AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53631

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53631.t1 MTR_1g046810 86.667 315 42 0 1 315 1 315 0.0 535
MS.gene53631.t1 MTR_1g052185 37.994 329 116 13 5 310 12 275 1.65e-40 143
MS.gene53631.t1 MTR_1g053530 38.053 226 93 7 63 281 39 224 6.35e-30 114
MS.gene53631.t1 MTR_1g085590 37.037 270 82 10 71 315 16 222 3.41e-29 113
MS.gene53631.t1 MTR_1g063150 37.788 217 53 7 94 310 36 170 2.18e-28 108
MS.gene53631.t1 MTR_1g063140 41.818 165 42 8 147 310 1 112 5.82e-20 85.9
MS.gene53631.t1 MTR_5g098470 30.622 209 83 9 14 210 46 204 1.14e-12 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 60 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATTGTTATATATGTCTTA+TGG 0.192869 1.1:+29671271 MS.gene53631:CDS
AACGAAGAGGAAACTGAATT+AGG 0.275756 1.1:+29671517 MS.gene53631:CDS
CATTGTTATATATGTCTTAT+GGG 0.313934 1.1:+29671272 MS.gene53631:CDS
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.1:-29670852 None:intergenic
ACTATCATCCACCGTATTGC+TGG 0.349548 1.1:-29671329 None:intergenic
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.1:-29671218 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.1:+29671296 MS.gene53631:CDS
ACGAAGAGGAAACTGAATTA+GGG 0.408588 1.1:+29671518 MS.gene53631:CDS
CACAAACATAATCATGATGA+TGG 0.427443 1.1:+29670968 MS.gene53631:CDS
AACAGAAAAGAAACACTAAC+TGG 0.431171 1.1:-29671602 None:intergenic
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1.1:-29670840 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.1:+29671111 MS.gene53631:CDS
TGTTACAAACATCACATGTA+TGG 0.446958 1.1:-29671003 None:intergenic
TGACTTTGTTCCAAGGAAGA+TGG 0.453168 1.1:-29671121 None:intergenic
GACTTTGTTCCAAGGAAGAT+GGG 0.458996 1.1:-29671120 None:intergenic
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.1:-29671157 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.1:-29670763 None:intergenic
TCATCCAACAGTGCTTTGAA+TGG 0.470969 1.1:+29671034 MS.gene53631:CDS
TATGAGATGGCATACTCAAA+AGG 0.486406 1.1:+29671060 MS.gene53631:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.1:-29670764 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1.1:+29670794 MS.gene53631:CDS
TACTCAAAAGGGTTCGAAGA+AGG 0.504806 1.1:+29671072 MS.gene53631:CDS
AATTAGGGTCAAGAGTTGTC+AGG 0.507473 1.1:+29671533 MS.gene53631:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.1:-29670892 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.1:-29670733 None:intergenic
CATGATCATGCTGTGAATAA+CGG 0.518528 1.1:+29670893 MS.gene53631:CDS
AACAAGGTGTGCTGCTAACA+AGG 0.519240 1.1:+29671365 MS.gene53631:CDS
ATGAGATGGCATACTCAAAA+GGG 0.526510 1.1:+29671061 MS.gene53631:CDS
GGATCTAGCTGTGATATTGA+AGG 0.530396 1.1:+29671481 MS.gene53631:CDS
ATTGTTATATATGTCTTATG+GGG 0.542437 1.1:+29671273 MS.gene53631:CDS
TCAAACATCGCAAGATTGCA+AGG 0.542865 1.1:+29671450 MS.gene53631:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.1:+29671318 MS.gene53631:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.1:-29670680 None:intergenic
ACTCAAAAGGGTTCGAAGAA+GGG 0.553906 1.1:+29671073 MS.gene53631:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1.1:+29670809 MS.gene53631:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.1:-29670847 None:intergenic
CAAGATTGCAAGGAACCTGC+AGG 0.562783 1.1:+29671460 MS.gene53631:CDS
TTGGTCTTATACGATATTGG+CGG 0.563784 1.1:-29671184 None:intergenic
CTCAAGATGACTTTGTTCCA+AGG 0.567999 1.1:-29671128 None:intergenic
ACAAACATAATCATGATGAT+GGG 0.568114 1.1:+29670969 MS.gene53631:CDS
ATGTCCATTCAAAGCACTGT+TGG 0.568123 1.1:-29671038 None:intergenic
GGATGATAGTGAAAAGATGA+AGG 0.573473 1.1:+29671342 MS.gene53631:CDS
TTCACCTCTGGTAAATCACT+TGG 0.575760 1.1:+29670806 MS.gene53631:CDS
ATATCACAGCTAGATCCTGC+AGG 0.585006 1.1:-29671475 None:intergenic
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.1:-29671105 None:intergenic
TCTTATACGATATTGGCGGC+AGG 0.588195 1.1:-29671180 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.1:-29671217 None:intergenic
TTGTTATATATGTCTTATGG+GGG 0.593530 1.1:+29671274 MS.gene53631:CDS
TCATCTTCGAAATCATCACT+TGG 0.604104 1.1:-29671577 None:intergenic
CAAGAAGAATATTAACGAAG+AGG 0.604934 1.1:+29671504 MS.gene53631:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.1:-29671112 None:intergenic
