AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016695.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016695.01.T01 MTR_3g093440 85.000 100 7 1 33 132 687 778 2.18e-47 164
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016695.01.T01 AT1G33400 39.640 111 55 4 22 131 523 622 3.33e-15 72.4
MsG0380016695.01.T01 AT1G33400 39.286 112 56 4 22 132 689 789 4.61e-15 72.0
MsG0380016695.01.T01 AT1G33400 39.286 112 56 4 22 132 701 801 6.29e-15 71.6

Find 21 sgRNAs with CRISPR-Local

Find 138 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTATCTCTGACTGTGTT+TGG 0.302118 3:-86664822 None:intergenic
TTCATCCGTCCAACTTTACT+TGG 0.341657 3:+86666826 MsG0380016695.01.T01:CDS
AGTGGGAGAATTACAATTAT+CGG 0.343600 3:+86665088 MsG0380016695.01.T01:CDS
TTCCTTATCTTCAGTACCTT+AGG 0.401357 3:+86666930 MsG0380016695.01.T01:CDS
GACAAGATTCATGAAATGTT+TGG 0.406111 3:+86664720 None:intergenic
TCATTGTAAAGCATCTATTC+AGG 0.417681 3:+86665114 MsG0380016695.01.T01:CDS
CTCCTAAGGTACTGAAGATA+AGG 0.430916 3:-86666932 None:intergenic
AATTTCTAATTTCTCTCCTA+AGG 0.456948 3:-86666946 None:intergenic
TTATGGACTTCATGCAGACT+TGG 0.466543 3:+86666904 MsG0380016695.01.T01:CDS
TAAGCAATAACTATATCATC+AGG 0.495058 3:-86666788 None:intergenic
GTCAACAGCATTGGTCGAAT+AGG 0.497911 3:+86666863 MsG0380016695.01.T01:CDS
AAAAGCATTCTCCTGAAGCT+TGG 0.537408 3:+86664766 MsG0380016695.01.T01:CDS
TATTGTCACCCAAGTAAAGT+TGG 0.540829 3:-86666835 None:intergenic
TCATCCGTCCAACTTTACTT+GGG 0.552845 3:+86666827 MsG0380016695.01.T01:CDS
TGAGAAAGCATTTGATTGAG+AGG 0.570566 3:-86666979 None:intergenic
GAGAAAGCATTTGATTGAGA+GGG 0.570983 3:-86666978 None:intergenic
AATAGTGCTGTCAACAGCAT+TGG 0.571018 3:+86666854 MsG0380016695.01.T01:CDS
CAAATGCTTTCTCAGCAAAG+TGG 0.580858 3:+86666988 MsG0380016695.01.T01:CDS
ATCTTCTCCAAAATCTGCAA+CGG 0.580987 3:-86666758 None:intergenic
AAATGCTTTCTCAGCAAAGT+GGG 0.621121 3:+86666989 MsG0380016695.01.T01:CDS
GTCACCCAAGTAAAGTTGGA+CGG 0.637144 3:-86666831 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAAAAAAAAAAGC+GGG + Chr3:86665206-86665225 MsG0380016695.01.T01:intron 10.0%
!! AAAAAAAAAAAAAAAAAGCG+GGG + Chr3:86665207-86665226 MsG0380016695.01.T01:intron 15.0%
!! ATATATATTATATATCGAGT+TGG + Chr3:86666238-86666257 MsG0380016695.01.T01:intron 15.0%
!!! TTTTTTTTTTTTTTGCAGAA+TGG - Chr3:86665186-86665205 None:intergenic 15.0%
!! AAAAAAAAAAAAAAAAGCGG+GGG + Chr3:86665208-86665227 MsG0380016695.01.T01:intron 20.0%
!! AAGTTACAGTAATAATGTAA+AGG - Chr3:86665920-86665939 None:intergenic 20.0%
