AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0890550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0890550 MtrunA17_Chr6g0471211 99.083 109 1 0 1 109 1 109 5.13e-63 187
Msa0890550 MtrunA17_Chr1g0203261 86.111 72 10 0 3 74 4 75 7.68e-26 92.4
Msa0890550 MtrunA17_Chr8g0387471 50.704 71 34 1 4 74 3 72 1.99e-17 72.0
Msa0890550 MtrunA17_Chr6g0469651 50.000 70 34 1 3 72 2 70 7.50e-16 68.2
Msa0890550 MtrunA17_Chr7g0233191 48.684 76 38 1 4 79 3 77 7.71e-16 67.4
Msa0890550 MtrunA17_Chr7g0248671 53.731 67 30 1 4 70 3 68 1.09e-15 68.6
Msa0890550 MtrunA17_Chr7g0233251 50.000 74 36 1 4 77 3 75 2.50e-15 66.2
Msa0890550 MtrunA17_Chr7g0233201 47.368 76 39 1 4 79 3 77 2.65e-15 66.2
Msa0890550 MtrunA17_Chr7g0233181 47.368 76 39 1 4 79 3 77 1.46e-14 63.9
Msa0890550 MtrunA17_Chr6g0469541 45.333 75 40 1 4 78 3 76 2.59e-14 63.5
Msa0890550 MtrunA17_Chr7g0233211 46.053 76 40 1 4 79 3 77 3.18e-14 63.2
Msa0890550 MtrunA17_Chr7g0233231 46.053 76 40 1 4 79 3 77 3.25e-14 63.2
Msa0890550 MtrunA17_Chr1g0202561 49.296 71 35 1 4 74 3 72 5.14e-14 63.5
Msa0890550 MtrunA17_Chr6g0469591 49.275 69 34 1 4 72 3 70 5.28e-14 63.2
Msa0890550 MtrunA17_Chr6g0469571 49.275 69 34 1 4 72 3 70 6.01e-14 63.2
Msa0890550 MtrunA17_Chr1g0202541 49.296 71 35 1 4 74 3 72 6.11e-14 63.2
Msa0890550 MtrunA17_Chr6g0469671 46.575 73 38 1 3 75 2 73 9.87e-14 62.0
Msa0890550 MtrunA17_Chr6g0469551 47.826 69 35 1 4 72 3 70 1.55e-13 62.0
Msa0890550 MtrunA17_Chr6g0469681 43.836 73 40 1 3 75 2 73 5.11e-13 60.8
Msa0890550 MtrunA17_Chr1g0202501 49.315 73 36 1 3 75 2 73 1.97e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0890550 AT5G23760.1 88.000 75 9 0 1 75 1 75 1.98e-28 99.8
Msa0890550 AT5G23760.2 85.938 64 9 0 12 75 1 64 7.72e-21 80.1
Msa0890550 AT1G01490.1 52.857 70 31 2 4 72 3 71 9.61e-16 69.3
Msa0890550 AT1G01490.2 52.857 70 31 2 4 72 3 71 9.61e-16 69.3
Msa0890550 AT1G01490.4 50.685 73 34 2 1 72 27 98 1.18e-15 69.7
Msa0890550 AT5G52740.1 48.571 70 33 2 3 72 2 68 8.25e-11 55.1

Find 19 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGAAGGTTGTGTTAA+AGG 0.218749 6_1:+63434400 Msa0890550:intron
GAAAGAAGAGAAGAAATAAA+AGG 0.242019 6_1:+63434817 Msa0890550:exon
AATTACAGAAAGTAAATAAA+AGG 0.324086 6_1:-63434983 None:intergenic
CCATTTGAAGAGGAGTTAGA+AGG 0.338959 6_1:-63434149 None:intergenic
AGAAAAGAAAGAAGAGAAGA+AGG 0.371134 6_1:+63434739 Msa0890550:CDS
GAGCAAAAGTTGACAGTGAT+TGG 0.373869 6_1:+63434623 Msa0890550:CDS
GAAGCAGCTGCAGATATCTT+TGG 0.401330 6_1:+63434464 Msa0890550:CDS
GTTGACAGTGATTGGTTCAA+TGG 0.405513 6_1:+63434631 Msa0890550:CDS
AGAGAAGAAAGAAGAGAAGA+AGG 0.411074 6_1:+63434787 Msa0890550:CDS
CCCTTTACCCACTACTATAT+AGG 0.419555 6_1:+63434065 None:intergenic
CCTTCTAACTCCTCTTCAAA+TGG 0.483238 6_1:+63434149 Msa0890550:exon
AACTCCTCTTCAAATGGCTC+AGG 0.489737 6_1:+63434155 Msa0890550:exon
TTCAATTGTAGCAGATGTAA+AGG 0.500702 6_1:+63434601 Msa0890550:CDS
GAAGAAAGAAGAGAAGAAGG+AGG 0.516884 6_1:+63434790 Msa0890550:CDS