TACATGTGATGTTTGTAACA+AGG 0.614171 1.1:+29671006 MS.gene53631:CDS
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.1:-29670718 None:intergenic
AGTGAAAAGATGAAGGAACA+AGG 0.617064 1.1:+29671349 MS.gene53631:CDS
GCGTATTGCTGATAATGATG+AGG 0.644357 1.1:+29671228 MS.gene53631:CDS
ACTTTGTTCCAAGGAAGATG+GGG 0.645998 1.1:-29671119 None:intergenic
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.1:+29671321 MS.gene53631:CDS
CTTTGAATGGACATATGAGA+TGG 0.684064 1.1:+29671047 MS.gene53631:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.1:-29670810 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.1:+29670896 MS.gene53631:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+TGG + chr1.1:29671271-29671290 MS.gene53631:CDS 20.0%
!! ATTGTTATATATGTCTTATG+GGG + chr1.1:29671273-29671292 MS.gene53631:CDS 20.0%
!! CATTGTTATATATGTCTTAT+GGG + chr1.1:29671272-29671291 MS.gene53631:CDS 20.0%
! ACAAACATAATCATGATGAT+GGG + chr1.1:29670969-29670988 MS.gene53631:CDS 25.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.1:29670927-29670946 MS.gene53631:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.1:29670928-29670947 MS.gene53631:CDS 25.0%
! GTTTGAAAAATCTTGTCTTT+AGG - chr1.1:29671436-29671455 None:intergenic 25.0%
! TATCGTATAAGACCAAAAAA+CGG + chr1.1:29671191-29671210 MS.gene53631:CDS 25.0%
! TTGTTATATATGTCTTATGG+GGG + chr1.1:29671274-29671293 MS.gene53631:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.1:29670924-29670943 None:intergenic 25.0%
!!! TTTTTGGTCTTATACGATAT+TGG - chr1.1:29671190-29671209 None:intergenic 25.0%
CAAGAAGAATATTAACGAAG+AGG + chr1.1:29671504-29671523 MS.gene53631:CDS 30.0%
CACAAACATAATCATGATGA+TGG + chr1.1:29670968-29670987 MS.gene53631:CDS 30.0%
TACATGTGATGTTTGTAACA+AGG + chr1.1:29671006-29671025 MS.gene53631:CDS 30.0%
TGTTACAAACATCACATGTA+TGG - chr1.1:29671006-29671025 None:intergenic 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.1:29670711-29670730 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.1:29670875-29670894 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.1:29670710-29670729 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.1:29670694-29670713 None:intergenic 30.0%
AACGAAGAGGAAACTGAATT+AGG + chr1.1:29671517-29671536 MS.gene53631:CDS 35.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.1:29670766-29670785 None:intergenic 35.0%
ACGAAGAGGAAACTGAATTA+GGG + chr1.1:29671518-29671537 MS.gene53631:CDS 35.0%
AGTGAAAAGATGAAGGAACA+AGG + chr1.1:29671349-29671368 MS.gene53631:CDS 35.0%
ATGAGATGGCATACTCAAAA+GGG + chr1.1:29671061-29671080 MS.gene53631:CDS 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.1:29670893-29670912 MS.gene53631:CDS 35.0%
CTTTGAATGGACATATGAGA+TGG + chr1.1:29671047-29671066 MS.gene53631:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.1:29670746-29670765 MS.gene53631:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.1:29671296-29671315 MS.gene53631:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.1:29671160-29671179 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.1:29670736-29670755 None:intergenic 35.0%
TATGAGATGGCATACTCAAA+AGG + chr1.1:29671060-29671079 MS.gene53631:CDS 35.0%
TCATCTTCGAAATCATCACT+TGG - chr1.1:29671580-29671599 None:intergenic 35.0%
TTGCCACAACGAAAAAAACT+TGG + chr1.1:29671393-29671412 MS.gene53631:CDS 35.0%
! GGATGATAGTGAAAAGATGA+AGG + chr1.1:29671342-29671361 MS.gene53631:CDS 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.1:29670721-29670740 None:intergenic 35.0%
!! TTGGTCTTATACGATATTGG+CGG - chr1.1:29671187-29671206 None:intergenic 35.0%
AATTAGGGTCAAGAGTTGTC+AGG + chr1.1:29671533-29671552 MS.gene53631:CDS 40.0%
ACTCAAAAGGGTTCGAAGAA+GGG + chr1.1:29671073-29671092 MS.gene53631:CDS 40.0%
ACTTTGTTCCAAGGAAGATG+GGG - chr1.1:29671122-29671141 None:intergenic 40.0%
ATGTCTTATGGGGGTTATGA+GGG + chr1.1:29671283-29671302 MS.gene53631:CDS 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.1:29670767-29670786 None:intergenic 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.1:29670895-29670914 None:intergenic 40.0%
CTCAAGATGACTTTGTTCCA+AGG - chr1.1:29671131-29671150 None:intergenic 40.0%