!! AGTTACAGTAATAATGTAAA+GGG - Chr3:86665919-86665938 None:intergenic 20.0%
!! GAAATATAAATAATTCTTGG+TGG + Chr3:86665325-86665344 MsG0380016695.01.T01:intron 20.0%
!! GAGTTTATAATAAAAAAGAG+AGG - Chr3:86666079-86666098 None:intergenic 20.0%
!! GTGGAAATATAAATAATTCT+TGG + Chr3:86665322-86665341 MsG0380016695.01.T01:intron 20.0%
!!! CATATTTGTTTTTAAAAGCT+TGG + Chr3:86666048-86666067 MsG0380016695.01.T01:intron 20.0%
! AATAAAACTATGGAGAATGT+TGG + Chr3:86665883-86665902 MsG0380016695.01.T01:intron 25.0%
! AATTACTTTACCATCATTCT+TGG - Chr3:86666727-86666746 None:intergenic 25.0%
! AATTTCTAATTTCTCTCCTA+AGG - Chr3:86666949-86666968 None:intergenic 25.0%
! TAAGCAATAACTATATCATC+AGG - Chr3:86666791-86666810 None:intergenic 25.0%
!! ACTTAATTTTCACTCAAGTT+CGG + Chr3:86666319-86666338 MsG0380016695.01.T01:intron 25.0%
!! TAACTTTCATTTTCTTGTCA+TGG + Chr3:86665020-86665039 MsG0380016695.01.T01:intron 25.0%
!!! ACAGTTTTGAAAACTTAGAT+AGG - Chr3:86666005-86666024 None:intergenic 25.0%
!!! ACCTTTTTTTAACTCAAGTT+CGG + Chr3:86665730-86665749 MsG0380016695.01.T01:intron 25.0%
!!! AGTTTCCAAGTAACTTTTTT+CGG + Chr3:86665297-86665316 MsG0380016695.01.T01:intron 25.0%
!!! TGCTCAATTTTAAAGTTCAA+AGG + Chr3:86665804-86665823 MsG0380016695.01.T01:intron 25.0%
AAATCATGGTGCATTTACAA+TGG + Chr3:86665385-86665404 MsG0380016695.01.T01:intron 30.0%
AGTGGGAGAATTACAATTAT+CGG + Chr3:86665088-86665107 MsG0380016695.01.T01:CDS 30.0%
! AAATCTTTTAACCAAGCTTC+AGG - Chr3:86664780-86664799 None:intergenic 30.0%
! AACAAACAAAAGCTTGCTTA+TGG - Chr3:86666636-86666655 None:intergenic 30.0%
! AGATTGATAACAAGACCATA+TGG - Chr3:86666693-86666712 None:intergenic 30.0%
! GATTGATAACAAGACCATAT+GGG - Chr3:86666692-86666711 None:intergenic 30.0%
! TCATTGTAAAGCATCTATTC+AGG + Chr3:86665114-86665133 MsG0380016695.01.T01:CDS 30.0%
!! GCTATTTTCTCACGTTATTA+TGG + Chr3:86666887-86666906 MsG0380016695.01.T01:CDS 30.0%
!!! ATCATAGGAATGTTTTAGCT+TGG + Chr3:86666533-86666552 MsG0380016695.01.T01:intron 30.0%
!!! TCATAGGAATGTTTTAGCTT+GGG + Chr3:86666534-86666553 MsG0380016695.01.T01:intron 30.0%
AAATGCTTTCTCAGCAAAGT+GGG + Chr3:86666989-86667008 MsG0380016695.01.T01:CDS 35.0%
AACCAGCAAACTAAGATAGT+AGG - Chr3:86665159-86665178 None:intergenic 35.0%
ACCAAGTGCATGTAATCATA+TGG + Chr3:86665436-86665455 MsG0380016695.01.T01:intron 35.0%
AGGTTTATGTGTTCATTAGG+AGG + Chr3:86665606-86665625 MsG0380016695.01.T01:intron 35.0%
AGTTGAACATGAGCTAAGTA+TGG - Chr3:86666285-86666304 None:intergenic 35.0%
