AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180001181.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180001181.01.T01 MTR_1g032630 82.474 97 17 0 1 97 85 181 3.18e-50 170
MsG0180001181.01.T01 MTR_1g032630 82.474 97 17 0 1 97 85 181 7.33e-50 169
MsG0180001181.01.T01 MTR_1g032720 81.707 82 14 1 1 81 87 168 1.74e-40 143
MsG0180001181.01.T01 MTR_1g032720 81.707 82 14 1 1 81 696 777 1.74e-40 143
MsG0180001181.01.T01 MTR_1g032610 63.265 98 35 1 1 97 87 184 4.47e-36 130
MsG0180001181.01.T01 MTR_1g032610 63.265 98 35 1 1 97 24 121 6.02e-36 130
MsG0180001181.01.T01 MTR_1g032590 40.789 76 44 1 4 78 85 160 6.42e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180001181.01.T01 AT1G14790 54.878 82 36 1 1 81 82 163 4.78e-25 99.0

Find 19 sgRNAs with CRISPR-Local

Find 140 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACGATGTTAAACTGTATTT+TGG 0.159141 1:+16921137 MsG0180001181.01.T01:CDS
GTGGATGCTAGTGTAGATTT+TGG 0.172622 1:+16921200 MsG0180001181.01.T01:CDS
AGCTTTCATATGAGAATATT+TGG 0.191630 1:+16921282 MsG0180001181.01.T01:CDS
TCCAAAGCCAAGGGCATTCT+TGG 0.267359 1:+16921106 MsG0180001181.01.T01:CDS
AGGAAAGATTCTCTATATTA+TGG 0.268444 1:+16921174 MsG0180001181.01.T01:CDS
TCCAAGAATGCCCTTGGCTT+TGG 0.307615 1:-16921107 None:intergenic
TGATCTTTCAGCCATCTTGC+AGG 0.325752 1:-16923280 None:intergenic
AGTTGATCCACTCAGAATAA+AGG 0.443637 1:+16923199 MsG0180001181.01.T01:CDS
TTGGGATTGGTATGAGAAAG+TGG 0.485612 1:+16921219 MsG0180001181.01.T01:CDS
TAGAAAGATGTACTATTCAA+AGG 0.487938 1:+16923243 MsG0180001181.01.T01:CDS
GATTGAGCTGCATCAACCAC+AGG 0.538892 1:+16921307 MsG0180001181.01.T01:CDS
AACTCAACCTTTATTCTGAG+TGG 0.564774 1:-16923206 None:intergenic
AAACTGTCCAAGAATGCCCT+TGG 0.565377 1:-16921113 None:intergenic
ATTCTCTATATTATGGAAGG+TGG 0.569959 1:+16921181 MsG0180001181.01.T01:CDS
TCTGTTATGAACCTGCAAGA+TGG 0.584270 1:+16923269 MsG0180001181.01.T01:CDS
AAGATTCTCTATATTATGGA+AGG 0.592994 1:+16921178 MsG0180001181.01.T01:CDS
GAGATATTGATCCAAAGCCA+AGG 0.607190 1:+16921096 MsG0180001181.01.T01:CDS
AGATATTGATCCAAAGCCAA+GGG 0.640291 1:+16921097 MsG0180001181.01.T01:CDS
ATTGAGCTGCATCAACCACA+GGG 0.682058 1:+16921308 MsG0180001181.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATATATATATATATTTTT+AGG + Chr1:16921527-16921546 MsG0180001181.01.T01:intron 0.0%
!!! AATATGGAATAATATTATTT+TGG + Chr1:16922080-16922099 MsG0180001181.01.T01:intron 10.0%
!!! ATTTTTTTTTTTTTGTATAC+CGG + Chr1:16921985-16922004 MsG0180001181.01.T01:intron 10.0%
