AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380017552.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017552.01.T01 MTR_3g108910 88.670 203 8 2 15 202 25 227 8.30e-94 274
MsG0380017552.01.T01 MTR_1g009640 52.551 196 53 7 33 200 43 226 1.37e-42 144
MsG0380017552.01.T01 MTR_1g045430 50.360 139 37 7 19 132 27 158 5.21e-24 94.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017552.01.T01 AT5G24890 48.062 129 45 5 15 122 46 173 7.07e-24 95.5
MsG0380017552.01.T01 AT4G31510 51.282 78 32 2 57 128 84 161 6.90e-16 73.6

Find 40 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATCAGCTTTCTATTCT+TGG 0.154622 3:-97797437 MsG0380017552.01.T01:CDS
CGACGGTCGCCACCTCTTCT+TGG 0.269356 3:-97797881 MsG0380017552.01.T01:CDS
TTCATCTTCCTCTAATTCAT+TGG 0.337534 3:-97797295 MsG0380017552.01.T01:CDS
TTGAACTTGAAAGGAAGAAA+TGG 0.345129 3:-97797758 MsG0380017552.01.T01:CDS
ATCCTCAGCCAATGAATTAG+AGG 0.354555 3:+97797287 None:intergenic
GACGGTCGCCACCTCTTCTT+GGG 0.391909 3:-97797880 MsG0380017552.01.T01:CDS
TTCCCTGCATATCTTGTTGT+GGG 0.400814 3:-97796945 MsG0380017552.01.T01:three_prime_UTR
CAAGAAGATCAGGTTCAAAT+TGG 0.407480 3:-97797258 MsG0380017552.01.T01:CDS
TGAACTTGAAAGGAAGAAAT+GGG 0.420141 3:-97797757 MsG0380017552.01.T01:intron
CACCGGCGGTTCATCGGAGC+CGG 0.426424 3:-97797843 MsG0380017552.01.T01:CDS
GACTTAGAAGCTTCAAGTCT+AGG 0.431880 3:-97797191 MsG0380017552.01.T01:CDS
TTATGAAGCTTTCATTACTT+TGG 0.443204 3:+97796918 None:intergenic
TCCTCGTTTACCGGCAAAAG+TGG 0.447534 3:+97797396 None:intergenic
TCATCGTTGTCACTGTCATC+AGG 0.463348 3:+97797797 None:intergenic
TCATCACGATCCTCGTTTAC+CGG 0.467994 3:+97797387 None:intergenic
ATTCCCTGCATATCTTGTTG+TGG 0.468779 3:-97796946 MsG0380017552.01.T01:three_prime_UTR
GGATAAGAAACAAGAAGATC+AGG 0.489836 3:-97797268 MsG0380017552.01.T01:CDS
CAGAGCAAGTTGAACTTGAA+AGG 0.490968 3:-97797767 MsG0380017552.01.T01:CDS
TGATTATGAAGATGAGGAAA+AGG 0.495795 3:-97797346 MsG0380017552.01.T01:CDS
TTCCTCTAATTCATTGGCTG+AGG 0.507116 3:-97797289 MsG0380017552.01.T01:CDS
CTCCGGCTCCGATGAACCGC+CGG 0.513710 3:+97797841 None:intergenic
GGCAAAAGTGGCATGGATTG+AGG 0.515046 3:+97797408 None:intergenic
AAGTCTCATTTCAGCAGCAT+AGG 0.520069 3:+97797215 None:intergenic
AGACCCACAACAAGATATGC+AGG 0.526730 3:+97796942 None:intergenic
GTTTACCGGCAAAAGTGGCA+TGG 0.586334 3:+97797401 None:intergenic
CAAGAAGAGGTGGCGACCGT+CGG 0.588379 3:+97797882 None:intergenic
CATGTTCTTGTAGATCTGCA+AGG 0.589439 3:+97797160 None:intergenic