ATCAGACTTTCCAAGAATGA+TGG + Chr3:86666714-86666733 MsG0380016695.01.T01:intron 35.0%
ATCTTCTCCAAAATCTGCAA+CGG - Chr3:86666761-86666780 None:intergenic 35.0%
CACAGGTTTATGTGTTCATT+AGG + Chr3:86665603-86665622 MsG0380016695.01.T01:intron 35.0%
CTAATGAACACATAAACCTG+TGG - Chr3:86665605-86665624 None:intergenic 35.0%
CTACTTACACTATCAAGTCT+TGG - Chr3:86664901-86664920 None:intergenic 35.0%
GCCGAACTTGAGTTAAAAAA+AGG - Chr3:86665734-86665753 None:intergenic 35.0%
GTATATAATAGCTCCTCCTA+GGG - Chr3:86666430-86666449 None:intergenic 35.0%
GTATCTCTTTCTGAATAGCT+AGG + Chr3:86665267-86665286 MsG0380016695.01.T01:intron 35.0%
TATTGTCACCCAAGTAAAGT+TGG - Chr3:86666838-86666857 None:intergenic 35.0%
TCCATATGATTACATGCACT+TGG - Chr3:86665440-86665459 None:intergenic 35.0%
TCCCACTAAACAAAAAGCTT+GGG - Chr3:86665075-86665094 None:intergenic 35.0%
TGCATGTAATCATATGGAGA+GGG + Chr3:86665442-86665461 MsG0380016695.01.T01:intron 35.0%
TGGAGAGGGAAATGAAAAAA+TGG + Chr3:86665533-86665552 MsG0380016695.01.T01:intron 35.0%
TTCCTTATCTTCAGTACCTT+AGG + Chr3:86666930-86666949 MsG0380016695.01.T01:CDS 35.0%
! AATTAAGTCTTGTAGAGCCA+TGG + Chr3:86666605-86666624 MsG0380016695.01.T01:intron 35.0%
! CTTTTATGCACATAGCATAC+AGG + Chr3:86666497-86666516 MsG0380016695.01.T01:intron 35.0%
! TTTTCAAAACTGTCCGATGT+GGG + Chr3:86666012-86666031 MsG0380016695.01.T01:intron 35.0%
! TTTTCATTTCCCTCTCCATA+TGG - Chr3:86665531-86665550 None:intergenic 35.0%
!! AACCTACTATCTTAGTTTGC+TGG + Chr3:86665154-86665173 MsG0380016695.01.T01:intron 35.0%
!! GAGAAAGCATTTGATTGAGA+GGG - Chr3:86666981-86667000 None:intergenic 35.0%
!! TGAGAAAGCATTTGATTGAG+AGG - Chr3:86666982-86667001 None:intergenic 35.0%
!!! AACTATTTTCGAGTTGGTTC+GGG + Chr3:86666394-86666413 MsG0380016695.01.T01:intron 35.0%
!!! CTTTTTTCCGTTGCAGATTT+TGG + Chr3:86666751-86666770 MsG0380016695.01.T01:CDS 35.0%
!!! GAACTATTTTCGAGTTGGTT+CGG + Chr3:86666393-86666412 MsG0380016695.01.T01:intron 35.0%
AAGACCTCTCATTCTCTCAA+TGG - Chr3:86666480-86666499 None:intergenic 40.0%
AATAGTGCTGTCAACAGCAT+TGG + Chr3:86666854-86666873 MsG0380016695.01.T01:CDS 40.0%
AGGAGCTATTATATACGTCC+TGG + Chr3:86666434-86666453 MsG0380016695.01.T01:intron 40.0%
ATCCAAACACAGTCAGAGAT+AGG + Chr3:86664820-86664839 MsG0380016695.01.T01:intron 40.0%
ATCCTATCTCTGACTGTGTT+TGG - Chr3:86664825-86664844 None:intergenic 40.0%
ATTCTCATTGCACTTCTCAG+CGG - Chr3:86665483-86665502 None:intergenic 40.0%
CAAATGCTTTCTCAGCAAAG+TGG + Chr3:86666988-86667007 MsG0380016695.01.T01:CDS 40.0%
CACTGCCGAAAAAAGTTACT+TGG - Chr3:86665305-86665324 None:intergenic 40.0%
CAGACTAATAAGTCCCACAT+CGG - Chr3:86666028-86666047 None:intergenic 40.0%
CGATTCGACAATTGAATCGT+TGG - Chr3:86666367-86666386 None:intergenic 40.0%
CGTATATAATAGCTCCTCCT+AGG - Chr3:86666431-86666450 None:intergenic 40.0%
CTAAACAAAAAGCTTGGGCA+AGG - Chr3:86665070-86665089 None:intergenic 40.0%
CTCCCACTAAACAAAAAGCT+TGG - Chr3:86665076-86665095 None:intergenic 40.0%
GAGTGAATGCATTTCCCATA+TGG + Chr3:86666675-86666694 MsG0380016695.01.T01:intron 40.0%
GGGAGTAGAAGTTTGGTTAT+TGG + Chr3:86665228-86665247 MsG0380016695.01.T01:intron 40.0%
GTGCATGTAATCATATGGAG+AGG + Chr3:86665441-86665460 MsG0380016695.01.T01:intron 40.0%
TAGCGTTACACTGGAAATCA+TGG + Chr3:86665371-86665390 MsG0380016695.01.T01:intron 40.0%
TATACGTCCTGGTAGATTTG+AGG + Chr3:86666445-86666464 MsG0380016695.01.T01:intron 40.0%
TCACGCTAATTCTCATAGCA+AGG - Chr3:86665414-86665433 None:intergenic 40.0%
TCACTCAAGTTCGGATCATT+TGG + Chr3:86666328-86666347 MsG0380016695.01.T01:intron 40.0%
TCATCCGTCCAACTTTACTT+GGG + Chr3:86666827-86666846 MsG0380016695.01.T01:CDS 40.0%
TTATGGACTTCATGCAGACT+TGG + Chr3:86666904-86666923 MsG0380016695.01.T01:CDS 40.0%
TTCATCCGTCCAACTTTACT+TGG + Chr3:86666826-86666845 MsG0380016695.01.T01:CDS 40.0%
TTTGTGCGACCTCAATTGAA+AGG + Chr3:86664948-86664967 MsG0380016695.01.T01:intron 40.0%
! AAATGGCTAGTTGCTGCATT+TGG + Chr3:86665550-86665569 MsG0380016695.01.T01:intron 40.0%
! AATGGCTAGTTGCTGCATTT+GGG + Chr3:86665551-86665570 MsG0380016695.01.T01:intron 40.0%
! GGTCGTGAGCATTTTATCAT+AGG + Chr3:86666518-86666537 MsG0380016695.01.T01:intron 40.0%
! GTTTTCAAAACTGTCCGATG+TGG + Chr3:86666011-86666030 MsG0380016695.01.T01:intron 40.0%
! TAAGTATGGTTCGACTCGTT+TGG - Chr3:86666271-86666290 None:intergenic 40.0%
! TCGACTCGATAAGAATGGTT+CGG + Chr3:86665679-86665698 MsG0380016695.01.T01:intron 40.0%
! TTTAAAGTCCACGAGCAACT+CGG + Chr3:86665757-86665776 MsG0380016695.01.T01:intron 40.0%
!! AAAAGCATTCTCCTGAAGCT+TGG + Chr3:86664766-86664785 MsG0380016695.01.T01:CDS 40.0%
!! CTCCTAAGGTACTGAAGATA+AGG - Chr3:86666935-86666954 None:intergenic 40.0%
!! GCCCAAGCTTTTTGTTTAGT+GGG + Chr3:86665071-86665090 MsG0380016695.01.T01:CDS 40.0%
!! TGCCCAAGCTTTTTGTTTAG+TGG + Chr3:86665070-86665089 MsG0380016695.01.T01:CDS 40.0%
!!! CAAGTAACTTTTTTCGGCAG+TGG + Chr3:86665303-86665322 MsG0380016695.01.T01:intron 40.0%
!!! GTCTCGAACTATTTTCGAGT+TGG + Chr3:86666388-86666407 MsG0380016695.01.T01:intron 40.0%
AAACACACCGAGAGAAAAGG+AGG - Chr3:86664931-86664950 None:intergenic 45.0%
ATGGAGAGGGAAATGACCTA+TGG + Chr3:86665455-86665474 MsG0380016695.01.T01:intron 45.0%
CACAAACACACCGAGAGAAA+AGG - Chr3:86664934-86664953 None:intergenic 45.0%
CACAAGTCCTCAAATCTACC+AGG - Chr3:86666455-86666474 None:intergenic 45.0%
CAGTCCATGCCTTTCAATTG+AGG - Chr3:86664960-86664979 None:intergenic 45.0%
CTTGGTGGAACTCACGAAAT+TGG + Chr3:86665340-86665359 MsG0380016695.01.T01:intron 45.0%
GATTTCCAGTGTAACGCTAC+AGG - Chr3:86665370-86665389 None:intergenic 45.0%
GTCACCCAAGTAAAGTTGGA+CGG - Chr3:86666834-86666853 None:intergenic 45.0%
GTGTTCATTAGGAGGAGCTA+GGG + Chr3:86665614-86665633 MsG0380016695.01.T01:intron 45.0%
TGGACTGTGTTCGACAAACA+AGG + Chr3:86664973-86664992 MsG0380016695.01.T01:intron 45.0%
TGTGTTCATTAGGAGGAGCT+AGG + Chr3:86665613-86665632 MsG0380016695.01.T01:intron 45.0%
! AGTTGCTGCATTTGGGATAG+AGG + Chr3:86665558-86665577 MsG0380016695.01.T01:intron 45.0%
! ATCTCCTCCTCCTTTTCTCT+CGG + Chr3:86664921-86664940 MsG0380016695.01.T01:intron 45.0%
! CAGACAAGTTCGATTCGACT+CGG - Chr3:86665651-86665670 None:intergenic 45.0%
! CGACAATTGAATCGTTGGCT+TGG - Chr3:86666362-86666381 None:intergenic 45.0%
! GTTGCTGCATTTGGGATAGA+GGG + Chr3:86665559-86665578 MsG0380016695.01.T01:intron 45.0%
! TCGACTCGACTCGATAAGAA+TGG + Chr3:86665674-86665693 MsG0380016695.01.T01:intron 45.0%
! TGTGCCATTGAGAGAATGAG+AGG + Chr3:86666473-86666492 MsG0380016695.01.T01:intron 45.0%
! TTGCTGCATTTGGGATAGAG+GGG + Chr3:86665560-86665579 MsG0380016695.01.T01:intron 45.0%
!! GTCAACAGCATTGGTCGAAT+AGG + Chr3:86666863-86666882 MsG0380016695.01.T01:CDS 45.0%
!! AAAAAAAAAAAAAAAAAAAG+CGG + Chr3:86665205-86665224 MsG0380016695.01.T01:intron 5.0%
!! ATAATAAAATAATAAAACTA+TGG + Chr3:86665873-86665892 MsG0380016695.01.T01:intron 5.0%
AAAGCGGGGGAGTAGAAGTT+TGG + Chr3:86665221-86665240 MsG0380016695.01.T01:intron 50.0%
ACCAACTGCACGTAGCCATA+TGG + Chr3:86665513-86665532 MsG0380016695.01.T01:intron 50.0%
ATAATAGCTCCTCCTAGGGC+TGG - Chr3:86666426-86666445 None:intergenic 50.0%
GCGACCTCAATTGAAAGGCA+TGG + Chr3:86664953-86664972 MsG0380016695.01.T01:intron 50.0%
GCTTGCTTATGGTGCATCCA+TGG - Chr3:86666625-86666644 None:intergenic 50.0%
TCCAGTGTAACGCTACAGGT+AGG - Chr3:86665366-86665385 None:intergenic 50.0%
TCCATATGGCTACGTGCAGT+TGG - Chr3:86665517-86665536 None:intergenic 50.0%
TGCACGTAGCCATATGGAGA+GGG + Chr3:86665519-86665538 MsG0380016695.01.T01:intron 50.0%
