AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84936

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84936.t1 MTR_1g053530 71.200 250 44 4 21 261 16 246 8.69e-118 338
MS.gene84936.t1 MTR_1g046810 37.621 311 130 11 21 278 16 315 2.29e-43 150
MS.gene84936.t1 MTR_1g052185 32.234 273 128 13 30 269 23 271 3.16e-24 99.0
MS.gene84936.t1 MTR_4g073310 32.016 253 121 11 29 277 22 227 6.35e-17 78.2
MS.gene84936.t1 MTR_5g098470 33.149 181 89 9 8 167 35 204 5.50e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 53 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGGTCCCGTATCTTAT+TGG 0.216824 1.3:+37559820 None:intergenic
AGCACCAGCAACTTTCTTAA+AGG 0.235125 1.3:-37560042 MS.gene84936:CDS
TACCCTTCTTCGAACCATTT+TGG 0.254107 1.3:+37559899 None:intergenic
AAACAAAATTAAACACTAAA+TGG 0.270394 1.3:+37559396 None:intergenic
ATAATCCCAGCTCCGTTTCT+TGG 0.289051 1.3:+37559804 None:intergenic
ATGAAATGGCACAGCCAAAA+TGG 0.332105 1.3:-37559913 MS.gene84936:CDS
GTTCTCTACATTGTTATCAT+TGG 0.335954 1.3:+37559534 None:intergenic
GTTTGAGTAATAAGTCCTTT+TGG 0.343516 1.3:+37559583 None:intergenic
TGAATCACCGTGACTGTAAA+AGG 0.346155 1.3:-37559705 MS.gene84936:CDS
TTTACCTTTAAGAAAGTTGC+TGG 0.374533 1.3:+37560038 None:intergenic
TGTTAACATTGCTGAAATAA+TGG 0.391363 1.3:-37559764 MS.gene84936:CDS
AACAAACACAAACATGCTAA+TGG 0.425038 1.3:-37560012 MS.gene84936:CDS
TTTCGATTTGAATGAGCTAC+TGG 0.444087 1.3:-37559443 MS.gene84936:CDS
CTCTACATTGTTATCATTGG+AGG 0.445625 1.3:+37559537 None:intergenic
CTTTGAATGGACACATGAAA+TGG 0.459517 1.3:-37559927 MS.gene84936:CDS
ACGGTGATTCACATTAAGAT+TGG 0.473501 1.3:+37559717 None:intergenic
CAATGGATGGAAACTGATCT+AGG 0.474117 1.3:+37559863 None:intergenic
TGGTGCTATGGAATTGTTTG+TGG 0.477702 1.3:+37560058 None:intergenic
TTGGTCCCGTATCTTATTGG+TGG 0.478295 1.3:+37559823 None:intergenic
TAAGAAAGTTGCTGGTGCTA+TGG 0.481986 1.3:+37560046 None:intergenic
ATCCGTTTCATCACCTTCAT+CGG 0.483860 1.3:+37559507 None:intergenic
CAGCCAAAATGGTTCGAAGA+AGG 0.488255 1.3:-37559902 MS.gene84936:CDS
CAAATACTTTGTCAGATCAA+TGG 0.494617 1.3:+37559846 None:intergenic
TTCATGTGTTCTTTGCAGCA+AGG 0.509354 1.3:-37559968 MS.gene84936:CDS
TACCGATGAAGGTGATGAAA+CGG 0.519602 1.3:-37559509 MS.gene84936:CDS
TGTGCTAGAGAATTCACCTC+TGG 0.520924 1.3:-37560096 MS.gene84936:CDS
CATGCTAATGGTATTAAGAT+CGG 0.524324 1.3:-37560000 MS.gene84936:CDS
GTGAGATTAAAGATTCCAAA+AGG 0.530313 1.3:-37559598 MS.gene84936:CDS
ACATTGTTATCATTGGAGGC+AGG 0.530674 1.3:+37559541 None:intergenic