GATCAGGTTCAAATTGGTCA+TGG 0.603769 3:-97797252 MsG0380017552.01.T01:CDS
ATGTTCTTGTAGATCTGCAA+GGG 0.608354 3:+97797161 None:intergenic
TTATTATGATTATGAAGATG+AGG 0.612831 3:-97797352 MsG0380017552.01.T01:CDS
CCACCTTCCAACCAGTCCGA+CGG 0.613709 3:-97797898 MsG0380017552.01.T01:intron
GATCGTGATGATCATGATGA+TGG 0.616588 3:-97797375 MsG0380017552.01.T01:CDS
AACTTGGTGGTCCCAAGAAG+AGG 0.619590 3:+97797869 None:intergenic
CCGGAGAGTTCATCGTCGAT+CGG 0.621696 3:-97797824 MsG0380017552.01.T01:CDS
CCGATCGACGATGAACTCTC+CGG 0.621857 3:+97797824 None:intergenic
TCTACAAGAACATGATGATG+AGG 0.622792 3:-97797151 MsG0380017552.01.T01:CDS
TTGGTGGTCCCAAGAAGAGG+TGG 0.647016 3:+97797872 None:intergenic
GATGAAGATGATGAACCAGA+TGG 0.654167 3:+97797312 None:intergenic
GACCCACAACAAGATATGCA+GGG 0.684854 3:+97796943 None:intergenic
TGATGACAGTGACAACGATG+AGG 0.687790 3:-97797795 MsG0380017552.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTAAATAAAATATATA+AGG + Chr3:97797080-97797099 None:intergenic 0.0%
!! AAAAAATAATAAGAGAAATG+AGG + Chr3:97797046-97797065 None:intergenic 15.0%
!!! GTATCTTTCTTTTTATTTTT+TGG - Chr3:97798402-97798421 MsG0380017552.01.T01:intron 15.0%
!! AAATCAAAAACACAATGAAA+AGG + Chr3:97797750-97797769 None:intergenic 20.0%
!! ATCAACATTATTAAGGTAAA+CGG - Chr3:97796938-97796957 MsG0380017552.01.T01:three_prime_UTR 20.0%
!! TTATTATGATTATGAAGATG+AGG - Chr3:97798057-97798076 MsG0380017552.01.T01:intron 20.0%
!!! ACTTTGATTTGATATTGATT+AGG - Chr3:97797810-97797829 MsG0380017552.01.T01:CDS 20.0%
!!! GAAAAAATGGAAATTTTTGT+GGG - Chr3:97797454-97797473 MsG0380017552.01.T01:CDS 20.0%
!!! TCTCATTCTTTTTTTCTTTT+TGG - Chr3:97797430-97797449 MsG0380017552.01.T01:CDS 20.0%
!!! TGAAAAAATGGAAATTTTTG+TGG - Chr3:97797453-97797472 MsG0380017552.01.T01:CDS 20.0%
!!! TTTTCTTTTTGGTGAAAAAA+TGG - Chr3:97797441-97797460 MsG0380017552.01.T01:CDS 20.0%
! AAAAATGAAATCTGCTAGTA+AGG - Chr3:97798434-97798453 MsG0380017552.01.T01:intron 25.0%
! AAATAAATGAAGTGTGTTGT+TGG + Chr3:97797131-97797150 None:intergenic 25.0%
! AGAAAAAAAGAATGAGAAGA+AGG + Chr3:97797427-97797446 None:intergenic 25.0%
! GATGATGATCAACATTATTA+AGG - Chr3:97796931-97796950 MsG0380017552.01.T01:three_prime_UTR 25.0%
! TGTTCATCTATAATCGTTAA+AGG + Chr3:97797197-97797216 None:intergenic 25.0%
! TTATGAAGCTTTCATTACTT+TGG + Chr3:97798494-97798513 None:intergenic 25.0%
!! AAAAAACATCATCGTTTTAG+TGG - Chr3:97797228-97797247 MsG0380017552.01.T01:CDS 25.0%
