
ACCAAATGATTATATGGTTG+TGG 0.479866 5.4:-65482605 MS.gene94239:CDS
TTTACCTGTGGTCGGGTACA+AGG 0.489187 5.4:-65482656 MS.gene94239:CDS
AAATTTGGTAAAACCCAGAA+AGG 0.519503 5.4:+65482022 None:intergenic
CAACCATTTCTTCAACAAGC+AGG 0.520003 5.4:-65482053 MS.gene94239:CDS
AATCATGCTGGACTTATGTA+TGG 0.521933 5.4:-65482534 MS.gene94239:CDS
ATTTATTGTGGATTTAGCCA+TGG 0.534223 5.4:-65482784 MS.gene94239:CDS
GGGATATATAATGTAAGAGA+TGG 0.535003 5.4:-65482100 MS.gene94239:CDS
AGTTGAACCACTAATCCCAT+TGG 0.545273 5.4:+65481999 None:intergenic
ATGGATGTTATGTTCTATGG+AGG 0.548376 5.4:-65482487 MS.gene94239:CDS
GTAAAACCCAGAAAGGTTGT+GGG 0.553567 5.4:+65482029 None:intergenic
ATACAAGTTTACCTGTGGTC+GGG 0.554481 5.4:-65482663 MS.gene94239:CDS
TAAAAGCGGGACAATCATGC+TGG 0.564345 5.4:-65482546 MS.gene94239:CDS
TATACAAGTTTACCTGTGGT+CGG 0.569637 5.4:-65482664 MS.gene94239:CDS
TATCTTGTGAAGTCATTAGA+GGG 0.571586 5.4:-65482352 MS.gene94239:CDS
TATGATCGATAATCGAGGGT+TGG 0.575237 5.4:+65482685 None:intergenic
GTGAAGAGTATGATGATCAA+AGG 0.582000 5.4:+65482075 None:intergenic
GTGACCTTGTACCCGACCAC+AGG 0.582047 5.4:+65482652 None:intergenic
CTATTGTTGCAAGCCAACCA+TGG 0.611822 5.4:+65482767 None:intergenic
TGTATATGATCGATAATCGA+GGG 0.630019 5.4:+65482681 None:intergenic
ATCATATACAAGTTTACCTG+TGG 0.632668 5.4:-65482668 MS.gene94239:CDS
AGTCATTAGAGGGAGACTTG+TGG 0.643188 5.4:-65482342 MS.gene94239:CDS
TTGTATATGATCGATAATCG+AGG 0.645288 5.4:+65482680 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAGATTTTTTACTTTTAA+GGG - chr5.4:65482516-65482535 MS.gene94239:CDS 10.0%
!! TAAATATGGTAATAAGAATT+TGG + chr5.4:65482030-65482049 None:intergenic 15.0%
!!! GAAAAGATTTTTTACTTTTA+AGG - chr5.4:65482515-65482534 MS.gene94239:CDS 15.0%
!! GATTCAATTTATTACATTCA+CGG - chr5.4:65482693-65482712 MS.gene94239:CDS 20.0%
!! TAAGAATTTGGCAATTTAAA+TGG + chr5.4:65482018-65482037 None:intergenic 20.0%
!! TCTTATTACCATATTTATTG+TGG - chr5.4:65482033-65482052 MS.gene94239:CDS 20.0%
!! TTATATATCCCTATATGAAA+TGG + chr5.4:65482720-65482739 None:intergenic 20.0%
! AACAAGACCAAATGATTATA+TGG - chr5.4:65482218-65482237 MS.gene94239:CDS 25.0%
! ATAGAACATAACATCCATAA+AGG + chr5.4:65482340-65482359 None:intergenic 25.0%
! TTTATGGATGTTATGTTCTA+TGG - chr5.4:65482339-65482358 MS.gene94239:CDS 25.0%
!! AGTATAGTATCTTTTAATCC+TGG - chr5.4:65482393-65482412 MS.gene94239:CDS 25.0%
!!! AATCATTTGGTCTTGTTATA+GGG + chr5.4:65482215-65482234 None:intergenic 25.0%
!!! TAATCATTTGGTCTTGTTAT+AGG + chr5.4:65482216-65482235 None:intergenic 25.0%
AAAAGGATGCAATAGTGTTA+TGG + chr5.4:65482100-65482119 None:intergenic 30.0%
AAATTTGGTAAAACCCAGAA+AGG + chr5.4:65482810-65482829 None:intergenic 30.0%
ACCAAATGATTATATGGTTG+TGG - chr5.4:65482224-65482243 MS.gene94239:CDS 30.0%