!!! GTATTTTTTTTTTTAATGAA+AGG - Chr1:16921645-16921664 None:intergenic 10.0%
!! AATTTCTTGATAAAATCTAA+GGG + Chr1:16921732-16921751 MsG0180001181.01.T01:intron 15.0%
!! TAGTTTATGGAATATTAATA+TGG + Chr1:16922064-16922083 MsG0180001181.01.T01:intron 15.0%
!!! TTTTTTTTTTTTTGTATACC+GGG + Chr1:16921986-16922005 MsG0180001181.01.T01:intron 15.0%
!! ATAAATAAGACTGAAATCTA+AGG - Chr1:16921619-16921638 None:intergenic 20.0%
!! CAATTTCTTGATAAAATCTA+AGG + Chr1:16921731-16921750 MsG0180001181.01.T01:intron 20.0%
!! TAAATAAGACTGAAATCTAA+GGG - Chr1:16921618-16921637 None:intergenic 20.0%
!! TATATATTATACAGCTAGAT+TGG + Chr1:16922251-16922270 MsG0180001181.01.T01:intron 20.0%
!! TCTATATGAATTATGAACAA+TGG + Chr1:16921486-16921505 MsG0180001181.01.T01:intron 20.0%
!!! GGTTTAAAACATTTAATGAA+AGG - Chr1:16921376-16921395 None:intergenic 20.0%
!!! TTATTGGCTAACATTAATTT+CGG + Chr1:16921706-16921725 MsG0180001181.01.T01:intron 20.0%
! AAAAAGGAAAATGAAGAACA+TGG - Chr1:16921397-16921416 None:intergenic 25.0%
! AAAGTTGAAGAGATCAAAAT+TGG - Chr1:16922671-16922690 None:intergenic 25.0%
! AACAAATAAGATTCACCATA+TGG - Chr1:16922761-16922780 None:intergenic 25.0%
! AAGATTCTCTATATTATGGA+AGG + Chr1:16921178-16921197 MsG0180001181.01.T01:CDS 25.0%
! ACAAATAAGATTCACCATAT+GGG - Chr1:16922760-16922779 None:intergenic 25.0%
! ACTTTAAACAAGATGTCAAA+TGG - Chr1:16923116-16923135 None:intergenic 25.0%
! AGCTTTCATATGAGAATATT+TGG + Chr1:16921282-16921301 MsG0180001181.01.T01:CDS 25.0%
! AGGAAAGATTCTCTATATTA+TGG + Chr1:16921174-16921193 MsG0180001181.01.T01:CDS 25.0%
! ATATGAATTATGAACAATGG+TGG + Chr1:16921489-16921508 MsG0180001181.01.T01:intron 25.0%
! GCTGTATAATATATAACACA+TGG - Chr1:16922246-16922265 None:intergenic 25.0%
! TAGAAAGATGTACTATTCAA+AGG + Chr1:16923243-16923262 MsG0180001181.01.T01:CDS 25.0%
!! AGCTCTTAGGTTTTTATATT+GGG + Chr1:16922374-16922393 MsG0180001181.01.T01:intron 25.0%
!! CTTGTTTAAAGTTAATTCCT+TGG + Chr1:16923124-16923143 MsG0180001181.01.T01:intron 25.0%
!! TATTGGCTAACATTAATTTC+GGG + Chr1:16921707-16921726 MsG0180001181.01.T01:intron 25.0%
!! TGTCATGATATATCTGATTT+TGG + Chr1:16921834-16921853 MsG0180001181.01.T01:intron 25.0%
!!! GTTTGAACTTCTTATTTTCA+TGG - Chr1:16921259-16921278 None:intergenic 25.0%
AATGGTATTTGAATTCCTTG+AGG - Chr1:16923098-16923117 None:intergenic 30.0%
AGAAAGATTCAAGAATGACA+TGG + Chr1:16921581-16921600 MsG0180001181.01.T01:intron 30.0%
AGAAAGATTCAAGAATGACA+TGG - Chr1:16921600-16921581 None:intergenic 30.0%