TAAGATACGGGACCAAGAAA+CGG 0.556029 1.3:-37559816 MS.gene84936:CDS
TATTTGCCACCAATAAGATA+CGG 0.556242 1.3:-37559829 MS.gene84936:CDS
AGCCAAAATGGTTCGAAGAA+GGG 0.561339 1.3:-37559901 MS.gene84936:CDS
ATGAAGGTGATGAAACGGAT+GGG 0.561647 1.3:-37559504 MS.gene84936:CDS
TGAATAGAATGATGAGAAGA+AGG 0.561791 1.3:+37560198 None:intergenic
GCAAAGAACACATGAATGGC+TGG 0.562308 1.3:+37559975 None:intergenic
GTAGAGAACAATACCGATGA+AGG 0.568109 1.3:-37559520 MS.gene84936:CDS
ACGGGACCAAGAAACGGAGC+TGG 0.570799 1.3:-37559810 MS.gene84936:CDS
TTCACCTCTGGTAATGCACT+CGG 0.587944 1.3:-37560084 MS.gene84936:CDS
CAATGAAAAGAACAGGTTGG+TGG 0.599420 1.3:-37559620 MS.gene84936:CDS
CGGGACCAAGAAACGGAGCT+GGG 0.599731 1.3:-37559809 MS.gene84936:CDS
CAAAATTAAACACTAAATGG+TGG 0.600626 1.3:+37559399 None:intergenic
TACTTTGTCAGATCAATGGA+TGG 0.603001 1.3:+37559850 None:intergenic
TGAAGGTGATGAAACGGATG+GGG 0.603593 1.3:-37559503 MS.gene84936:CDS
ATTTGCCACCAATAAGATAC+GGG 0.609267 1.3:-37559828 MS.gene84936:CDS
GATGAAGGTGATGAAACGGA+TGG 0.616100 1.3:-37559505 MS.gene84936:CDS
AAACAATGAAAAGAACAGGT+TGG 0.620052 1.3:-37559623 MS.gene84936:CDS
TGCTGCAAAGAACACATGAA+TGG 0.640126 1.3:+37559971 None:intergenic
TAACATTGCTGAAATAATGG+TGG 0.655107 1.3:-37559761 MS.gene84936:CDS
GCCGCCGAGTGCATTACCAG+AGG 0.670268 1.3:+37560080 None:intergenic
GAAAATGAGAAACATCAACA+AGG 0.726705 1.3:-37560144 MS.gene84936:CDS
ACCTCTGGTAATGCACTCGG+CGG 0.742189 1.3:-37560081 MS.gene84936:CDS
GATGTGAAGATCAATGAACA+AGG 0.760498 1.3:-37559652 MS.gene84936:CDS
GTGAAGATCAATGAACAAGG+TGG 0.773369 1.3:-37559649 MS.gene84936:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTAAAAACAATGAAAAGAAC+AGG - chr1.3:37560015-37560034 MS.gene84936:CDS 25.0%
! TGTTAACATTGCTGAAATAA+TGG - chr1.3:37559878-37559897 MS.gene84936:CDS 25.0%
!! AATTAGAGTCACACATTTTT+CGG - chr1.3:37560174-37560193 MS.gene84936:CDS 25.0%
AAACAATGAAAAGAACAGGT+TGG - chr1.3:37560019-37560038 MS.gene84936:CDS 30.0%
AACAAACACAAACATGCTAA+TGG - chr1.3:37559630-37559649 MS.gene84936:CDS 30.0%
CAAATACTTTGTCAGATCAA+TGG + chr1.3:37559799-37559818 None:intergenic 30.0%
CATGCTAATGGTATTAAGAT+CGG - chr1.3:37559642-37559661 MS.gene84936:CDS 30.0%
GAAAATGAGAAACATCAACA+AGG - chr1.3:37559498-37559517 MS.gene84936:CDS 30.0%
GTGAGATTAAAGATTCCAAA+AGG - chr1.3:37560044-37560063 MS.gene84936:CDS 30.0%
GTTCTCTACATTGTTATCAT+TGG + chr1.3:37560111-37560130 None:intergenic 30.0%
TAACATTGCTGAAATAATGG+TGG - chr1.3:37559881-37559900 MS.gene84936:CDS 30.0%
TATTTGCCACCAATAAGATA+CGG - chr1.3:37559813-37559832 MS.gene84936:CDS 30.0%