TTGTCATGGTCTGCTGTTGC+AGG + Chr3:86665034-86665053 MsG0380016695.01.T01:intron 50.0%
CACACCGAGAGAAAAGGAGG+AGG - Chr3:86664928-86664947 None:intergenic 55.0%
CGTGATCTAGTAGGCTCCAC+AGG + Chr3:86665586-86665605 MsG0380016695.01.T01:intron 55.0%
CTGCACGTAGCCATATGGAG+AGG + Chr3:86665518-86665537 MsG0380016695.01.T01:intron 55.0%
GCCTACCTGTAGCGTTACAC+TGG + Chr3:86665362-86665381 MsG0380016695.01.T01:intron 55.0%
! GAGGGGAAGCGTGATCTAGT+AGG + Chr3:86665577-86665596 MsG0380016695.01.T01:intron 55.0%
! GCAACTCGGTTCGACTCGTT+AGG + Chr3:86665771-86665790 MsG0380016695.01.T01:intron 55.0%
GAGTCGAACCGAGTTGCTCG+TGG - Chr3:86665768-86665787 None:intergenic 60.0%
GCACTTCTCAGCGGCACCAT+AGG - Chr3:86665474-86665493 None:intergenic 60.0%
TTCGGGTCATTGCCAGCCCT+AGG + Chr3:86666411-86666430 MsG0380016695.01.T01:intron 60.0%
GGGTCATTGCCAGCCCTAGG+AGG + Chr3:86666414-86666433 MsG0380016695.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 86664735 86667048 86664735 ID=MsG0380016695.01;Name=MsG0380016695.01
Chr3 mRNA 86664735 86667048 86664735 ID=MsG0380016695.01.T01;Parent=MsG0380016695.01;Name=MsG0380016695.01.T01;_AED=0.50;_eAED=0.69;_QI=0|0|0.33|1|0|0|3|0|160
Chr3 exon 86664735 86664830 86664735 ID=MsG0380016695.01.T01:exon:21973;Parent=MsG0380016695.01.T01
Chr3 exon 86665056 86665135 86665056 ID=MsG0380016695.01.T01:exon:21974;Parent=MsG0380016695.01.T01
Chr3 exon 86666742 86667048 86666742 ID=MsG0380016695.01.T01:exon:21975;Parent=MsG0380016695.01.T01
Chr3 CDS 86664735 86664830 86664735 ID=MsG0380016695.01.T01:cds;Parent=MsG0380016695.01.T01
Chr3 CDS 86665056 86665135 86665056 ID=MsG0380016695.01.T01:cds;Parent=MsG0380016695.01.T01
Chr3 CDS 86666742 86667048 86666742 ID=MsG0380016695.01.T01:cds;Parent=MsG0380016695.01.T01
Gene Sequence

>MsG0380016695.01.T01

ATGTTTGGCGTAGTTTTTTGTTTTGTTCTGCAAAAGCATTCTCCTGAAGCTTGGTTAAAAGATTTATTTAACTCAGAATATGCTAATCCAAACACAGCAGAAGACAACCTTGCCCAAGCTTTTTGTTTAGTGGGAGAATTACAATTATCGGCGATCATTGTAAAGCATCTATTCAGTAATTCATTCTTTTTTCCGTTGCAGATTTTGGAGAAGATATATGATCCTGATGATATAGTTATTGCTTATGAACTTGTGAAGCTTTCATCCGTCCAACTTTACTTGGGTGACAATAGTGCTGTCAACAGCATTGGTCGAATAGGTGCTATTTTCTCACGTTATTATGGACTTCATGCAGACTTGGTCTTTCCTTATCTTCAGTACCTTAGGAGAGAAATTAGAAATTTCAGTGAAGCCCTCTCAATCAAATGCTTTCTCAGCAAAGTGGGCTATAAAGTGATAGAAAAATCATCAATCACAGCTTAA
Protein sequence

>MsG0380016695.01.T01

MFGVVFCFVLQKHSPEAWLKDLFNSEYANPNTAEDNLAQAFCLVGELQLSAIIVKHLFSNSFFFPLQILEKIYDPDDIVIAYELVKLSSVQLYLGDNSAVNSIGRIGAIFSRYYGLHADLVFPYLQYLRREIRNFSEALSIKCFLSKVGYKVIEKSSITA*