ATTCTCTATATTATGGAAGG+TGG + Chr1:16921181-16921200 MsG0180001181.01.T01:CDS 30.0%
CTCTTCTGTTTGTAGTTAAT+TGG + Chr1:16922783-16922802 MsG0180001181.01.T01:intron 30.0%
GAAATAAAAATTGCTGCTGT+TGG - Chr1:16922563-16922582 None:intergenic 30.0%
TAAACTAACAATGTTCCACA+AGG - Chr1:16922051-16922070 None:intergenic 30.0%
TCTCTGTAATAGTTCTTCAA+AGG - Chr1:16922862-16922881 None:intergenic 30.0%
TGTGGAAGAAATGATATTGA+AGG - Chr1:16922346-16922365 None:intergenic 30.0%
! ACACAGTTTTCCTTGAAATT+CGG - Chr1:16922988-16923007 None:intergenic 30.0%
! ATTGGTTTATGGTACATCTA+TGG + Chr1:16922208-16922227 MsG0180001181.01.T01:intron 30.0%
! CAGCTCTTAGGTTTTTATAT+TGG + Chr1:16922373-16922392 MsG0180001181.01.T01:intron 30.0%
! GACGATGTTAAACTGTATTT+TGG + Chr1:16921137-16921156 MsG0180001181.01.T01:CDS 30.0%
! TGTGGAACATTGTTAGTTTA+TGG + Chr1:16922051-16922070 MsG0180001181.01.T01:intron 30.0%
!! TGCAAAGTATCTATTGATTC+AGG + Chr1:16921337-16921356 MsG0180001181.01.T01:intron 30.0%
!!! CTTTGAGTAGTTTTGTCTTT+AGG + Chr1:16921929-16921948 MsG0180001181.01.T01:intron 30.0%
!!! TTATTTTGGTTTGTAGCTCA+AGG + Chr1:16922094-16922113 MsG0180001181.01.T01:intron 30.0%
AACTCAACCTTTATTCTGAG+TGG - Chr1:16923209-16923228 None:intergenic 35.0%
AATTTGATGCACATCCCATA+TGG + Chr1:16922743-16922762 MsG0180001181.01.T01:intron 35.0%
ACATTACACTCAAAAACACG+AGG - Chr1:16922813-16922832 None:intergenic 35.0%
AGATATTGATCCAAAGCCAA+GGG + Chr1:16921097-16921116 MsG0180001181.01.T01:CDS 35.0%
AGATTGGCAGTAAGATTTGA+AGG + Chr1:16922267-16922286 MsG0180001181.01.T01:intron 35.0%
AGTTGATCCACTCAGAATAA+AGG + Chr1:16923199-16923218 MsG0180001181.01.T01:CDS 35.0%
ATTAGTGCTCTTGAGAACAT+TGG + Chr1:16922190-16922209 MsG0180001181.01.T01:intron 35.0%
CTTGCTCAACATGAAATCAA+AGG - Chr1:16922319-16922338 None:intergenic 35.0%
GGAAAACTGTGTTCATTATG+AGG + Chr1:16922996-16923015 MsG0180001181.01.T01:intron 35.0%
GGATCTTCATATACACTTGT+TGG - Chr1:16922841-16922860 None:intergenic 35.0%
TAAGCAGTGCTTATAAAGCT+TGG - Chr1:16922443-16922462 None:intergenic 35.0%
TAGCCAATAAAATCTCAGCT+TGG - Chr1:16921696-16921715 None:intergenic 35.0%
TGTTCATTATGAGGAATCGA+GGG + Chr1:16923005-16923024 MsG0180001181.01.T01:intron 35.0%
TTCGGAAAATCTCTGTTACT+AGG - Chr1:16922970-16922989 None:intergenic 35.0%
! CAGAGATTTTCCGAATTTCA+AGG + Chr1:16922975-16922994 MsG0180001181.01.T01:intron 35.0%
! CTTCATATACACTTGTTGGT+AGG - Chr1:16922837-16922856 None:intergenic 35.0%