TGAATAGAATGATGAGAAGA+AGG + chr1.3:37559447-37559466 None:intergenic 30.0%
! ATTAGAGTCACACATTTTTC+GGG - chr1.3:37560175-37560194 MS.gene84936:CDS 30.0%
! GTTTGAGTAATAAGTCCTTT+TGG + chr1.3:37560062-37560081 None:intergenic 30.0%
! TTTACCTTTAAGAAAGTTGC+TGG + chr1.3:37559607-37559626 None:intergenic 30.0%
!! TCATCGAAAAAAGCTTTGAA+TGG - chr1.3:37559702-37559721 MS.gene84936:CDS 30.0%
ACGGTGATTCACATTAAGAT+TGG + chr1.3:37559928-37559947 None:intergenic 35.0%
ATTTGCCACCAATAAGATAC+GGG - chr1.3:37559814-37559833 MS.gene84936:CDS 35.0%
CTCTACATTGTTATCATTGG+AGG + chr1.3:37560108-37560127 None:intergenic 35.0%
CTTTGAATGGACACATGAAA+TGG - chr1.3:37559715-37559734 MS.gene84936:CDS 35.0%
GATGTGAAGATCAATGAACA+AGG - chr1.3:37559990-37560009 MS.gene84936:CDS 35.0%
TACTTTGTCAGATCAATGGA+TGG + chr1.3:37559795-37559814 None:intergenic 35.0%
! GTTTCATCCTTTTACAGTCA+CGG + chr1.3:37559947-37559966 None:intergenic 35.0%
! TTTCGATTTGAATGAGCTAC+TGG - chr1.3:37560199-37560218 MS.gene84936:CDS 35.0%
!! TGATCAACAGCATTGCTTTT+TGG + chr1.3:37559477-37559496 None:intergenic 35.0%
ACATTGTTATCATTGGAGGC+AGG + chr1.3:37560104-37560123 None:intergenic 40.0%
AGCACCAGCAACTTTCTTAA+AGG - chr1.3:37559600-37559619 MS.gene84936:CDS 40.0%
AGCCAAAATGGTTCGAAGAA+GGG - chr1.3:37559741-37559760 MS.gene84936:CDS 40.0%
ATCCGTTTCATCACCTTCAT+CGG + chr1.3:37560138-37560157 None:intergenic 40.0%
ATGAAATGGCACAGCCAAAA+TGG - chr1.3:37559729-37559748 MS.gene84936:CDS 40.0%
ATGAAGGTGATGAAACGGAT+GGG - chr1.3:37560138-37560157 MS.gene84936:CDS 40.0%
CAATGGATGGAAACTGATCT+AGG + chr1.3:37559782-37559801 None:intergenic 40.0%
GTAGAGAACAATACCGATGA+AGG - chr1.3:37560122-37560141 MS.gene84936:CDS 40.0%
GTGAAGATCAATGAACAAGG+TGG - chr1.3:37559993-37560012 MS.gene84936:CDS 40.0%
TAAGATACGGGACCAAGAAA+CGG - chr1.3:37559826-37559845 MS.gene84936:CDS 40.0%
TACCGATGAAGGTGATGAAA+CGG - chr1.3:37560133-37560152 MS.gene84936:CDS 40.0%
TGAATCACCGTGACTGTAAA+AGG - chr1.3:37559937-37559956 MS.gene84936:CDS 40.0%
TGCTGCAAAGAACACATGAA+TGG + chr1.3:37559674-37559693 None:intergenic 40.0%
TTCATGTGTTCTTTGCAGCA+AGG - chr1.3:37559674-37559693 MS.gene84936:CDS 40.0%
TTCTTGGTCCCGTATCTTAT+TGG + chr1.3:37559825-37559844 None:intergenic 40.0%
! CAATGAAAAGAACAGGTTGG+TGG - chr1.3:37560022-37560041 MS.gene84936:CDS 40.0%
! TAAGAAAGTTGCTGGTGCTA+TGG + chr1.3:37559599-37559618 None:intergenic 40.0%
! TACCCTTCTTCGAACCATTT+TGG + chr1.3:37559746-37559765 None:intergenic 40.0%