ATAGGAGCAACATTCTTAAA+AGG + chr5.4:65482117-65482136 None:intergenic 30.0%
ATCATATACAAGTTTACCTG+TGG - chr5.4:65482161-65482180 MS.gene94239:CDS 30.0%
ATTTATTGTGGATTTAGCCA+TGG - chr5.4:65482045-65482064 MS.gene94239:CDS 30.0%
GGCTAAATCCACAATAAATA+TGG + chr5.4:65482044-65482063 None:intergenic 30.0%
GGGATATATAATGTAAGAGA+TGG - chr5.4:65482729-65482748 MS.gene94239:CDS 30.0%
TATCTTGTGAAGTCATTAGA+GGG - chr5.4:65482477-65482496 MS.gene94239:CDS 30.0%
TGTATATGATCGATAATCGA+GGG + chr5.4:65482151-65482170 None:intergenic 30.0%
TTATCTTGTGAAGTCATTAG+AGG - chr5.4:65482476-65482495 MS.gene94239:CDS 30.0%
TTGTATATGATCGATAATCG+AGG + chr5.4:65482152-65482171 None:intergenic 30.0%
! CTTTTAATCCTGGTCATAAA+AGG - chr5.4:65482403-65482422 MS.gene94239:CDS 30.0%
! GGTTTTACCAAATTTCCAAT+GGG - chr5.4:65482815-65482834 MS.gene94239:CDS 30.0%
!! ACGTTTCGCTTTTATAAAAG+CGG - chr5.4:65482269-65482288 MS.gene94239:CDS 30.0%
!!! TGATTTTCAAGTGTACAAGT+TGG - chr5.4:65482539-65482558 MS.gene94239:CDS 30.0%
AATCATGCTGGACTTATGTA+TGG - chr5.4:65482295-65482314 MS.gene94239:CDS 35.0%
ATGGATGTTATGTTCTATGG+AGG - chr5.4:65482342-65482361 MS.gene94239:CDS 35.0%
ATTCACGGTCCATTTCATAT+AGG - chr5.4:65482708-65482727 MS.gene94239:CDS 35.0%
GATAACTCCAAATCCAATTC+AGG - chr5.4:65482425-65482444 MS.gene94239:CDS 35.0%
GCAATTCACACTAACATTGA+TGG - chr5.4:65482246-65482265 MS.gene94239:CDS 35.0%
GCCACAACCATATAATCATT+TGG + chr5.4:65482228-65482247 None:intergenic 35.0%
TATACAAGTTTACCTGTGGT+CGG - chr5.4:65482165-65482184 MS.gene94239:CDS 35.0%
TGAAAAGCTATGTCCTGAAT+TGG + chr5.4:65482441-65482460 None:intergenic 35.0%
TTCACGGTCCATTTCATATA+GGG - chr5.4:65482709-65482728 MS.gene94239:CDS 35.0%
! ACTGATTCAATTTCTGCATC+AGG - chr5.4:65482642-65482661 MS.gene94239:CDS 35.0%
! ATTCAGGACATAGCTTTTCA+TGG - chr5.4:65482441-65482460 MS.gene94239:CDS 35.0%
! GGGTTTTACCAAATTTCCAA+TGG - chr5.4:65482814-65482833 MS.gene94239:CDS 35.0%
! GTGAAGAGTATGATGATCAA+AGG + chr5.4:65482757-65482776 None:intergenic 35.0%
!! CGTTTCGCTTTTATAAAAGC+GGG - chr5.4:65482270-65482289 MS.gene94239:CDS 35.0%
!! GGAGACAATGTTTTGTTCTT+GGG - chr5.4:65482615-65482634 MS.gene94239:CDS 35.0%
!! TGGAGACAATGTTTTGTTCT+TGG - chr5.4:65482614-65482633 MS.gene94239:CDS 35.0%
ATACAAGTTTACCTGTGGTC+GGG - chr5.4:65482166-65482185 MS.gene94239:CDS 40.0%
ATGCTAAAGCTTGAGAGTCT+TGG - chr5.4:65482594-65482613 MS.gene94239:CDS 40.0%
ATTGTGGATTTAGCCATGGT+TGG - chr5.4:65482049-65482068 MS.gene94239:CDS 40.0%
CAACCATTTCTTCAACAAGC+AGG - chr5.4:65482776-65482795 MS.gene94239:CDS 40.0%
GCTATGTCCTGAATTGGATT+TGG + chr5.4:65482435-65482454 None:intergenic 40.0%
GTAAAACCCAGAAAGGTTGT+GGG + chr5.4:65482803-65482822 None:intergenic 40.0%
TATGATCGATAATCGAGGGT+TGG + chr5.4:65482147-65482166 None:intergenic 40.0%
TTGGAATTCGATGTTGAGAC+TGG - chr5.4:65482558-65482577 MS.gene94239:CDS 40.0%
! GGAGTTATCCTTTTATGACC+AGG + chr5.4:65482414-65482433 None:intergenic 40.0%
!! GCTTTTCATGGAAGCTCTAA+AGG - chr5.4:65482453-65482472 MS.gene94239:CDS 40.0%
AGTCATTAGAGGGAGACTTG+TGG - chr5.4:65482487-65482506 MS.gene94239:CDS 45.0%
CTATTGTTGCAAGCCAACCA+TGG + chr5.4:65482065-65482084 None:intergenic 45.0%
CTTATGTATGGTTCTCGAGC+TGG - chr5.4:65482307-65482326 MS.gene94239:CDS 45.0%
GCATCAGGTTCATACTTCTC+TGG - chr5.4:65482657-65482676 MS.gene94239:CDS 45.0%
GGTAAAACCCAGAAAGGTTG+TGG + chr5.4:65482804-65482823 None:intergenic 45.0%
TAAAAGCGGGACAATCATGC+TGG - chr5.4:65482283-65482302 MS.gene94239:CDS 45.0%
TCGAGGGTTGGAAGACTAAT+AGG + chr5.4:65482135-65482154 None:intergenic 45.0%
! GAGCTGGCTTCATTCCTTTA+TGG - chr5.4:65482323-65482342 MS.gene94239:CDS 45.0%
! GGTCCTGCTTGTTGAAGAAA+TGG + chr5.4:65482782-65482801 None:intergenic 45.0%
TTTACCTGTGGTCGGGTACA+AGG - chr5.4:65482173-65482192 MS.gene94239:CDS 50.0%
AGCAGGACCCACAACCTTTC+TGG - chr5.4:65482793-65482812 MS.gene94239:CDS 55.0%
GCAGGACCCACAACCTTTCT+GGG - chr5.4:65482794-65482813 MS.gene94239:CDS 55.0%
GTGACCTTGTACCCGACCAC+AGG + chr5.4:65482180-65482199 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 65482009 65482842 65482009 ID=MS.gene94239
chr5.4 mRNA 65482009 65482842 65482009 ID=MS.gene94239.t1;Parent=MS.gene94239
chr5.4 exon 65482009 65482842 65482009 ID=MS.gene94239.t1.exon1;Parent=MS.gene94239.t1
chr5.4 CDS 65482009 65482842 65482009 ID=cds.MS.gene94239.t1;Parent=MS.gene94239.t1
Gene Sequence

>MS.gene94239

ATGTATCCATTTAAATTGCCAAATTCTTATTACCATATTTATTGTGGATTTAGCCATGGTTGGCTTGCAACAATAGATAAAAGTCATGCCATAACACTATTGCATCCTTTTAAGAATGTTGCTCCTATTAGTCTTCCAACCCTCGATTATCGATCATATACAAGTTTACCTGTGGTCGGGTACAAGGTCACTCTTTCTGCTGACCCTATAACAAGACCAAATGATTATATGGTTGTGGCAATTCACACTAACATTGATGGACGTTTCGCTTTTATAAAAGCGGGACAATCATGCTGGACTTATGTATGGTTCTCGAGCTGGCTTCATTCCTTTATGGATGTTATGTTCTATGGAGGTTTAGTTTATGCTGTGAGTAAATATCACAGTATAGTATCTTTTAATCCTGGTCATAAAAGGATAACTCCAAATCCAATTCAGGACATAGCTTTTCATGGAAGCTCTAAAGGTTATCTTGTGAAGTCATTAGAGGGAGACTTGTGGATAGTGAAAAGATTTTTTACTTTTAAGGGTGATTTTCAAGTGTACAAGTTGGAATTCGATGTTGAGACTGGAAAGTTTAAACAAATGCTAAAGCTTGAGAGTCTTGGAGACAATGTTTTGTTCTTGGGAGACACTGATTCAATTTCTGCATCAGGTTCATACTTCTCTGGTTGTTTGAAAAAAGATTCAATTTATTACATTCACGGTCCATTTCATATAGGGATATATAATGTAAGAGATGGAACCTTTGATCATCATACTCTTCACAACCATTTCTTCAACAAGCAGGACCCACAACCTTTCTGGGTTTTACCAAATTTCCAATGGGATTAG
Protein sequence

>MS.gene94239.t1

MYPFKLPNSYYHIYCGFSHGWLATIDKSHAITLLHPFKNVAPISLPTLDYRSYTSLPVVGYKVTLSADPITRPNDYMVVAIHTNIDGRFAFIKAGQSCWTYVWFSSWLHSFMDVMFYGGLVYAVSKYHSIVSFNPGHKRITPNPIQDIAFHGSSKGYLVKSLEGDLWIVKRFFTFKGDFQVYKLEFDVETGKFKQMLKLESLGDNVLFLGDTDSISASGSYFSGCLKKDSIYYIHGPFHIGIYNVRDGTFDHHTLHNHFFNKQDPQPFWVLPNFQWD