AAAGTTGATATTGTATCTGT+TGG 0.520457 6_1:+63434692 Msa0890550:CDS
CATTTGAAGAGGAGTTAGAA+GGG 0.523137 6_1:-63434148 None:intergenic
GAAAACAAGAAAGAAAATGA+AGG 0.596787 6_1:-63434119 None:intergenic
TATACCTGAGCCATTTGAAG+AGG 0.613212 6_1:-63434159 None:intergenic
ATTTGAAGAGGAGTTAGAAG+GGG 0.632377 6_1:-63434147 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTAAATTAAATAGGAT+AGG - chr6_1:63434210-63434229 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG - chr6_1:63434215-63434234 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG + chr6_1:63434215-63434234 Msa0890550:intron 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_1:63434535-63434554 Msa0890550:intron 10.0%
!!! TTATTTTTCTAATTTTTCTT+TGG + chr6_1:63434889-63434908 Msa0890550:three_prime_UTR 10.0%
!!! AAATTGTCTATAATTTTTTT+TGG + chr6_1:63434957-63434976 Msa0890550:three_prime_UTR 10.0%
!! AAAATTAAATTAAATAGGAT+AGG - chr6_1:63434210-63434229 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG - chr6_1:63434215-63434234 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG + chr6_1:63434215-63434234 Msa0890550:intron 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_1:63434535-63434554 Msa0890550:intron 10.0%
!!! TTATTTTTCTAATTTTTCTT+TGG + chr6_1:63434889-63434908 Msa0890550:three_prime_UTR 10.0%
!!! AAATTGTCTATAATTTTTTT+TGG + chr6_1:63434957-63434976 Msa0890550:three_prime_UTR 10.0%
!! TAAGAGAATGAAAAAAAAAA+AGG - chr6_1:63434358-63434377 None:intergenic 15.0%
!! AATTACAGAAAGTAAATAAA+AGG - chr6_1:63434986-63435005 None:intergenic 15.0%
!! TAAGAGAATGAAAAAAAAAA+AGG - chr6_1:63434358-63434377 None:intergenic 15.0%
!! AATTACAGAAAGTAAATAAA+AGG - chr6_1:63434986-63435005 None:intergenic 15.0%
!! TAAATTAAATAGGATAGGAT+AGG - chr6_1:63434205-63434224 None:intergenic 20.0%
!! ATTCTCTTATTCTTTCATAT+TGG + chr6_1:63434369-63434388 Msa0890550:intron 20.0%
!! TAAATTAAATAGGATAGGAT+AGG - chr6_1:63434205-63434224 None:intergenic 20.0%
!! ATTCTCTTATTCTTTCATAT+TGG + chr6_1:63434369-63434388 Msa0890550:intron 20.0%
! GAAAACAAGAAAGAAAATGA+AGG - chr6_1:63434122-63434141 None:intergenic 25.0%
! ACATATATAGCTAAATCATG+AGG - chr6_1:63434282-63434301 None:intergenic 25.0%
!!! TGTTGTTGATTTTGATGAAT+AGG + chr6_1:63434572-63434591 Msa0890550:intron 25.0%
!!! GTTGTTGATTTTGATGAATA+GGG + chr6_1:63434573-63434592 Msa0890550:intron 25.0%
!!! TTGTTGATTTTGATGAATAG+GGG + chr6_1:63434574-63434593 Msa0890550:intron 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_1:63434692-63434711 Msa0890550:CDS 25.0%
! AGAAAAAAAAGAGGAGAAAA+AGG + chr6_1:63434763-63434782 Msa0890550:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_1:63434817-63434836 Msa0890550:exon 25.0%
! GAAAACAAGAAAGAAAATGA+AGG - chr6_1:63434122-63434141 None:intergenic 25.0%
! ACATATATAGCTAAATCATG+AGG - chr6_1:63434282-63434301 None:intergenic 25.0%
!!! TGTTGTTGATTTTGATGAAT+AGG + chr6_1:63434572-63434591 Msa0890550:intron 25.0%
!!! GTTGTTGATTTTGATGAATA+GGG + chr6_1:63434573-63434592 Msa0890550:intron 25.0%