!! TCCTTTTAACAAAAGAAGAA+GGG - Chr3:97797925-97797944 MsG0380017552.01.T01:intron 25.0%
!! TGATTTGATATTGATTAGGA+GGG - Chr3:97797814-97797833 MsG0380017552.01.T01:CDS 25.0%
!! TGATTTTCTTGAAAATTTGG+AGG + Chr3:97797960-97797979 None:intergenic 25.0%
!! TTGATTTGATATTGATTAGG+AGG - Chr3:97797813-97797832 MsG0380017552.01.T01:CDS 25.0%
!!! AGCTGATTTTCTTGAAAATT+TGG + Chr3:97797963-97797982 None:intergenic 25.0%
AAAATAGAGAAAGAGATGAG+GGG + Chr3:97797171-97797190 None:intergenic 30.0%
ACATTATTAAGGTAAACGGA+CGG - Chr3:97796942-97796961 MsG0380017552.01.T01:three_prime_UTR 30.0%
AGAAAATAGAGAAAGAGATG+AGG + Chr3:97797173-97797192 None:intergenic 30.0%
ATAATAAGAGAAATGAGGTG+AGG + Chr3:97797041-97797060 None:intergenic 30.0%
ATCATCATCATCATCATCAT+GGG + Chr3:97796920-97796939 None:intergenic 30.0%
GAAAATAGAGAAAGAGATGA+GGG + Chr3:97797172-97797191 None:intergenic 30.0%
GAAAATCAGCTTTCTATTCT+TGG - Chr3:97797972-97797991 MsG0380017552.01.T01:intron 30.0%
GAGGGGAAAAAAAAAAAAGA+AGG + Chr3:97797154-97797173 None:intergenic 30.0%
TCAAAAACACAATGAAAAGG+AGG + Chr3:97797747-97797766 None:intergenic 30.0%
TCTTAGGTTTCCAAGTAAAA+GGG + Chr3:97797360-97797379 None:intergenic 30.0%
TGAACTTGAAAGGAAGAAAT+GGG - Chr3:97797652-97797671 MsG0380017552.01.T01:intron 30.0%
TGATTATGAAGATGAGGAAA+AGG - Chr3:97798063-97798082 MsG0380017552.01.T01:intron 30.0%
TTCATCTTCCTCTAATTCAT+TGG - Chr3:97798114-97798133 MsG0380017552.01.T01:intron 30.0%
TTGAACTTGAAAGGAAGAAA+TGG - Chr3:97797651-97797670 MsG0380017552.01.T01:intron 30.0%
! ACCCTTCTTCTTTTGTTAAA+AGG + Chr3:97797929-97797948 None:intergenic 30.0%
! GATTTGATATTGATTAGGAG+GGG - Chr3:97797815-97797834 MsG0380017552.01.T01:CDS 30.0%
! GTCCTTTTAACAAAAGAAGA+AGG - Chr3:97797924-97797943 MsG0380017552.01.T01:intron 30.0%
AGAAAGGAACAAACTTGATG+GGG + Chr3:97797710-97797729 None:intergenic 35.0%
AGAGAAAGGAACAAACTTGA+TGG + Chr3:97797712-97797731 None:intergenic 35.0%
ATGTTCTTGTAGATCTGCAA+GGG + Chr3:97798251-97798270 None:intergenic 35.0%
CAAGAAGATCAGGTTCAAAT+TGG - Chr3:97798151-97798170 MsG0380017552.01.T01:intron 35.0%
CTTAGGTTTCCAAGTAAAAG+GGG + Chr3:97797359-97797378 None:intergenic 35.0%
GAGAAAGGAACAAACTTGAT+GGG + Chr3:97797711-97797730 None:intergenic 35.0%
GATCATCATCATCATCATCA+TGG + Chr3:97796921-97796940 None:intergenic 35.0%
GGATAAGAAACAAGAAGATC+AGG - Chr3:97798141-97798160 MsG0380017552.01.T01:intron 35.0%
GTCTTAGGTTTCCAAGTAAA+AGG + Chr3:97797361-97797380 None:intergenic 35.0%
