AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene061755

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061755.t1 MTR_1g046810 86.667 315 42 0 1 315 1 315 0.0 535
MS.gene061755.t1 MTR_1g052185 37.994 329 116 13 5 310 12 275 1.10e-40 143
MS.gene061755.t1 MTR_1g053530 37.611 226 94 7 63 281 39 224 3.03e-29 112
MS.gene061755.t1 MTR_1g085590 36.667 270 83 10 71 315 16 222 1.01e-28 112
MS.gene061755.t1 MTR_1g063150 36.866 217 55 7 94 310 36 170 3.83e-27 105
MS.gene061755.t1 MTR_1g063140 40.964 166 44 8 147 311 1 113 1.97e-18 82.0
MS.gene061755.t1 MTR_5g098470 30.144 209 84 9 14 210 46 204 7.69e-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 58 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATTGTTATATATGTCTTA+TGG 0.192869 1.2:+29632808 MS.gene061755:CDS
AGCGAAGATGAAACTGAATT+AGG 0.276698 1.2:+29633054 MS.gene061755:CDS
CATTGTTATATATGTCTTAT+GGG 0.313934 1.2:+29632809 MS.gene061755:CDS
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.2:-29632389 None:intergenic
CTTTGAATGGACATATTAGA+TGG 0.355165 1.2:+29632584 MS.gene061755:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1.2:-29632866 None:intergenic
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.2:-29632755 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.2:+29632833 MS.gene061755:CDS
GCGAAGATGAAACTGAATTA+GGG 0.408376 1.2:+29633055 MS.gene061755:CDS
GACTTTGTTCCAAGGAAGAT+GGG 0.419216 1.2:-29632657 None:intergenic
CACAAGCATAATCATGATGA+TGG 0.420773 1.2:+29632505 MS.gene061755:CDS
TCATCCAACAATGCTTTGAA+TGG 0.423695 1.2:+29632571 MS.gene061755:CDS
AACAGAAAAGAAACACTAAC+TGG 0.431171 1.2:-29633139 None:intergenic
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1.2:-29632377 None:intergenic
TGACTTTGTTCCAAGGAAGA+TGG 0.439982 1.2:-29632658 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.2:+29632648 MS.gene061755:CDS
TATTAGATGGCATACTCAAA+AGG 0.453871 1.2:+29632597 MS.gene061755:CDS
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.2:-29632694 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.2:-29632300 None:intergenic
ATGTCCATTCAAAGCATTGT+TGG 0.483556 1.2:-29632575 None:intergenic
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.2:-29632301 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1.2:+29632331 MS.gene061755:CDS
TACTCAAAAGGGTTCGAAGA+AGG 0.504806 1.2:+29632609 MS.gene061755:CDS
AATTAGGGTCAAGAGTTGTC+AGG 0.507473 1.2:+29633070 MS.gene061755:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.2:-29632429 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.2:-29632270 None:intergenic
CATGATCATGCTGTGAATAA+CGG 0.518528 1.2:+29632430 MS.gene061755:CDS
AACAAGGTGTGCTGCTAACA+AGG 0.519240 1.2:+29632902 MS.gene061755:CDS
ATTAGATGGCATACTCAAAA+GGG 0.526510 1.2:+29632598 MS.gene061755:CDS
GGATCTAGCTGTGATATTGA+AGG 0.530396 1.2:+29633018 MS.gene061755:CDS
CACATGTGATGTTTGTAACA+AGG 0.533818 1.2:+29632543 MS.gene061755:CDS
CTCAAGTTGACTTTGTTCCA+AGG 0.540256 1.2:-29632665 None:intergenic
ATTGTTATATATGTCTTATG+GGG 0.542437 1.2:+29632810 MS.gene061755:CDS
TCAAACATCGCAAGATTGCA+AGG 0.542865 1.2:+29632987 MS.gene061755:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.2:+29632855 MS.gene061755:CDS
TTGGTCTTATACGATATTGG+CGG 0.553676 1.2:-29632721 None:intergenic
ACTCAAAAGGGTTCGAAGAA+GGG 0.553906 1.2:+29632610 MS.gene061755:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1.2:+29632346 MS.gene061755:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.2:-29632384 None:intergenic
CAAGATTGCAAGGAACCTGC+AGG 0.562783 1.2:+29632997 MS.gene061755:CDS
TTCACCTCTGGTAAATCACT+TGG 0.575760 1.2:+29632343 MS.gene061755:CDS
GGATGATAATGAGAAGATGA+AGG 0.579672 1.2:+29632879 MS.gene061755:CDS
ACAAGCATAATCATGATGAT+GGG 0.583581 1.2:+29632506 MS.gene061755:CDS
TCAAACGAATGGTAAGAAGA+AGG 0.583642 1.2:-29632217 None:intergenic
ATATCACAGCTAGATCCTGC+AGG 0.585006 1.2:-29633012 None:intergenic
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.2:-29632642 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.2:-29632754 None:intergenic
TTGTTATATATGTCTTATGG+GGG 0.593530 1.2:+29632811 MS.gene061755:CDS
TCATCTTCGAAATCATCACT+TGG 0.604104 1.2:-29633114 None:intergenic