!!! TTGTTGATTTTGATGAATAG+GGG + chr6_1:63434574-63434593 Msa0890550:intron 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_1:63434692-63434711 Msa0890550:CDS 25.0%
! AGAAAAAAAAGAGGAGAAAA+AGG + chr6_1:63434763-63434782 Msa0890550:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_1:63434817-63434836 Msa0890550:exon 25.0%
TAAATAGGATAGGATAGGAT+AGG - chr6_1:63434200-63434219 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_1:63434271-63434290 None:intergenic 30.0%
TTCAATTGTAGCAGATGTAA+AGG + chr6_1:63434601-63434620 Msa0890550:CDS 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_1:63434739-63434758 Msa0890550:CDS 30.0%
GAAGAAGGAAGAAAAAAAAG+AGG + chr6_1:63434754-63434773 Msa0890550:CDS 30.0%
TAAATAGGATAGGATAGGAT+AGG - chr6_1:63434200-63434219 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_1:63434271-63434290 None:intergenic 30.0%
TTCAATTGTAGCAGATGTAA+AGG + chr6_1:63434601-63434620 Msa0890550:CDS 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_1:63434739-63434758 Msa0890550:CDS 30.0%
GAAGAAGGAAGAAAAAAAAG+AGG + chr6_1:63434754-63434773 Msa0890550:CDS 30.0%
!! AGGCTAAGAGAATTTTGATG+AGG - chr6_1:63434102-63434121 None:intergenic 35.0%
ATTTGAAGAGGAGTTAGAAG+GGG - chr6_1:63434150-63434169 None:intergenic 35.0%
CATTTGAAGAGGAGTTAGAA+GGG - chr6_1:63434151-63434170 None:intergenic 35.0%
GATAGGATAGGATATGAAAG+AGG - chr6_1:63434188-63434207 None:intergenic 35.0%
CACAGGAAAATCTAAGAGAT+AGG - chr6_1:63434254-63434273 None:intergenic 35.0%
! TTGGATTGATTCAAAGCAGA+AGG + chr6_1:63434388-63434407 Msa0890550:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_1:63434400-63434419 Msa0890550:intron 35.0%
! TGCTTCTATAGCTTTTTGCT+TGG - chr6_1:63434450-63434469 None:intergenic 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_1:63434668-63434687 Msa0890550:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_1:63434719-63434738 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_1:63434787-63434806 Msa0890550:CDS 35.0%
! ACAATTTTTGCAGCTTACAC+TGG - chr6_1:63434944-63434963 None:intergenic 35.0%
!! AGGCTAAGAGAATTTTGATG+AGG - chr6_1:63434102-63434121 None:intergenic 35.0%
ATTTGAAGAGGAGTTAGAAG+GGG - chr6_1:63434150-63434169 None:intergenic 35.0%
CATTTGAAGAGGAGTTAGAA+GGG - chr6_1:63434151-63434170 None:intergenic 35.0%
GATAGGATAGGATATGAAAG+AGG - chr6_1:63434188-63434207 None:intergenic 35.0%
CACAGGAAAATCTAAGAGAT+AGG - chr6_1:63434254-63434273 None:intergenic 35.0%
! TTGGATTGATTCAAAGCAGA+AGG + chr6_1:63434388-63434407 Msa0890550:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_1:63434400-63434419 Msa0890550:intron 35.0%
! TGCTTCTATAGCTTTTTGCT+TGG - chr6_1:63434450-63434469 None:intergenic 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_1:63434668-63434687 Msa0890550:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_1:63434719-63434738 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_1:63434787-63434806 Msa0890550:CDS 35.0%