! TGGATGCTAGTGTAGATTTT+GGG + Chr1:16921201-16921220 MsG0180001181.01.T01:CDS 35.0%
!! CTCTTGAGAACATTGGTTTA+TGG + Chr1:16922197-16922216 MsG0180001181.01.T01:intron 35.0%
!!! GTCAACTTTTTCATGCAATC+CGG + Chr1:16923049-16923068 MsG0180001181.01.T01:intron 35.0%
AAGGAGTGAAATCTATCGCA+CGG - Chr1:16922906-16922925 None:intergenic 40.0%
AATCGAGGGTCAATACACAT+TGG + Chr1:16923019-16923038 MsG0180001181.01.T01:intron 40.0%
ACCCAAATGCTGCAATTAGA+TGG + Chr1:16922506-16922525 MsG0180001181.01.T01:intron 40.0%
AGCCATCTAATTGCAGCATT+TGG - Chr1:16922511-16922530 None:intergenic 40.0%
AGTAGTCGTCTAACTTTGTC+AGG + Chr1:16921866-16921885 MsG0180001181.01.T01:intron 40.0%
CAATAAAATCTCAGCTTGGC+CGG - Chr1:16921692-16921711 None:intergenic 40.0%
CCTTACAAAACCAGCTTGTA+CGG + Chr1:16922407-16922426 MsG0180001181.01.T01:intron 40.0%
GAGATATTGATCCAAAGCCA+AGG + Chr1:16921096-16921115 MsG0180001181.01.T01:CDS 40.0%
GCCATCTAATTGCAGCATTT+GGG - Chr1:16922510-16922529 None:intergenic 40.0%
GGTATTTGAATTCCTTGAGG+AGG - Chr1:16923095-16923114 None:intergenic 40.0%
GTGTTCATTATGAGGAATCG+AGG + Chr1:16923004-16923023 MsG0180001181.01.T01:intron 40.0%
GTTAATTCCTTGGTTCAGCA+CGG + Chr1:16923134-16923153 MsG0180001181.01.T01:intron 40.0%
TCACTCCTTGCAGTTGTATT+GGG + Chr1:16922917-16922936 MsG0180001181.01.T01:intron 40.0%
TCTGTTATGAACCTGCAAGA+TGG + Chr1:16923269-16923288 MsG0180001181.01.T01:CDS 40.0%
TGGAAATTCCGCTTTCATTG+TGG - Chr1:16922543-16922562 None:intergenic 40.0%
TTAATTCCTTGGTTCAGCAC+GGG + Chr1:16923135-16923154 MsG0180001181.01.T01:intron 40.0%
TTCACTCCTTGCAGTTGTAT+TGG + Chr1:16922916-16922935 MsG0180001181.01.T01:intron 40.0%
! GTGGATGCTAGTGTAGATTT+TGG + Chr1:16921200-16921219 MsG0180001181.01.T01:CDS 40.0%
! TACTTTGCAGTTTTACCCTG+TGG - Chr1:16921326-16921345 None:intergenic 40.0%
! TTGGGATTGGTATGAGAAAG+TGG + Chr1:16921219-16921238 MsG0180001181.01.T01:CDS 40.0%
!! GTTCTCAAGAGCACTAATCT+TGG - Chr1:16922188-16922207 None:intergenic 40.0%
!! TTTTGGCTGTCAGATCTCAA+AGG + Chr1:16921154-16921173 MsG0180001181.01.T01:CDS 40.0%
!!! GCTAGTGTAGATTTTGGGAT+TGG + Chr1:16921206-16921225 MsG0180001181.01.T01:CDS 40.0%
AAACTGTCCAAGAATGCCCT+TGG - Chr1:16921116-16921135 None:intergenic 45.0%
AATCTATCGCACGGATCCAT+TGG - Chr1:16922897-16922916 None:intergenic 45.0%
ACAATTCTCACCGTACAAGC+TGG - Chr1:16922420-16922439 None:intergenic 45.0%
ACTGCTTATGCCATATCTCC+GGG + Chr1:16922455-16922474 MsG0180001181.01.T01:intron 45.0%
ATTGAGCTGCATCAACCACA+GGG + Chr1:16921308-16921327 MsG0180001181.01.T01:CDS 45.0%