!! TGGTGCTATGGAATTGTTTG+TGG + chr1.3:37559587-37559606 None:intergenic 40.0%
ATAATCCCAGCTCCGTTTCT+TGG + chr1.3:37559841-37559860 None:intergenic 45.0%
CAGCCAAAATGGTTCGAAGA+AGG - chr1.3:37559740-37559759 MS.gene84936:CDS 45.0%
GATGAAGGTGATGAAACGGA+TGG - chr1.3:37560137-37560156 MS.gene84936:CDS 45.0%
GCAAAGAACACATGAATGGC+TGG + chr1.3:37559670-37559689 None:intergenic 45.0%
TGAAGGTGATGAAACGGATG+GGG - chr1.3:37560139-37560158 MS.gene84936:CDS 45.0%
TGTGCTAGAGAATTCACCTC+TGG - chr1.3:37559546-37559565 MS.gene84936:CDS 45.0%
TTGGTCCCGTATCTTATTGG+TGG + chr1.3:37559822-37559841 None:intergenic 45.0%
! TTCACCTCTGGTAATGCACT+CGG - chr1.3:37559558-37559577 MS.gene84936:CDS 45.0%
! ACCTCTGGTAATGCACTCGG+CGG - chr1.3:37559561-37559580 MS.gene84936:CDS 55.0%
ACGGGACCAAGAAACGGAGC+TGG - chr1.3:37559832-37559851 MS.gene84936:CDS 60.0%
CGGGACCAAGAAACGGAGCT+GGG - chr1.3:37559833-37559852 MS.gene84936:CDS 60.0%
GCCGCCGAGTGCATTACCAG+AGG + chr1.3:37559565-37559584 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 37559411 37560253 37559411 ID=MS.gene84936
chr1.3 mRNA 37559411 37560253 37559411 ID=MS.gene84936.t1;Parent=MS.gene84936
chr1.3 exon 37559411 37560253 37559411 ID=MS.gene84936.t1.exon1;Parent=MS.gene84936.t1
chr1.3 CDS 37559411 37560253 37559411 ID=cds.MS.gene84936.t1;Parent=MS.gene84936.t1
Gene Sequence

>MS.gene84936

ATGATGAAGAATTCTTTTTCTTCTTCTTCTTCACCTTCTTCTCATCATTCTATTCATCAAAAGCCAAAAAGCAATGCTGTTGATCATGAAAATGAGAAACATCAACAAGGTGCAAGACTTCACAAATGTGATTTGTGTGCTAGAGAATTCACCTCTGGTAATGCACTCGGCGGCCACAAACAATTCCATAGCACCAGCAACTTTCTTAAAGGTAAAATCAACAAACACAAACATGCTAATGGTATTAAGATCGGAACCAGCCATTCATGTGTTCTTTGCAGCAAGGCTTTTTCATCGAAAAAAGCTTTGAATGGACACATGAAATGGCACAGCCAAAATGGTTCGAAGAAGGGTAGTAACAATTATGACCTAGATCAGTTTCCATCCATTGATCTGACAAAGTATTTGCCACCAATAAGATACGGGACCAAGAAACGGAGCTGGGATTATATTCTTGATGTTGAAACTGTTAACATTGCTGAAATAATGGTGGATATGTCTCAGCTATCATCTGCCAATCTTAATGTGAATCACCGTGACTGTAAAAGGATGAAACTTTGCAGCAATGTTGATGATGATGATGTGAAGATCAATGAACAAGGTGGTAAAAACAATGAAAAGAACAGGTTGGTGGTGAGATTAAAGATTCCAAAAGGACTTATTACTCAAACATCTCAAGCTAGCAAGCAACCTGCCTCCAATGATAACAATGTAGAGAACAATACCGATGAAGGTGATGAAACGGATGGGGAATCAACTCTTGAATTAGAGTCACACATTTTTCGGGATTTCGATTTGAATGAGCTACTGGAAGATGATGTTGTAGATGAAACCACCATTTAG
Protein sequence

>MS.gene84936.t1

MMKNSFSSSSSPSSHHSIHQKPKSNAVDHENEKHQQGARLHKCDLCAREFTSGNALGGHKQFHSTSNFLKGKINKHKHANGIKIGTSHSCVLCSKAFSSKKALNGHMKWHSQNGSKKGSNNYDLDQFPSIDLTKYLPPIRYGTKKRSWDYILDVETVNIAEIMVDMSQLSSANLNVNHRDCKRMKLCSNVDDDDVKINEQGGKNNEKNRLVVRLKIPKGLITQTSQASKQPASNDNNVENNTDEGDETDGESTLELESHIFRDFDLNELLEDDVVDETTI