! ACAATTTTTGCAGCTTACAC+TGG - chr6_1:63434944-63434963 None:intergenic 35.0%
CCATTTGAAGAGGAGTTAGA+AGG - chr6_1:63434152-63434171 None:intergenic 40.0%
CCTTCTAACTCCTCTTCAAA+TGG + chr6_1:63434149-63434168 Msa0890550:exon 40.0%
TATACCTGAGCCATTTGAAG+AGG - chr6_1:63434162-63434181 None:intergenic 40.0%
GAGCAAAAGTTGACAGTGAT+TGG + chr6_1:63434623-63434642 Msa0890550:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG + chr6_1:63434631-63434650 Msa0890550:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_1:63434790-63434809 Msa0890550:CDS 40.0%
CCATTTGAAGAGGAGTTAGA+AGG - chr6_1:63434152-63434171 None:intergenic 40.0%
CCTTCTAACTCCTCTTCAAA+TGG + chr6_1:63434149-63434168 Msa0890550:exon 40.0%
TATACCTGAGCCATTTGAAG+AGG - chr6_1:63434162-63434181 None:intergenic 40.0%
GAGCAAAAGTTGACAGTGAT+TGG + chr6_1:63434623-63434642 Msa0890550:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG + chr6_1:63434631-63434650 Msa0890550:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_1:63434790-63434809 Msa0890550:CDS 40.0%
AACTCCTCTTCAAATGGCTC+AGG + chr6_1:63434155-63434174 Msa0890550:exon 45.0%
GAAGCAGCTGCAGATATCTT+TGG + chr6_1:63434464-63434483 Msa0890550:CDS 45.0%
AACTCCTCTTCAAATGGCTC+AGG + chr6_1:63434155-63434174 Msa0890550:exon 45.0%
GAAGCAGCTGCAGATATCTT+TGG + chr6_1:63434464-63434483 Msa0890550:CDS 45.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 63434080 63435028 63434080 ID=Msa0890550;Name=Msa0890550
chr6_1 mRNA 63434080 63435028 63434080 ID=Msa0890550-mRNA-1;Parent=Msa0890550;Name=Msa0890550-mRNA-1;_AED=0.17;_eAED=0.17;_QI=88|1|1|1|1|1|3|193|109
chr6_1 exon 63434080 63434176 63434080 ID=Msa0890550-mRNA-1:exon:11556;Parent=Msa0890550-mRNA-1
chr6_1 exon 63434407 63434485 63434407 ID=Msa0890550-mRNA-1:exon:11557;Parent=Msa0890550-mRNA-1
chr6_1 exon 63434594 63435028 63434594 ID=Msa0890550-mRNA-1:exon:11558;Parent=Msa0890550-mRNA-1
chr6_1 five_prime_UTR 63434080 63434167 63434080 ID=Msa0890550-mRNA-1:five_prime_utr;Parent=Msa0890550-mRNA-1
chr6_1 CDS 63434168 63434176 63434168 ID=Msa0890550-mRNA-1:cds;Parent=Msa0890550-mRNA-1
chr6_1 CDS 63434407 63434485 63434407 ID=Msa0890550-mRNA-1:cds;Parent=Msa0890550-mRNA-1
chr6_1 CDS 63434594 63434835 63434594 ID=Msa0890550-mRNA-1:cds;Parent=Msa0890550-mRNA-1
chr6_1 three_prime_UTR 63434836 63435028 63434836 ID=Msa0890550-mRNA-1:three_prime_utr;Parent=Msa0890550-mRNA-1
Gene Sequence

>Msa0890550

ATGGCTCAGAAGGTTGTGTTAAAGGTGTTAACTATGACAGATGACAAAACCAAGCAAAAAGCTATAGAAGCAGCTGCAGATATCTTTGGGGTTGATTCAATTGTAGCAGATGTAAAGGAGCAAAAGTTGACAGTGATTGGTTCAATGGATACAGTGAAAATTGTGAAGAAGCTGAAAAAAGTAGGAAAAGTTGATATTGTATCTGTTGGTCCTGCAAAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAGAAGAAGGAAGAAAAAAAAGAGGAGAAAAAGGAAGAGAAGAAAGAAGAGAAGAAGGAGGAAAAGAAAGAAGAGAAGAAATAA

Protein sequence

>Msa0890550

MAQKVVLKVLTMTDDKTKQKAIEAAADIFGVDSIVADVKEQKLTVIGSMDTVKIVKKLKKVGKVDIVSVGPAKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKK*