AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90006


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90006.t1 MTR_1g053530 72.112 251 41 5 20 261 16 246 2.30e-117 337
MS.gene90006.t1 MTR_1g046810 35.235 298 133 9 29 278 30 315 8.15e-42 146
MS.gene90006.t1 MTR_1g052185 31.884 276 134 12 29 273 23 275 2.64e-25 102
MS.gene90006.t1 MTR_4g073310 31.746 252 124 9 28 277 22 227 3.03e-20 87.0
MS.gene90006.t1 MTR_1g085590 31.472 197 96 9 88 273 73 241 2.89e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGGTCTCGTATCTTAT+TGG 0.208428 1.4:-40282189 None:intergenic
AGCACCAACAACTTTCTTAA+AGG 0.236987 1.4:+40281964 MS.gene90006:CDS
TACCCTTCTTCGAACCATTT+TGG 0.254107 1.4:-40282110 None:intergenic
ATAATCCCAGCTCCGTTTCT+TGG 0.287583 1.4:-40282205 None:intergenic
ATGAAATGGCACAGCCAAAA+TGG 0.332105 1.4:+40282096 MS.gene90006:CDS
GTTCTCTACATTGTCATCAT+TGG 0.335954 1.4:-40282475 None:intergenic
GTTTGAGTAATAAGTCCTTT+TGG 0.343516 1.4:-40282426 None:intergenic
TGAATCACCGTGACTGTAAA+AGG 0.346155 1.4:+40282304 MS.gene90006:CDS
CAAATTTAAACGCTAAATAG+TGG 0.394892 1.4:-40282610 None:intergenic
TTTACCTTTAAGAAAGTTGT+TGG 0.419418 1.4:-40281968 None:intergenic
TCATCTACAACATCATTTGC+CGG 0.440063 1.4:-40282585 None:intergenic
TAAGAAAGTTGTTGGTGCTA+TGG 0.440297 1.4:-40281960 None:intergenic
CTTTGAATGGACACATGAAA+TGG 0.459517 1.4:+40282082 MS.gene90006:CDS
CTCTACATTGTCATCATTGG+AGG 0.472478 1.4:-40282472 None:intergenic
TTGGTCTCGTATCTTATTGG+TGG 0.473127 1.4:-40282186 None:intergenic
ACGGTGATTCACATTAAGAT+TGG 0.473501 1.4:-40282292 None:intergenic
CAATGGATGGAAACTGATCT+AGG 0.474117 1.4:-40282146 None:intergenic
ATCCGTTTCATCACCTTCAT+CGG 0.483860 1.4:-40282502 None:intergenic
TGGTGCTATGGAATTGTTTG+TGG 0.484496 1.4:-40281948 None:intergenic
CAGCCAAAATGGTTCGAAGA+AGG 0.488255 1.4:+40282107 MS.gene90006:CDS
TGTGCTAGAGAATTCACAAC+TGG 0.492819 1.4:+40281910 MS.gene90006:CDS
CAAATACTTTGTCAGATCAA+TGG 0.494617 1.4:-40282163 None:intergenic
GAATTGTTTGTGGCCGCCGA+GGG 0.497780 1.4:-40281938 None:intergenic
TACCGATGAAGGTGATGAAA+CGG 0.519602 1.4:+40282500 MS.gene90006:CDS
GTGAGATTAAAGATTCCAAA+AGG 0.530313 1.4:+40282411 MS.gene90006:CDS
ACGAGACCAAGAAACGGAGC+TGG 0.539882 1.4:+40282199 MS.gene90006:CDS
AAAGACAAACATGCTGATGA+TGG 0.542758 1.4:+40281997 MS.gene90006:CDS
ACATTGTCATCATTGGAGGC+AGG 0.544139 1.4:-40282468 None:intergenic
TGTTAACATTGCTGAAACAA+TGG 0.555726 1.4:+40282245 MS.gene90006:CDS
GGAATTGTTTGTGGCCGCCG+AGG 0.556033 1.4:-40281939 None:intergenic
TTCACAACTGGTAATGCCCT+CGG 0.558819 1.4:+40281922 MS.gene90006:CDS
AGCCAAAATGGTTCGAAGAA+GGG 0.561339 1.4:+40282108 MS.gene90006:CDS
ATGAAGGTGATGAAACGGAT+GGG 0.561647 1.4:+40282505 MS.gene90006:CDS
TGAATAGAATGATGAGAAGA+AGG 0.561791 1.4:-40281808 None:intergenic
GCTGATGATGGTATTAAGAT+CGG 0.564146 1.4:+40282009 MS.gene90006:CDS
GTAGAGAACAATACCGATGA+AGG 0.568109 1.4:+40282489 MS.gene90006:CDS
TTCATGTGTTCTTTGCAACA+AGG 0.570989 1.4:+40282041 MS.gene90006:CDS
CGAGACCAAGAAACGGAGCT+GGG 0.594941 1.4:+40282200 MS.gene90006:CDS
CAATGAAAAGAACAGGTTGG+TGG 0.599420 1.4:+40282389 MS.gene90006:CDS
TACTTTGTCAGATCAATGGA+TGG 0.603001 1.4:-40282159 None:intergenic
TGAAGGTGATGAAACGGATG+GGG 0.603593 1.4:+40282506 MS.gene90006:CDS
TAAGATACGAGACCAAGAAA+CGG 0.610128 1.4:+40282193 MS.gene90006:CDS
GCAAAGAACACATGAATGGT+TGG 0.613792 1.4:-40282034 None:intergenic
GATGAAGGTGATGAAACGGA+TGG 0.616100 1.4:+40282504 MS.gene90006:CDS
AAACAATGAAAAGAACAGGT+TGG 0.620052 1.4:+40282386 MS.gene90006:CDS
TGTTGCAAAGAACACATGAA+TGG 0.632355 1.4:-40282038 None:intergenic
TAACATTGCTGAAACAATGG+TGG 0.675593 1.4:+40282248 MS.gene90006:CDS
ACAACTGGTAATGCCCTCGG+CGG 0.704742 1.4:+40281925 MS.gene90006:CDS
GAAAATGAGAAACATCAACA+AGG 0.726705 1.4:+40281862 MS.gene90006:CDS
GATGTGAAGATCAATGAACA+AGG 0.760498 1.4:+40282357 MS.gene90006:CDS
GTGAAGATCAATGAACAAGG+TGG 0.773369 1.4:+40282360 MS.gene90006:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTAAAAACAATGAAAAGAAC+AGG + chr1.4:40282382-40282401 MS.gene90006:CDS 25.0%
!! ATTTTCATGATCAACAACAT+TGG - chr1.4:40281848-40281867 None:intergenic 25.0%
!! TTTACCTTTAAGAAAGTTGT+TGG - chr1.4:40281971-40281990 None:intergenic 25.0%
AAACAATGAAAAGAACAGGT+TGG + chr1.4:40282386-40282405 MS.gene90006:CDS 30.0%
CAAATACTTTGTCAGATCAA+TGG - chr1.4:40282166-40282185 None:intergenic 30.0%
GAAAATGAGAAACATCAACA+AGG + chr1.4:40281862-40281881 MS.gene90006:CDS 30.0%
GTGAGATTAAAGATTCCAAA+AGG + chr1.4:40282411-40282430 MS.gene90006:CDS 30.0%
TGAATAGAATGATGAGAAGA+AGG - chr1.4:40281811-40281830 None:intergenic 30.0%
TGTTAACATTGCTGAAACAA+TGG + chr1.4:40282245-40282264 MS.gene90006:CDS 30.0%
! ATTCGAGTCAAACATTTTTC+AGG + chr1.4:40282542-40282561 MS.gene90006:CDS 30.0%
! GTTTGAGTAATAAGTCCTTT+TGG - chr1.4:40282429-40282448 None:intergenic 30.0%
!! TCATCGAAAAAAGCTTTGAA+TGG + chr1.4:40282069-40282088 MS.gene90006:CDS 30.0%
!!! TGATCAACAACATTGGTTTT+TGG - chr1.4:40281841-40281860 None:intergenic 30.0%
!!! TTTTGATTTGAATGAGCTAC+CGG + chr1.4:40282566-40282585 MS.gene90006:CDS 30.0%
AAAGACAAACATGCTGATGA+TGG + chr1.4:40281997-40282016 MS.gene90006:CDS 35.0%
ACGGTGATTCACATTAAGAT+TGG - chr1.4:40282295-40282314 None:intergenic 35.0%
AGCACCAACAACTTTCTTAA+AGG + chr1.4:40281964-40281983 MS.gene90006:CDS 35.0%
CTTTGAATGGACACATGAAA+TGG + chr1.4:40282082-40282101 MS.gene90006:CDS 35.0%
GATGTGAAGATCAATGAACA+AGG + chr1.4:40282357-40282376 MS.gene90006:CDS 35.0%
GTTCTCTACATTGTCATCAT+TGG - chr1.4:40282478-40282497 None:intergenic 35.0%
TAACATTGCTGAAACAATGG+TGG + chr1.4:40282248-40282267 MS.gene90006:CDS 35.0%
TAAGATACGAGACCAAGAAA+CGG + chr1.4:40282193-40282212 MS.gene90006:CDS 35.0%
TACTTTGTCAGATCAATGGA+TGG - chr1.4:40282162-40282181 None:intergenic 35.0%
TCATCTACAACATCATTTGC+CGG - chr1.4:40282588-40282607 None:intergenic 35.0%
TGTTGCAAAGAACACATGAA+TGG - chr1.4:40282041-40282060 None:intergenic 35.0%
TTCATGTGTTCTTTGCAACA+AGG + chr1.4:40282041-40282060 MS.gene90006:CDS 35.0%
TTCTTGGTCTCGTATCTTAT+TGG - chr1.4:40282192-40282211 None:intergenic 35.0%
! GTTTCATCCTTTTACAGTCA+CGG - chr1.4:40282314-40282333 None:intergenic 35.0%
!! GCTGATGATGGTATTAAGAT+CGG + chr1.4:40282009-40282028 MS.gene90006:CDS 35.0%
!! TAAGAAAGTTGTTGGTGCTA+TGG - chr1.4:40281963-40281982 None:intergenic 35.0%
AGCCAAAATGGTTCGAAGAA+GGG + chr1.4:40282108-40282127 MS.gene90006:CDS 40.0%
ATCCGTTTCATCACCTTCAT+CGG - chr1.4:40282505-40282524 None:intergenic 40.0%
ATGAAATGGCACAGCCAAAA+TGG + chr1.4:40282096-40282115 MS.gene90006:CDS 40.0%
ATGAAGGTGATGAAACGGAT+GGG + chr1.4:40282505-40282524 MS.gene90006:CDS 40.0%
CAATGGATGGAAACTGATCT+AGG - chr1.4:40282149-40282168 None:intergenic 40.0%
CTCTACATTGTCATCATTGG+AGG - chr1.4:40282475-40282494 None:intergenic 40.0%
GCAAAGAACACATGAATGGT+TGG - chr1.4:40282037-40282056 None:intergenic 40.0%
GTAGAGAACAATACCGATGA+AGG + chr1.4:40282489-40282508 MS.gene90006:CDS 40.0%
GTGAAGATCAATGAACAAGG+TGG + chr1.4:40282360-40282379 MS.gene90006:CDS 40.0%
TACCGATGAAGGTGATGAAA+CGG + chr1.4:40282500-40282519 MS.gene90006:CDS 40.0%
TGAATCACCGTGACTGTAAA+AGG + chr1.4:40282304-40282323 MS.gene90006:CDS 40.0%
TGTGCTAGAGAATTCACAAC+TGG + chr1.4:40281910-40281929 MS.gene90006:CDS 40.0%
TTGGTCTCGTATCTTATTGG+TGG - chr1.4:40282189-40282208 None:intergenic 40.0%
! CAATGAAAAGAACAGGTTGG+TGG + chr1.4:40282389-40282408 MS.gene90006:CDS 40.0%
! TACCCTTCTTCGAACCATTT+TGG - chr1.4:40282113-40282132 None:intergenic 40.0%
!! TGGTGCTATGGAATTGTTTG+TGG - chr1.4:40281951-40281970 None:intergenic 40.0%
ACATTGTCATCATTGGAGGC+AGG - chr1.4:40282471-40282490 None:intergenic 45.0%
ATAATCCCAGCTCCGTTTCT+TGG - chr1.4:40282208-40282227 None:intergenic 45.0%
CAGCCAAAATGGTTCGAAGA+AGG + chr1.4:40282107-40282126 MS.gene90006:CDS 45.0%
GATGAAGGTGATGAAACGGA+TGG + chr1.4:40282504-40282523 MS.gene90006:CDS 45.0%
TGAAGGTGATGAAACGGATG+GGG + chr1.4:40282506-40282525 MS.gene90006:CDS 45.0%
! TTCACAACTGGTAATGCCCT+CGG + chr1.4:40281922-40281941 MS.gene90006:CDS 45.0%
ACGAGACCAAGAAACGGAGC+TGG + chr1.4:40282199-40282218 MS.gene90006:CDS 55.0%
CGAGACCAAGAAACGGAGCT+GGG + chr1.4:40282200-40282219 MS.gene90006:CDS 55.0%
GAATTGTTTGTGGCCGCCGA+GGG - chr1.4:40281941-40281960 None:intergenic 55.0%
! ACAACTGGTAATGCCCTCGG+CGG + chr1.4:40281925-40281944 MS.gene90006:CDS 55.0%
GGAATTGTTTGTGGCCGCCG+AGG - chr1.4:40281942-40281961 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 40281778 40282620 40281778 ID=MS.gene90006
chr1.4 mRNA 40281778 40282620 40281778 ID=MS.gene90006.t1;Parent=MS.gene90006
chr1.4 exon 40281778 40282620 40281778 ID=MS.gene90006.t1.exon1;Parent=MS.gene90006.t1
chr1.4 CDS 40281778 40282620 40281778 ID=cds.MS.gene90006.t1;Parent=MS.gene90006.t1
Gene Sequence

>MS.gene90006

ATGATGAAGAATTCTTTTTCTTCTTCTTCACCTTCTTCTCATCATTCTATTCATCATAAGCCAAAAACCAATGTTGTTGATCATGAAAATGAGAAACATCAACAAGGTGCAAGACTTCACAAATGTGATTTGTGTGCTAGAGAATTCACAACTGGTAATGCCCTCGGCGGCCACAAACAATTCCATAGCACCAACAACTTTCTTAAAGGTAAAATCAACAAAGACAAACATGCTGATGATGGTATTAAGATCGGAACCAACCATTCATGTGTTCTTTGCAACAAGGCTTTTTCATCGAAAAAAGCTTTGAATGGACACATGAAATGGCACAGCCAAAATGGTTCGAAGAAGGGTAGTAACAATTACGACCTAGATCAGTTTCCATCCATTGATCTGACAAAGTATTTGCCACCAATAAGATACGAGACCAAGAAACGGAGCTGGGATTATATTCTTGATGTTGAAACTGTTAACATTGCTGAAACAATGGTGGAAATGTCTCAGCTATCATCTGCCAATCTTAATGTGAATCACCGTGACTGTAAAAGGATGAAACTTTGCAGCAATGTTGATGATGATGATGTGAAGATCAATGAACAAGGTGGTAAAAACAATGAAAAGAACAGGTTGGTGGTGAGATTAAAGATTCCAAAAGGACTTATTACTCAAACATCTCAAGCTAGCAAGCAACCTGCCTCCAATGATGACAATGTAGAGAACAATACCGATGAAGGTGATGAAACGGATGGGGAATCAACTCTTGAATTCGAGTCAAACATTTTTCAGGATTTTGATTTGAATGAGCTACCGGCAAATGATGTTGTAGATGAAACCACTATTTAG

Protein sequence

>MS.gene90006.t1

MMKNSFSSSSPSSHHSIHHKPKTNVVDHENEKHQQGARLHKCDLCAREFTTGNALGGHKQFHSTNNFLKGKINKDKHADDGIKIGTNHSCVLCNKAFSSKKALNGHMKWHSQNGSKKGSNNYDLDQFPSIDLTKYLPPIRYETKKRSWDYILDVETVNIAETMVEMSQLSSANLNVNHRDCKRMKLCSNVDDDDVKINEQGGKNNEKNRLVVRLKIPKGLITQTSQASKQPASNDDNVENNTDEGDETDGESTLEFESNIFQDFDLNELPANDVVDETTI