CACTGCTTATGCCATATCTC+CGG + Chr1:16922454-16922473 MsG0180001181.01.T01:intron 45.0%
CTGCAATTAGATGGCTAGAG+GGG + Chr1:16922515-16922534 MsG0180001181.01.T01:intron 45.0%
GCTGCAATTAGATGGCTAGA+GGG + Chr1:16922514-16922533 MsG0180001181.01.T01:intron 45.0%
GGTCAATACACATTGGAGAG+CGG + Chr1:16923026-16923045 MsG0180001181.01.T01:intron 45.0%
GTCAATACACATTGGAGAGC+GGG + Chr1:16923027-16923046 MsG0180001181.01.T01:intron 45.0%
TGCAATTAGATGGCTAGAGG+GGG + Chr1:16922516-16922535 MsG0180001181.01.T01:intron 45.0%
TGCTGCAATTAGATGGCTAG+AGG + Chr1:16922513-16922532 MsG0180001181.01.T01:intron 45.0%
TGTGTTGGAGGCTACAATGA+AGG + Chr1:16922481-16922500 MsG0180001181.01.T01:intron 45.0%
! CGGCCAAGCTGAGATTTTAT+TGG + Chr1:16921690-16921709 MsG0180001181.01.T01:intron 45.0%
!!! CCGTACAAGCTGGTTTTGTA+AGG - Chr1:16922410-16922429 None:intergenic 45.0%
!!! AACAAAATTTAAAATAAAAA+AGG - Chr1:16921413-16921432 None:intergenic 5.0%
ACGGATCCATTGGTCATCAG+GGG - Chr1:16922887-16922906 None:intergenic 50.0%
AGACTATCCATCGAGCCTTG+TGG + Chr1:16922033-16922052 MsG0180001181.01.T01:intron 50.0%
ATCCTCTGCATGCACAACTG+CGG + Chr1:16922010-16922029 MsG0180001181.01.T01:intron 50.0%
CAACACATTGCCCGGAGATA+TGG - Chr1:16922468-16922487 None:intergenic 50.0%
CAATGTTCCACAAGGCTCGA+TGG - Chr1:16922043-16922062 None:intergenic 50.0%
CACGGATCCATTGGTCATCA+GGG - Chr1:16922888-16922907 None:intergenic 50.0%
CATATCTCCGGGCAATGTGT+TGG + Chr1:16922466-16922485 MsG0180001181.01.T01:intron 50.0%
CCACAAGAGTTGCAGCTCTT+AGG + Chr1:16922361-16922380 MsG0180001181.01.T01:intron 50.0%
CCTAAGAGCTGCAACTCTTG+TGG - Chr1:16922364-16922383 None:intergenic 50.0%
GACTGCCCAATACAACTGCA+AGG - Chr1:16922925-16922944 None:intergenic 50.0%
GAGATTCCCCTGATGACCAA+TGG + Chr1:16922878-16922897 MsG0180001181.01.T01:intron 50.0%
GATTGAGCTGCATCAACCAC+AGG + Chr1:16921307-16921326 MsG0180001181.01.T01:CDS 50.0%
TCAGCTTGGCCGGAAATCAT+GGG - Chr1:16921682-16921701 None:intergenic 50.0%
TCCAAGAATGCCCTTGGCTT+TGG - Chr1:16921110-16921129 None:intergenic 50.0%
TTGTGCATGCAGAGGATACC+CGG - Chr1:16922007-16922026 None:intergenic 50.0%
!! TCCAAAGCCAAGGGCATTCT+TGG + Chr1:16921106-16921125 MsG0180001181.01.T01:CDS 50.0%
AAGACACCCGTGCTGAACCA+AGG - Chr1:16923144-16923163 None:intergenic 55.0%
ACCCACCACCCCATGATTTC+CGG + Chr1:16921670-16921689 MsG0180001181.01.T01:intron 55.0%
ATCTCCGGGCAATGTGTTGG+AGG + Chr1:16922469-16922488 MsG0180001181.01.T01:intron 55.0%