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.2:+29632886 MS.gene061755:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.2:-29632649 None:intergenic
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.2:-29632255 None:intergenic
ACTTTGTTCCAAGGAAGATG+GGG 0.644016 1.2:-29632656 None:intergenic
GCGTATTGCTGATAATGATG+AGG 0.644357 1.2:+29632765 MS.gene061755:CDS
TGTTACAAACATCACATGTG+TGG 0.651192 1.2:-29632540 None:intergenic
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.2:+29632858 MS.gene061755:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.2:-29632347 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.2:+29632433 MS.gene061755:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+TGG + chr1.2:29632808-29632827 MS.gene061755:CDS 20.0%
!! ATTGTTATATATGTCTTATG+GGG + chr1.2:29632810-29632829 MS.gene061755:CDS 20.0%
!! CATTGTTATATATGTCTTAT+GGG + chr1.2:29632809-29632828 MS.gene061755:CDS 20.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.2:29632464-29632483 MS.gene061755:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.2:29632465-29632484 MS.gene061755:CDS 25.0%
! GTTTGAAAAATCTTGTCTTT+AGG - chr1.2:29632973-29632992 None:intergenic 25.0%
! TATCGTATAAGACCAAAAAA+CGG + chr1.2:29632728-29632747 MS.gene061755:CDS 25.0%
! TTGTTATATATGTCTTATGG+GGG + chr1.2:29632811-29632830 MS.gene061755:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.2:29632461-29632480 None:intergenic 25.0%
!!! TTTTTGGTCTTATACGATAT+TGG - chr1.2:29632727-29632746 None:intergenic 25.0%
ACAAGCATAATCATGATGAT+GGG + chr1.2:29632506-29632525 MS.gene061755:CDS 30.0%
ATTAGATGGCATACTCAAAA+GGG + chr1.2:29632598-29632617 MS.gene061755:CDS 30.0%
CTTTGAATGGACATATTAGA+TGG + chr1.2:29632584-29632603 MS.gene061755:CDS 30.0%
TATTAGATGGCATACTCAAA+AGG + chr1.2:29632597-29632616 MS.gene061755:CDS 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.2:29632248-29632267 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.2:29632412-29632431 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.2:29632247-29632266 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.2:29632231-29632250 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.2:29632303-29632322 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.2:29632886-29632905 MS.gene061755:CDS 35.0%
AGCGAAGATGAAACTGAATT+AGG + chr1.2:29633054-29633073 MS.gene061755:CDS 35.0%
CACAAGCATAATCATGATGA+TGG + chr1.2:29632505-29632524 MS.gene061755:CDS 35.0%
CACATGTGATGTTTGTAACA+AGG + chr1.2:29632543-29632562 MS.gene061755:CDS 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.2:29632430-29632449 MS.gene061755:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.2:29632283-29632302 MS.gene061755:CDS 35.0%
GCGAAGATGAAACTGAATTA+GGG + chr1.2:29633055-29633074 MS.gene061755:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.2:29632833-29632852 MS.gene061755:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.2:29632697-29632716 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.2:29632273-29632292 None:intergenic 35.0%
TCAAACGAATGGTAAGAAGA+AGG - chr1.2:29632220-29632239 None:intergenic 35.0%
TCATCTTCGAAATCATCACT+TGG - chr1.2:29633117-29633136 None:intergenic 35.0%
TGTTACAAACATCACATGTG+TGG - chr1.2:29632543-29632562 None:intergenic 35.0%
TTGCCACAACGAAAAAAACT+TGG + chr1.2:29632930-29632949 MS.gene061755:CDS 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.2:29632879-29632898 MS.gene061755:CDS 35.0%
! TCATCCAACAATGCTTTGAA+TGG + chr1.2:29632571-29632590 MS.gene061755:CDS 35.0%
!! ATGTCCATTCAAAGCATTGT+TGG - chr1.2:29632578-29632597 None:intergenic 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.2:29632258-29632277 None:intergenic 35.0%
!! TTGGTCTTATACGATATTGG+CGG - chr1.2:29632724-29632743 None:intergenic 35.0%
AATTAGGGTCAAGAGTTGTC+AGG + chr1.2:29633070-29633089 MS.gene061755:CDS 40.0%
ACTCAAAAGGGTTCGAAGAA+GGG + chr1.2:29632610-29632629 MS.gene061755:CDS 40.0%
ACTTTGTTCCAAGGAAGATG+GGG - chr1.2:29632659-29632678 None:intergenic 40.0%
