AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53633

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53633.t1 MTR_1g046810 86.667 315 42 0 1 315 1 315 0.0 535
MS.gene53633.t1 MTR_1g052185 37.994 329 116 13 5 310 12 275 1.65e-40 143
MS.gene53633.t1 MTR_1g053530 38.053 226 93 7 63 281 39 224 6.35e-30 114
MS.gene53633.t1 MTR_1g085590 37.037 270 82 10 71 315 16 222 3.41e-29 113
MS.gene53633.t1 MTR_1g063150 37.788 217 53 7 94 310 36 170 2.18e-28 108
MS.gene53633.t1 MTR_1g063140 41.818 165 42 8 147 310 1 112 5.82e-20 85.9
MS.gene53633.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:+29679441 MS.gene53633:CDS
AACGAAGAGGAAACTGAATT+AGG 0.275756 1.1:+29679687 MS.gene53633:CDS
CATTGTTATATATGTCTTAT+GGG 0.313934 1.1:+29679442 MS.gene53633:CDS
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.1:-29679022 None:intergenic
ACTATCATCCACCGTATTGC+TGG 0.349548 1.1:-29679499 None:intergenic
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.1:-29679388 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.1:+29679466 MS.gene53633:CDS
ACGAAGAGGAAACTGAATTA+GGG 0.408588 1.1:+29679688 MS.gene53633:CDS
CACAAACATAATCATGATGA+TGG 0.427443 1.1:+29679138 MS.gene53633:CDS
AACAGAAAAGAAACACTAAC+TGG 0.431171 1.1:-29679772 None:intergenic
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1.1:-29679010 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.1:+29679281 MS.gene53633:CDS
TGTTACAAACATCACATGTA+TGG 0.446958 1.1:-29679173 None:intergenic
TGACTTTGTTCCAAGGAAGA+TGG 0.453168 1.1:-29679291 None:intergenic
GACTTTGTTCCAAGGAAGAT+GGG 0.458996 1.1:-29679290 None:intergenic
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.1:-29679327 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.1:-29678933 None:intergenic
TCATCCAACAGTGCTTTGAA+TGG 0.470969 1.1:+29679204 MS.gene53633:CDS
TATGAGATGGCATACTCAAA+AGG 0.486406 1.1:+29679230 MS.gene53633:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.1:-29678934 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1.1:+29678964 MS.gene53633:CDS
TACTCAAAAGGGTTCGAAGA+AGG 0.504806 1.1:+29679242 MS.gene53633:CDS
AATTAGGGTCAAGAGTTGTC+AGG 0.507473 1.1:+29679703 MS.gene53633:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.1:-29679062 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.1:-29678903 None:intergenic
CATGATCATGCTGTGAATAA+CGG 0.518528 1.1:+29679063 MS.gene53633:CDS
AACAAGGTGTGCTGCTAACA+AGG 0.519240 1.1:+29679535 MS.gene53633:CDS
ATGAGATGGCATACTCAAAA+GGG 0.526510 1.1:+29679231 MS.gene53633:CDS
GGATCTAGCTGTGATATTGA+AGG 0.530396 1.1:+29679651 MS.gene53633:CDS
ATTGTTATATATGTCTTATG+GGG 0.542437 1.1:+29679443 MS.gene53633:CDS
TCAAACATCGCAAGATTGCA+AGG 0.542865 1.1:+29679620 MS.gene53633:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.1:+29679488 MS.gene53633:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.1:-29678850 None:intergenic
ACTCAAAAGGGTTCGAAGAA+GGG 0.553906 1.1:+29679243 MS.gene53633:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1.1:+29678979 MS.gene53633:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.1:-29679017 None:intergenic
CAAGATTGCAAGGAACCTGC+AGG 0.562783 1.1:+29679630 MS.gene53633:CDS
TTGGTCTTATACGATATTGG+CGG 0.563784 1.1:-29679354 None:intergenic
CTCAAGATGACTTTGTTCCA+AGG 0.567999 1.1:-29679298 None:intergenic
ACAAACATAATCATGATGAT+GGG 0.568114 1.1:+29679139 MS.gene53633:CDS
ATGTCCATTCAAAGCACTGT+TGG 0.568123 1.1:-29679208 None:intergenic
GGATGATAGTGAAAAGATGA+AGG 0.573473 1.1:+29679512 MS.gene53633:CDS
TTCACCTCTGGTAAATCACT+TGG 0.575760 1.1:+29678976 MS.gene53633:CDS
ATATCACAGCTAGATCCTGC+AGG 0.585006 1.1:-29679645 None:intergenic
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.1:-29679275 None:intergenic
TCTTATACGATATTGGCGGC+AGG 0.588195 1.1:-29679350 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.1:-29679387 None:intergenic
TTGTTATATATGTCTTATGG+GGG 0.593530 1.1:+29679444 MS.gene53633:CDS
TCATCTTCGAAATCATCACT+TGG 0.604104 1.1:-29679747 None:intergenic
CAAGAAGAATATTAACGAAG+AGG 0.604934 1.1:+29679674 MS.gene53633:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.1:-29679282 None:intergenic