! TCTACAAGAACATGATGATG+AGG - Chr3:97798258-97798277 MsG0380017552.01.T01:intron 35.0%
! TTGAAAGGAAGAAATGGGTT+GGG - Chr3:97797657-97797676 MsG0380017552.01.T01:intron 35.0%
!! ATCGTTTTAGTGGTTGCAAA+AGG - Chr3:97797238-97797257 MsG0380017552.01.T01:CDS 35.0%
!! GGATTATCGAGTCATTTTGA+AGG - Chr3:97797836-97797855 MsG0380017552.01.T01:CDS 35.0%
AAGACAAAGCGAAGAAGAAC+AGG - Chr3:97797376-97797395 MsG0380017552.01.T01:CDS 40.0%
AAGGCTAGAAAAATGCCATC+TGG - Chr3:97798082-97798101 MsG0380017552.01.T01:intron 40.0%
AAGTCTCATTTCAGCAGCAT+AGG + Chr3:97798197-97798216 None:intergenic 40.0%
ATCCTCAGCCAATGAATTAG+AGG + Chr3:97798125-97798144 None:intergenic 40.0%
ATTCCCTGCATATCTTGTTG+TGG - Chr3:97798463-97798482 MsG0380017552.01.T01:intron 40.0%
CATCATCATCATCATGGGTA+GGG + Chr3:97796915-97796934 None:intergenic 40.0%
CATGTTCTTGTAGATCTGCA+AGG + Chr3:97798252-97798271 None:intergenic 40.0%
CTTGAAAGGAAGAAATGGGT+TGG - Chr3:97797656-97797675 MsG0380017552.01.T01:intron 40.0%
GACTTAGAAGCTTCAAGTCT+AGG - Chr3:97798218-97798237 MsG0380017552.01.T01:intron 40.0%
GATCAGGTTCAAATTGGTCA+TGG - Chr3:97798157-97798176 MsG0380017552.01.T01:intron 40.0%
GATCGTGATGATCATGATGA+TGG - Chr3:97798034-97798053 MsG0380017552.01.T01:intron 40.0%
GATGAAGATGATGAACCAGA+TGG + Chr3:97798100-97798119 None:intergenic 40.0%
GTAGATAGAGAGAGAGAGAA+GGG + Chr3:97797019-97797038 None:intergenic 40.0%
GTTCTTCTTCGCTTTGTCTT+AGG + Chr3:97797376-97797395 None:intergenic 40.0%
TCATCATCATCATCATGGGT+AGG + Chr3:97796916-97796935 None:intergenic 40.0%
! CAGAGCAAGTTGAACTTGAA+AGG - Chr3:97797642-97797661 MsG0380017552.01.T01:intron 40.0%
! TGACAAACACCCCTTTTACT+TGG - Chr3:97797347-97797366 MsG0380017552.01.T01:CDS 40.0%
! TTCCCTGCATATCTTGTTGT+GGG - Chr3:97798464-97798483 MsG0380017552.01.T01:intron 40.0%
! TTCCTCTAATTCATTGGCTG+AGG - Chr3:97798120-97798139 MsG0380017552.01.T01:intron 40.0%
!! AAGAAATGGGTTGGGTTCAT+TGG - Chr3:97797665-97797684 MsG0380017552.01.T01:intron 40.0%
AAGCGAAGAAGAACAGGACA+AGG - Chr3:97797382-97797401 MsG0380017552.01.T01:CDS 45.0%
AGACCCACAACAAGATATGC+AGG + Chr3:97798470-97798489 None:intergenic 45.0%
AGCGAAGAAGAACAGGACAA+GGG - Chr3:97797383-97797402 MsG0380017552.01.T01:CDS 45.0%
GACCCACAACAAGATATGCA+GGG + Chr3:97798469-97798488 None:intergenic 45.0%
GGAACGTCAATGGTGAAAGT+AGG + Chr3:97797481-97797500 None:intergenic 45.0%
GGTAGATAGAGAGAGAGAGA+AGG + Chr3:97797020-97797039 None:intergenic 45.0%
TCATCACGATCCTCGTTTAC+CGG + Chr3:97798025-97798044 None:intergenic 45.0%
