AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1366250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1366250 MtrunA17_Chr4g0031161 59.341 182 71 2 1 179 1 182 1.24e-64 196
Msa1366250 MtrunA17_Chr1g0187701 51.667 180 58 6 2 179 4 156 2.90e-46 149
Msa1366250 MtrunA17_Chr1g0187511 34.104 173 73 5 13 179 8 145 4.89e-20 81.6
Msa1366250 MtrunA17_Chr1g0187541 33.136 169 78 5 13 179 11 146 7.18e-17 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACATTACTATTGGAAAATT+TGG 0.112651 tig0018446:-102731 None:intergenic
GAAAATGGGTTGTCATTAAT+TGG 0.221537 tig0018446:-102634 None:intergenic
ACAACCTCTCATGTCATCTT+TGG 0.248681 tig0018446:+102880 Msa1366250:CDS
GAGCGAAATGAGACTGAAAA+TGG 0.269352 tig0018446:-102649 None:intergenic
CAAAATGTGCAGGCAAAATA+AGG 0.288111 tig0018446:-102590 None:intergenic
CAACCTCTCATGTCATCTTT+GGG 0.292269 tig0018446:+102881 Msa1366250:CDS
GAGGGAACTTATGGAAGTTT+TGG 0.297913 tig0018446:+102758 Msa1366250:CDS
TGCAAGAATTGATTTGTTAT+TGG 0.301298 tig0018446:-102833 None:intergenic
CCCTCCATCAACATTACTAT+TGG 0.305799 tig0018446:-102740 None:intergenic
GTACTCTTTGAGAGTTAATC+TGG 0.323940 tig0018446:-102700 None:intergenic
ATGTTGATGGAGGGAACTTA+TGG 0.372547 tig0018446:+102749 Msa1366250:CDS
GGTAAAGACTTCTCGTGATA+AGG 0.409305 tig0018446:-102679 None:intergenic
ATCGGTTGGAGACACCTCTA+TGG 0.420654 tig0018446:-102969 None:intergenic
TAAGATATATATCGACCAAC+TGG 0.437521 tig0018446:+102997 Msa1366250:CDS
ACAAACACATTGTTATCGAT+TGG 0.463185 tig0018446:-103025 None:intergenic
TATCGATTGGTTTATCCAGT+TGG 0.481056 tig0018446:-103012 None:intergenic
GGTTGTCATTAATTGGTAGT+TGG 0.481188 tig0018446:-102627 None:intergenic
ATTGGTAGTTGGTGAAAACT+TGG 0.517484 tig0018446:-102616 None:intergenic
AGCAACCACCACAACAACCT+TGG 0.526275 tig0018446:+102798 Msa1366250:CDS
TCCAATAGTAATGTTGATGG+AGG 0.540613 tig0018446:+102739 Msa1366250:CDS
AACTTGGCTGCAAAATGTGC+AGG 0.547777 tig0018446:-102600 None:intergenic
ATGTGCAGGCAAAATAAGGC+TGG 0.570360 tig0018446:-102586 None:intergenic
CCAATAGTAATGTTGATGGA+GGG 0.570777 tig0018446:+102740 Msa1366250:CDS
AGGCAAAATAAGGCTGGTTG+AGG 0.574955 tig0018446:-102580 None:intergenic
TAGAGAAAATGCTGCCATAG+AGG 0.582088 tig0018446:+102955 Msa1366250:CDS
AGCGAAATGAGACTGAAAAT+GGG 0.587414 tig0018446:-102648 None:intergenic
GACATCAACCAAGGTTGTTG+TGG 0.605926 tig0018446:-102806 None:intergenic
AACCTCTCATGTCATCTTTG+GGG 0.617848 tig0018446:+102882 Msa1366250:CDS
AATTGGTGGAGCTACAAATG+AGG 0.628180 tig0018446:-102930 None:intergenic
ATCAACCAAGGTTGTTGTGG+TGG 0.645799 tig0018446:-102803 None:intergenic
ATTGGTTGAGACATCAACCA+AGG 0.645904 tig0018446:-102815 None:intergenic
TTCCCCAAAGATGACATGAG+AGG 0.655028 tig0018446:-102884 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATATATATCTTAGTTTTAT+CGG - tig0018446:102990-103009 None:intergenic 15.0%
!! AACATTACTATTGGAAAATT+TGG - tig0018446:102734-102753 None:intergenic 20.0%
!! TTTTCCAATAGTAATGTTGA+TGG + tig0018446:102736-102755 Msa1366250:CDS 25.0%
!!! TGCAAGAATTGATTTGTTAT+TGG - tig0018446:102836-102855 None:intergenic 25.0%
!!! TATATCTTAGTTTTATCGGT+TGG - tig0018446:102986-103005 None:intergenic 25.0%
!! GAAAATGGGTTGTCATTAAT+TGG - tig0018446:102637-102656 None:intergenic 30.0%
TAAGATATATATCGACCAAC+TGG + tig0018446:102997-103016 Msa1366250:CDS 30.0%
ACAAACACATTGTTATCGAT+TGG - tig0018446:103028-103047 None:intergenic 30.0%
CAAAATGTGCAGGCAAAATA+AGG - tig0018446:102593-102612 None:intergenic 35.0%
!! ATTGGTAGTTGGTGAAAACT+TGG - tig0018446:102619-102638 None:intergenic 35.0%
! GGTTGTCATTAATTGGTAGT+TGG - tig0018446:102630-102649 None:intergenic 35.0%
AGCGAAATGAGACTGAAAAT+GGG - tig0018446:102651-102670 None:intergenic 35.0%
! GTACTCTTTGAGAGTTAATC+TGG - tig0018446:102703-102722 None:intergenic 35.0%
! TCCAATAGTAATGTTGATGG+AGG + tig0018446:102739-102758 Msa1366250:CDS 35.0%
! CCAATAGTAATGTTGATGGA+GGG + tig0018446:102740-102759 Msa1366250:CDS 35.0%
!! GCATTTTCTCTAGAAATTGG+TGG - tig0018446:102947-102966 None:intergenic 35.0%
!! GCAGCATTTTCTCTAGAAAT+TGG - tig0018446:102950-102969 None:intergenic 35.0%
!! TATCGATTGGTTTATCCAGT+TGG - tig0018446:103015-103034 None:intergenic 35.0%
GTTGAGGATGAAAAACATGG+CGG - tig0018446:102567-102586 None:intergenic 40.0%
CTGGTTGAGGATGAAAAACA+TGG - tig0018446:102570-102589 None:intergenic 40.0%
GAGCGAAATGAGACTGAAAA+TGG - tig0018446:102652-102671 None:intergenic 40.0%
GGTAAAGACTTCTCGTGATA+AGG - tig0018446:102682-102701 None:intergenic 40.0%
CCCTCCATCAACATTACTAT+TGG - tig0018446:102743-102762 None:intergenic 40.0%
! ATGTTGATGGAGGGAACTTA+TGG + tig0018446:102749-102768 Msa1366250:CDS 40.0%
! GAGGGAACTTATGGAAGTTT+TGG + tig0018446:102758-102777 Msa1366250:CDS 40.0%
!! GGAACTTATGGAAGTTTTGG+TGG + tig0018446:102761-102780 Msa1366250:CDS 40.0%
ATTGGTTGAGACATCAACCA+AGG - tig0018446:102818-102837 None:intergenic 40.0%
ACAACCTCTCATGTCATCTT+TGG + tig0018446:102880-102899 Msa1366250:CDS 40.0%
CAACCTCTCATGTCATCTTT+GGG + tig0018446:102881-102900 Msa1366250:CDS 40.0%
AACCTCTCATGTCATCTTTG+GGG + tig0018446:102882-102901 Msa1366250:CDS 40.0%
AATTGGTGGAGCTACAAATG+AGG - tig0018446:102933-102952 None:intergenic 40.0%
TAGAGAAAATGCTGCCATAG+AGG + tig0018446:102955-102974 Msa1366250:CDS 40.0%
! AGGCAAAATAAGGCTGGTTG+AGG - tig0018446:102583-102602 None:intergenic 45.0%
ATGTGCAGGCAAAATAAGGC+TGG - tig0018446:102589-102608 None:intergenic 45.0%
AACTTGGCTGCAAAATGTGC+AGG - tig0018446:102603-102622 None:intergenic 45.0%
ATCAACCAAGGTTGTTGTGG+TGG - tig0018446:102806-102825 None:intergenic 45.0%
GACATCAACCAAGGTTGTTG+TGG - tig0018446:102809-102828 None:intergenic 45.0%
TTCCCCAAAGATGACATGAG+AGG - tig0018446:102887-102906 None:intergenic 45.0%
AGCAACCACCACAACAACCT+TGG + tig0018446:102798-102817 Msa1366250:CDS 50.0%
ATCGGTTGGAGACACCTCTA+TGG - tig0018446:102972-102991 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0018446 gene 102560 103099 102560 ID=Msa1366250;Name=Msa1366250
tig0018446 mRNA 102560 103099 102560 ID=Msa1366250-mRNA-1;Parent=Msa1366250;Name=Msa1366250-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|179
tig0018446 exon 102560 103099 102560 ID=Msa1366250-mRNA-1:exon:15024;Parent=Msa1366250-mRNA-1
tig0018446 CDS 102560 103099 102560 ID=Msa1366250-mRNA-1:cds;Parent=Msa1366250-mRNA-1
Gene Sequence

>Msa1366250

ATGGCCGCCATGTTTTTCATCCTCAACCAGCCTTATTTTGCCTGCACATTTTGCAGCCAAGTTTTCACCAACTACCAATTAATGACAACCCATTTTCAGTCTCATTTCGCTCAAGAAAACCTTATCACGAGAAGTCTTTACCAGATTAACTCTCAAAGAGTACTTTTGCAACCAAATTTTCCAATAGTAATGTTGATGGAGGGAACTTATGGAAGTTTTGGTGGAAATATAGTTTTTCAGCAACCACCACAACAACCTTGGTTGATGTCTCAACCAATAACAAATCAATTCTTGCATACTAACATGCAAGTTGTTGCTTCACAACCTCTCATGTCATCTTTGGGGAACAATGTTAATGCTAATAACGTGACCTCATTTGTAGCTCCACCAATTTCTAGAGAAAATGCTGCCATAGAGGTGTCTCCAACCGATAAAACTAAGATATATATCGACCAACTGGATAAACCAATCGATAACAATGTGTTTGTCAATTCTGCTGATATCAATGACGACTCATTGAATCTGCAGTTAGAACTCTAG
Protein sequence

>Msa1366250

MAAMFFILNQPYFACTFCSQVFTNYQLMTTHFQSHFAQENLITRSLYQINSQRVLLQPNFPIVMLMEGTYGSFGGNIVFQQPPQQPWLMSQPITNQFLHTNMQVVASQPLMSSLGNNVNANNVTSFVAPPISRENAAIEVSPTDKTKIYIDQLDKPIDNNVFVNSADINDDSLNLQLEL*