TACATGTGATGTTTGTAACA+AGG 0.614171 1.1:+29679176 MS.gene53633:CDS
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.1:-29678888 None:intergenic
AGTGAAAAGATGAAGGAACA+AGG 0.617064 1.1:+29679519 MS.gene53633:CDS
GCGTATTGCTGATAATGATG+AGG 0.644357 1.1:+29679398 MS.gene53633:CDS
ACTTTGTTCCAAGGAAGATG+GGG 0.645998 1.1:-29679289 None:intergenic
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.1:+29679491 MS.gene53633:CDS
CTTTGAATGGACATATGAGA+TGG 0.684064 1.1:+29679217 MS.gene53633:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.1:-29678980 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.1:+29679066 MS.gene53633:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+TGG + chr1.1:29679441-29679460 MS.gene53633:CDS 20.0%
!! ATTGTTATATATGTCTTATG+GGG + chr1.1:29679443-29679462 MS.gene53633:CDS 20.0%
!! CATTGTTATATATGTCTTAT+GGG + chr1.1:29679442-29679461 MS.gene53633:CDS 20.0%
! ACAAACATAATCATGATGAT+GGG + chr1.1:29679139-29679158 MS.gene53633:CDS 25.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.1:29679097-29679116 MS.gene53633:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.1:29679098-29679117 MS.gene53633:CDS 25.0%
! GTTTGAAAAATCTTGTCTTT+AGG - chr1.1:29679606-29679625 None:intergenic 25.0%
! TATCGTATAAGACCAAAAAA+CGG + chr1.1:29679361-29679380 MS.gene53633:CDS 25.0%
! TTGTTATATATGTCTTATGG+GGG + chr1.1:29679444-29679463 MS.gene53633:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.1:29679094-29679113 None:intergenic 25.0%
!!! TTTTTGGTCTTATACGATAT+TGG - chr1.1:29679360-29679379 None:intergenic 25.0%
CAAGAAGAATATTAACGAAG+AGG + chr1.1:29679674-29679693 MS.gene53633:CDS 30.0%
CACAAACATAATCATGATGA+TGG + chr1.1:29679138-29679157 MS.gene53633:CDS 30.0%
TACATGTGATGTTTGTAACA+AGG + chr1.1:29679176-29679195 MS.gene53633:CDS 30.0%
TGTTACAAACATCACATGTA+TGG - chr1.1:29679176-29679195 None:intergenic 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.1:29678881-29678900 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.1:29679045-29679064 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.1:29678880-29678899 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.1:29678864-29678883 None:intergenic 30.0%
AACGAAGAGGAAACTGAATT+AGG + chr1.1:29679687-29679706 MS.gene53633:CDS 35.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.1:29678936-29678955 None:intergenic 35.0%
ACGAAGAGGAAACTGAATTA+GGG + chr1.1:29679688-29679707 MS.gene53633:CDS 35.0%
AGTGAAAAGATGAAGGAACA+AGG + chr1.1:29679519-29679538 MS.gene53633:CDS 35.0%
ATGAGATGGCATACTCAAAA+GGG + chr1.1:29679231-29679250 MS.gene53633:CDS 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.1:29679063-29679082 MS.gene53633:CDS 35.0%
CTTTGAATGGACATATGAGA+TGG + chr1.1:29679217-29679236 MS.gene53633:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.1:29678916-29678935 MS.gene53633:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.1:29679466-29679485 MS.gene53633:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.1:29679330-29679349 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.1:29678906-29678925 None:intergenic 35.0%
TATGAGATGGCATACTCAAA+AGG + chr1.1:29679230-29679249 MS.gene53633:CDS 35.0%
TCATCTTCGAAATCATCACT+TGG - chr1.1:29679750-29679769 None:intergenic 35.0%
TTGCCACAACGAAAAAAACT+TGG + chr1.1:29679563-29679582 MS.gene53633:CDS 35.0%
! GGATGATAGTGAAAAGATGA+AGG + chr1.1:29679512-29679531 MS.gene53633:CDS 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.1:29678891-29678910 None:intergenic 35.0%
!! TTGGTCTTATACGATATTGG+CGG - chr1.1:29679357-29679376 None:intergenic 35.0%
AATTAGGGTCAAGAGTTGTC+AGG + chr1.1:29679703-29679722 MS.gene53633:CDS 40.0%
ACTCAAAAGGGTTCGAAGAA+GGG + chr1.1:29679243-29679262 MS.gene53633:CDS 40.0%
ACTTTGTTCCAAGGAAGATG+GGG - chr1.1:29679292-29679311 None:intergenic 40.0%
ATGTCTTATGGGGGTTATGA+GGG + chr1.1:29679453-29679472 MS.gene53633:CDS 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.1:29678937-29678956 None:intergenic 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.1:29679065-29679084 None:intergenic 40.0%
CTCAAGATGACTTTGTTCCA+AGG - chr1.1:29679301-29679320 None:intergenic 40.0%