TCATCGTTGTCACTGTCATC+AGG + Chr3:97797615-97797634 None:intergenic 45.0%
TGATGACAGTGACAACGATG+AGG - Chr3:97797614-97797633 MsG0380017552.01.T01:intron 45.0%
! TAAACGGACGGATTCTATCC+AGG - Chr3:97796954-97796973 MsG0380017552.01.T01:three_prime_UTR 45.0%
!!! AAGGGTGGTTTTGACACGTT+GGG + Chr3:97797001-97797020 None:intergenic 45.0%
!!! TCAATCCATGCCACTTTTGC+CGG - Chr3:97798003-97798022 MsG0380017552.01.T01:intron 45.0%
CGGAGATGAAGGAACGTCAA+TGG + Chr3:97797491-97797510 None:intergenic 50.0%
GATAGAGAGAGAGAGAAGGG+TGG + Chr3:97797016-97797035 None:intergenic 50.0%
GATGGGGAGAGAGTCTTCTA+AGG + Chr3:97797694-97797713 None:intergenic 50.0%
GGAGAGAGAGAGAGAGAGAA+AGG + Chr3:97797726-97797745 None:intergenic 50.0%
GTTTACCGGCAAAAGTGGCA+TGG + Chr3:97798011-97798030 None:intergenic 50.0%
TCCTCGTTTACCGGCAAAAG+TGG + Chr3:97798016-97798035 None:intergenic 50.0%
TGAACCGCCGGTGAAAAACT+TGG + Chr3:97797559-97797578 None:intergenic 50.0%
TTGACACGTTGGGAATGACG+TGG + Chr3:97796991-97797010 None:intergenic 50.0%
! AACTTGGTGGTCCCAAGAAG+AGG + Chr3:97797543-97797562 None:intergenic 50.0%
! ACCACCAAGTTTTTCACCGG+CGG - Chr3:97797552-97797571 MsG0380017552.01.T01:CDS 50.0%
! GGCAAAAGTGGCATGGATTG+AGG + Chr3:97798004-97798023 None:intergenic 50.0%
! GGGACCACCAAGTTTTTCAC+CGG - Chr3:97797549-97797568 MsG0380017552.01.T01:CDS 50.0%
! GTTTTTCACCGGCGGTTCAT+CGG - Chr3:97797560-97797579 MsG0380017552.01.T01:CDS 50.0%
!!! GAAGGGTGGTTTTGACACGT+TGG + Chr3:97797002-97797021 None:intergenic 50.0%
ACCGCCGGTGAAAAACTTGG+TGG + Chr3:97797556-97797575 None:intergenic 55.0%
CCGATCGACGATGAACTCTC+CGG + Chr3:97797588-97797607 None:intergenic 55.0%
CCGGAGAGTTCATCGTCGAT+CGG - Chr3:97797585-97797604 MsG0380017552.01.T01:intron 55.0%
! GGACGGATTCTATCCAGGCT+AGG - Chr3:97796959-97796978 MsG0380017552.01.T01:three_prime_UTR 55.0%
! TTGGTGGTCCCAAGAAGAGG+TGG + Chr3:97797540-97797559 None:intergenic 55.0%
!! TTGGAAGGTGGCGGAGATGA+AGG + Chr3:97797502-97797521 None:intergenic 55.0%
!!! GCCACTTTTGCCGGTAAACG+AGG - Chr3:97798012-97798031 MsG0380017552.01.T01:intron 55.0%
CAAGAAGAGGTGGCGACCGT+CGG + Chr3:97797530-97797549 None:intergenic 60.0%
CCACCTTCCAACCAGTCCGA+CGG - Chr3:97797511-97797530 MsG0380017552.01.T01:CDS 60.0%
GACGGTCGCCACCTCTTCTT+GGG - Chr3:97797529-97797548 MsG0380017552.01.T01:CDS 60.0%
GACGTGGCAAGAACCTAGCC+TGG + Chr3:97796975-97796994 None:intergenic 60.0%
!! TCGGACTGGTTGGAAGGTGG+CGG + Chr3:97797511-97797530 None:intergenic 60.0%