ATGTCTTATGGGGGTTATGA+GGG + chr1.2:29632820-29632839 MS.gene061755:CDS 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.2:29632869-29632888 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.2:29632304-29632323 None:intergenic 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.2:29632432-29632451 None:intergenic 40.0%
GACTTTGTTCCAAGGAAGAT+GGG - chr1.2:29632660-29632679 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.2:29632855-29632874 MS.gene061755:CDS 40.0%
GGATCTAGCTGTGATATTGA+AGG + chr1.2:29633018-29633037 MS.gene061755:CDS 40.0%
TACTCAAAAGGGTTCGAAGA+AGG + chr1.2:29632609-29632628 MS.gene061755:CDS 40.0%
TATGTCTTATGGGGGTTATG+AGG + chr1.2:29632819-29632838 MS.gene061755:CDS 40.0%
TCAAACATCGCAAGATTGCA+AGG + chr1.2:29632987-29633006 MS.gene061755:CDS 40.0%
TGACTTTGTTCCAAGGAAGA+TGG - chr1.2:29632661-29632680 None:intergenic 40.0%
TGTCACAAAACATTCACCTC+TGG + chr1.2:29632331-29632350 MS.gene061755:CDS 40.0%
TTCACCTCTGGTAAATCACT+TGG + chr1.2:29632343-29632362 MS.gene061755:CDS 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.2:29632765-29632784 MS.gene061755:CDS 40.0%
!! ACGAAAAAAACTTGGTGCTG+AGG + chr1.2:29632938-29632957 MS.gene061755:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.2:29632392-29632411 None:intergenic 40.0%
!! CTCAAGTTGACTTTGTTCCA+AGG - chr1.2:29632668-29632687 None:intergenic 40.0%
!!! GCACCAAGTTTTTTTCGTTG+TGG - chr1.2:29632936-29632955 None:intergenic 40.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.2:29632350-29632369 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.2:29632346-29632365 MS.gene061755:CDS 45.0%
ATATCACAGCTAGATCCTGC+AGG - chr1.2:29633015-29633034 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.2:29632858-29632877 MS.gene061755:CDS 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.2:29632433-29632452 MS.gene061755:CDS 45.0%
! AACAAGGTGTGCTGCTAACA+AGG + chr1.2:29632902-29632921 MS.gene061755:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.2:29632387-29632406 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.2:29632743-29632762 MS.gene061755:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.2:29632737-29632756 MS.gene061755:CDS 50.0%
AGTGTTAGAGGAGCGGTGAA+TGG - chr1.2:29632380-29632399 None:intergenic 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.2:29632758-29632777 None:intergenic 50.0%
CAAGATTGCAAGGAACCTGC+AGG + chr1.2:29632997-29633016 MS.gene061755:CDS 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.2:29632757-29632776 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.2:29632743-29632762 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.2:29632652-29632671 None:intergenic 55.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.2:29632645-29632664 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.2:29632648-29632667 MS.gene061755:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 29632196 29633146 29632196 ID=MS.gene061755
chr1.2 mRNA 29632196 29633146 29632196 ID=MS.gene061755.t1;Parent=MS.gene061755
chr1.2 exon 29632196 29633146 29632196 ID=MS.gene061755.t1.exon1;Parent=MS.gene061755.t1
chr1.2 CDS 29632196 29633146 29632196 ID=cds.MS.gene061755.t1;Parent=MS.gene061755.t1
Gene Sequence

>MS.gene061755

ATGAACAAACACTATTCTTCACCTTCTTCTTACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAGCATAATCATGATGATGGGAAACTGAAGAACCACACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAATGCTTTGAATGGACATATTAGATGGCATACTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTTGGAACAAAGTCAACTTGAGTTTCTACCATCTACTGACTTGTCAAAGTACTTGCCGCCAATATCGTATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATTGCTGCAAAAACATTGTTATATATGTCTTATGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGCTGCTAACAAGGTGTGTTTGCCACAACGAAAAAAACTTGGTGCTGAGGTTGAAGATTCCTAAAGACAAGATTTTTCAAACATCGCAAGATTGCAAGGAACCTGCAGGATCTAGCTGTGATATTGAAGGCAAGAAGAATATTAGCGAAGATGAAACTGAATTAGGGTCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTCGAAGATGAAACCAGTTAG
Protein sequence

>MS.gene061755.t1

MNKHYSSPSSYHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKLKNHTCDVCNKVFSSNNALNGHIRWHTQKGSKKGVIIHSPTAPSSLEQSQLEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVLLTRCVCHNEKNLVLRLKIPKDKIFQTSQDCKEPAGSSCDIEGKKNISEDETELGSRVVRNFDLNELPSDDFEDETS