GACTTTGTTCCAAGGAAGAT+GGG - chr1.1:29671123-29671142 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.1:29671318-29671337 MS.gene53631:CDS 40.0%
GGATCTAGCTGTGATATTGA+AGG + chr1.1:29671481-29671500 MS.gene53631:CDS 40.0%
TACTCAAAAGGGTTCGAAGA+AGG + chr1.1:29671072-29671091 MS.gene53631:CDS 40.0%
TATGTCTTATGGGGGTTATG+AGG + chr1.1:29671282-29671301 MS.gene53631:CDS 40.0%
TCAAACATCGCAAGATTGCA+AGG + chr1.1:29671450-29671469 MS.gene53631:CDS 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.1:29670683-29670702 None:intergenic 40.0%
TGACTTTGTTCCAAGGAAGA+TGG - chr1.1:29671124-29671143 None:intergenic 40.0%
TGTCACAAAACATTCACCTC+TGG + chr1.1:29670794-29670813 MS.gene53631:CDS 40.0%
TTCACCTCTGGTAAATCACT+TGG + chr1.1:29670806-29670825 MS.gene53631:CDS 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.1:29671228-29671247 MS.gene53631:CDS 40.0%
! TCATCCAACAGTGCTTTGAA+TGG + chr1.1:29671034-29671053 MS.gene53631:CDS 40.0%
!! ACGAAAAAAACTTGGTGCTG+AGG + chr1.1:29671401-29671420 MS.gene53631:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.1:29670855-29670874 None:intergenic 40.0%
!! ATGTCCATTCAAAGCACTGT+TGG - chr1.1:29671041-29671060 None:intergenic 40.0%
!!! GCACCAAGTTTTTTTCGTTG+TGG - chr1.1:29671399-29671418 None:intergenic 40.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.1:29670813-29670832 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.1:29670809-29670828 MS.gene53631:CDS 45.0%
ACTATCATCCACCGTATTGC+TGG - chr1.1:29671332-29671351 None:intergenic 45.0%
ATATCACAGCTAGATCCTGC+AGG - chr1.1:29671478-29671497 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.1:29671321-29671340 MS.gene53631:CDS 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.1:29670896-29670915 MS.gene53631:CDS 45.0%
TCTTATACGATATTGGCGGC+AGG - chr1.1:29671183-29671202 None:intergenic 45.0%
! AACAAGGTGTGCTGCTAACA+AGG + chr1.1:29671365-29671384 MS.gene53631:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.1:29670850-29670869 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.1:29671206-29671225 MS.gene53631:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.1:29671200-29671219 MS.gene53631:CDS 50.0%
AGTGTTAGAGGAGCGGTGAA+TGG - chr1.1:29670843-29670862 None:intergenic 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.1:29671221-29671240 None:intergenic 50.0%
CAAGATTGCAAGGAACCTGC+AGG + chr1.1:29671460-29671479 MS.gene53631:CDS 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.1:29671220-29671239 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.1:29671206-29671225 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.1:29671115-29671134 None:intergenic 55.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.1:29671108-29671127 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.1:29671111-29671130 MS.gene53631:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 29670659 29671609 29670659 ID=MS.gene53631
chr1.1 mRNA 29670659 29671609 29670659 ID=MS.gene53631.t1;Parent=MS.gene53631
chr1.1 exon 29670659 29671609 29670659 ID=MS.gene53631.t1.exon1;Parent=MS.gene53631.t1
chr1.1 CDS 29670659 29671609 29670659 ID=cds.MS.gene53631.t1;Parent=MS.gene53631.t1
Gene Sequence

>MS.gene53631

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAACATAATCATGATGATGGGAAACTGAAGAACCATACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAGTGCTTTGAATGGACATATGAGATGGCATACTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTTGGAACAAAGTCATCTTGAGTTTCTACCATCTACTGACTTGTCAAAGTACCTGCCGCCAATATCGTATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATCGCTGCAAAAACATTGTTATATATGTCTTATGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAGTGAAAAGATGAAGGAACAAGGTGTGCTGCTAACAAGGTGTGTTTGCCACAACGAAAAAAACTTGGTGCTGAGGTTGAAGATTCCTAAAGACAAGATTTTTCAAACATCGCAAGATTGCAAGGAACCTGCAGGATCTAGCTGTGATATTGAAGGCAAGAAGAATATTAACGAAGAGGAAACTGAATTAGGGTCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTCGAAGATGAAACCAGTTAG
Protein sequence

>MS.gene53631.t1

MNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKLKNHTCDVCNKVFSSNSALNGHMRWHTQKGSKKGVIIHSPTAPSSLEQSHLEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDSEKMKEQGVLLTRCVCHNEKNLVLRLKIPKDKIFQTSQDCKEPAGSSCDIEGKKNINEEETELGSRVVRNFDLNELPSDDFEDETS