CGACGGTCGCCACCTCTTCT+TGG - Chr3:97797528-97797547 MsG0380017552.01.T01:CDS 65.0%
!! CCGTCGGACTGGTTGGAAGG+TGG + Chr3:97797514-97797533 None:intergenic 65.0%
!! CGACCGTCGGACTGGTTGGA+AGG + Chr3:97797517-97797536 None:intergenic 65.0%
AGAGGTGGCGACCGTCGGAC+TGG + Chr3:97797525-97797544 None:intergenic 70.0%
CACCGGCGGTTCATCGGAGC+CGG - Chr3:97797566-97797585 MsG0380017552.01.T01:CDS 70.0%
CTCCGGCTCCGATGAACCGC+CGG + Chr3:97797571-97797590 None:intergenic 70.0%
!! GTGGCGACCGTCGGACTGGT+TGG + Chr3:97797521-97797540 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 97796885 97798546 97796885 ID=MsG0380017552.01;Name=MsG0380017552.01
Chr3 mRNA 97796885 97798546 97796885 ID=MsG0380017552.01.T01;Parent=MsG0380017552.01;Name=MsG0380017552.01.T01;_AED=0.22;_eAED=0.22;_QI=0|0|0.33|0.66|1|1|3|237|214
Chr3 exon 97796885 97797599 97796885 ID=MsG0380017552.01.T01:exon:21370;Parent=MsG0380017552.01.T01
Chr3 exon 97797758 97797905 97797758 ID=MsG0380017552.01.T01:exon:21369;Parent=MsG0380017552.01.T01
Chr3 exon 97798528 97798546 97798528 ID=MsG0380017552.01.T01:exon:21368;Parent=MsG0380017552.01.T01
Chr3 CDS 97798528 97798546 97798528 ID=MsG0380017552.01.T01:cds;Parent=MsG0380017552.01.T01
Chr3 CDS 97797758 97797905 97797758 ID=MsG0380017552.01.T01:cds;Parent=MsG0380017552.01.T01
Chr3 CDS 97797122 97797599 97797122 ID=MsG0380017552.01.T01:cds;Parent=MsG0380017552.01.T01
Chr3 three_prime_UTR 97796885 97797121 97796885 ID=MsG0380017552.01.T01:three_prime_utr;Parent=MsG0380017552.01.T01
Gene Sequence

>MsG0380017552.01.T01

ATGAATGAGATAAGAGTTATCCGACGGTCGCCACCTCTTCTTGGGACCACCAAGTTTTTCACCGGCGGTTCATCGGAGCCGGAGAGTTCATCGTCGATCGGAACTCCTGATGACAGTGACAACGATGAGGAAGTGCAGAGCAAGTTGAACTTGAAAGGAAGAAATGGGAGGGGATTATCGAGTCATTTTGAAGGAAAATCAAAGTCATTCACAGATCTATCACAAGTAAACAATTTGAATGAATTGCAAAAGCAAGAGAGTCCTTTTAACAAAAGAAGAAGGGTTCTAATTGCCTCCAAATTTTCAAGAAAATCAGCTTTCTATTCTTGGTCAAATCCTCAATCCATGCCACTTTTGCCGGTAAACGAGGATCGTGATGATCATGATGATGGTTATTATGATTATGAAGATGAGGAAAAGGCTAGAAAAATGCCATCTGGTTCATCATCTTCATCTTCCTCTAATTCATTGGCTGAGGATAAGAAACAAGAAGATCAGGTTCAAATTGGTCATGGTAGAATGCATGAATCCTATGCTGCTGAAATGAGACTTAGACTTAGAAGCTTCAAGTCTAGGAGTTATTCCCTTGCAGATCTACAAGAACATGATGATGAGGAAGATGATGATGATGATGATGATAACTAA
Protein sequence

>MsG0380017552.01.T01

MNEIRVIRRSPPLLGTTKFFTGGSSEPESSSSIGTPDDSDNDEEVQSKLNLKGRNGRGLSSHFEGKSKSFTDLSQVNNLNELQKQESPFNKRRRVLIASKFSRKSAFYSWSNPQSMPLLPVNEDRDDHDDGYYDYEDEEKARKMPSGSSSSSSSNSLAEDKKQEDQVQIGHGRMHESYAAEMRLRLRSFKSRSYSLADLQEHDDEEDDDDDDDN*