GACTTTGTTCCAAGGAAGAT+GGG - chr1.1:29679293-29679312 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.1:29679488-29679507 MS.gene53633:CDS 40.0%
GGATCTAGCTGTGATATTGA+AGG + chr1.1:29679651-29679670 MS.gene53633:CDS 40.0%
TACTCAAAAGGGTTCGAAGA+AGG + chr1.1:29679242-29679261 MS.gene53633:CDS 40.0%
TATGTCTTATGGGGGTTATG+AGG + chr1.1:29679452-29679471 MS.gene53633:CDS 40.0%
TCAAACATCGCAAGATTGCA+AGG + chr1.1:29679620-29679639 MS.gene53633:CDS 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.1:29678853-29678872 None:intergenic 40.0%
TGACTTTGTTCCAAGGAAGA+TGG - chr1.1:29679294-29679313 None:intergenic 40.0%
TGTCACAAAACATTCACCTC+TGG + chr1.1:29678964-29678983 MS.gene53633:CDS 40.0%
TTCACCTCTGGTAAATCACT+TGG + chr1.1:29678976-29678995 MS.gene53633:CDS 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.1:29679398-29679417 MS.gene53633:CDS 40.0%
! TCATCCAACAGTGCTTTGAA+TGG + chr1.1:29679204-29679223 MS.gene53633:CDS 40.0%
!! ACGAAAAAAACTTGGTGCTG+AGG + chr1.1:29679571-29679590 MS.gene53633:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.1:29679025-29679044 None:intergenic 40.0%
!! ATGTCCATTCAAAGCACTGT+TGG - chr1.1:29679211-29679230 None:intergenic 40.0%
!!! GCACCAAGTTTTTTTCGTTG+TGG - chr1.1:29679569-29679588 None:intergenic 40.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.1:29678983-29679002 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.1:29678979-29678998 MS.gene53633:CDS 45.0%
ACTATCATCCACCGTATTGC+TGG - chr1.1:29679502-29679521 None:intergenic 45.0%
ATATCACAGCTAGATCCTGC+AGG - chr1.1:29679648-29679667 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.1:29679491-29679510 MS.gene53633:CDS 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.1:29679066-29679085 MS.gene53633:CDS 45.0%
TCTTATACGATATTGGCGGC+AGG - chr1.1:29679353-29679372 None:intergenic 45.0%
! AACAAGGTGTGCTGCTAACA+AGG + chr1.1:29679535-29679554 MS.gene53633:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.1:29679020-29679039 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.1:29679376-29679395 MS.gene53633:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.1:29679370-29679389 MS.gene53633:CDS 50.0%
AGTGTTAGAGGAGCGGTGAA+TGG - chr1.1:29679013-29679032 None:intergenic 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.1:29679391-29679410 None:intergenic 50.0%
CAAGATTGCAAGGAACCTGC+AGG + chr1.1:29679630-29679649 MS.gene53633:CDS 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.1:29679390-29679409 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.1:29679376-29679395 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.1:29679285-29679304 None:intergenic 55.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.1:29679278-29679297 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.1:29679281-29679300 MS.gene53633:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 29678829 29679779 29678829 ID=MS.gene53633
chr1.1 mRNA 29678829 29679779 29678829 ID=MS.gene53633.t1;Parent=MS.gene53633
chr1.1 exon 29678829 29679779 29678829 ID=MS.gene53633.t1.exon1;Parent=MS.gene53633.t1
chr1.1 CDS 29678829 29679779 29678829 ID=cds.MS.gene53633.t1;Parent=MS.gene53633.t1
Gene Sequence

>MS.gene53633

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAACATAATCATGATGATGGGAAACTGAAGAACCATACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAGTGCTTTGAATGGACATATGAGATGGCATACTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTTGGAACAAAGTCATCTTGAGTTTCTACCATCTACTGACTTGTCAAAGTACCTGCCGCCAATATCGTATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATCGCTGCAAAAACATTGTTATATATGTCTTATGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAGTGAAAAGATGAAGGAACAAGGTGTGCTGCTAACAAGGTGTGTTTGCCACAACGAAAAAAACTTGGTGCTGAGGTTGAAGATTCCTAAAGACAAGATTTTTCAAACATCGCAAGATTGCAAGGAACCTGCAGGATCTAGCTGTGATATTGAAGGCAAGAAGAATATTAACGAAGAGGAAACTGAATTAGGGTCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTCGAAGATGAAACCAGTTAG
Protein sequence

>MS.gene53633.t1

MNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKLKNHTCDVCNKVFSSNSALNGHMRWHTQKGSKKGVIIHSPTAPSSLEQSHLEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDSEKMKEQGVLLTRCVCHNEKNLVLRLKIPKDKIFQTSQDCKEPAGSSCDIEGKKNINEEETELGSRVVRNFDLNELPSDDFEDETS