CAATCCGGATGTTGTCCCCA+TGG + Chr1:16923064-16923083 MsG0180001181.01.T01:intron 55.0%
CAGCTTGGCCGGAAATCATG+GGG - Chr1:16921681-16921700 None:intergenic 55.0%
CCTTGAGGAGGAGCAACCAT+GGG - Chr1:16923083-16923102 None:intergenic 55.0%
CTCAGCTTGGCCGGAAATCA+TGG - Chr1:16921683-16921702 None:intergenic 55.0%
CTTGAGGAGGAGCAACCATG+GGG - Chr1:16923082-16923101 None:intergenic 55.0%
GAGGGGGACCACAATGAAAG+CGG + Chr1:16922532-16922551 MsG0180001181.01.T01:intron 55.0%
GCAACCATGGGGACAACATC+CGG - Chr1:16923071-16923090 None:intergenic 55.0%
GCACGGATCCATTGGTCATC+AGG - Chr1:16922889-16922908 None:intergenic 55.0%
GTAGCCTCCAACACATTGCC+CGG - Chr1:16922476-16922495 None:intergenic 55.0%
GTTCAGCACGGGTGTCTTTC+AGG + Chr1:16923146-16923165 MsG0180001181.01.T01:intron 55.0%
TCCTTGAGGAGGAGCAACCA+TGG - Chr1:16923084-16923103 None:intergenic 55.0%
CCCATGGTTGCTCCTCCTCA+AGG + Chr1:16923080-16923099 MsG0180001181.01.T01:intron 60.0%
CTCCGCAGTTGTGCATGCAG+AGG - Chr1:16922015-16922034 None:intergenic 60.0%
CTTGGCCGGAAATCATGGGG+TGG - Chr1:16921678-16921697 None:intergenic 60.0%
GCCGGAAATCATGGGGTGGT+GGG - Chr1:16921674-16921693 None:intergenic 60.0%
GGCCGGAAATCATGGGGTGG+TGG - Chr1:16921675-16921694 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 16921089 16923295 16921089 ID=MsG0180001181.01;Name=MsG0180001181.01
Chr1 mRNA 16921089 16923295 16921089 ID=MsG0180001181.01.T01;Parent=MsG0180001181.01;Name=MsG0180001181.01.T01;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|1|1|2|0|122
Chr1 exon 16921089 16921329 16921089 ID=MsG0180001181.01.T01:exon:31556;Parent=MsG0180001181.01.T01
Chr1 exon 16923168 16923295 16923168 ID=MsG0180001181.01.T01:exon:31557;Parent=MsG0180001181.01.T01
Chr1 CDS 16921089 16921329 16921089 ID=MsG0180001181.01.T01:cds;Parent=MsG0180001181.01.T01
Chr1 CDS 16923168 16923295 16923168 ID=MsG0180001181.01.T01:cds;Parent=MsG0180001181.01.T01
Gene Sequence

>MsG0180001181.01.T01

ATGGAAAGAGATATTGATCCAAAGCCAAGGGCATTCTTGGACAGTTTAGACGATGTTAAACTGTATTTTGGCTGTCAGATCTCAAAGGAAAGATTCTCTATATTATGGAAGGTGGATGCTAGTGTAGATTTTGGGATTGGTATGAGAAAGTGGCGATTCTCTATGCTCCATGAAAATAAGAAGTTCAAACTTGAGCTTTCATATGAGAATATTTGGAAGATTGAGCTGCATCAACCACAGGGTTCTGAACTTGATAATGCTTTCTATCGTCTAGTTGATCCACTCAGAATAAAGGTTGAGTTTATCGAACATGCTTTAGAAAGATGTACTATTCAAAGGATTTCTGTTATGAACCTGCAAGATGGCTGA
Protein sequence

>MsG0180001181.01.T01

MERDIDPKPRAFLDSLDDVKLYFGCQISKERFSILWKVDASVDFGIGMRKWRFSMLHENKKFKLELSYENIWKIELHQPQGSELDNAFYRLVDPLRIKVEFIEHALERCTIQRISVMNLQDG*