AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880042186.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042186.01.T01 MTR_5g077900 97.101 69 2 0 1 69 1 69 4.13e-44 144
MsG0880042186.01.T01 MTR_5g077900 81.013 79 14 1 51 129 147 224 2.97e-39 131
MsG0880042186.01.T01 MTR_7g046380 97.101 69 2 0 1 69 183 251 5.08e-44 148
MsG0880042186.01.T01 MTR_7g046380 78.571 70 14 1 51 120 329 397 5.90e-31 114
MsG0880042186.01.T01 MTR_0002s1270 95.652 69 3 0 1 69 175 243 2.70e-42 144
MsG0880042186.01.T01 MTR_0002s1270 81.013 79 14 1 51 129 321 398 1.89e-38 134
MsG0880042186.01.T01 MTR_0057s0200 94.915 59 3 0 73 131 1 59 6.32e-37 120
MsG0880042186.01.T01 MTR_4g066320 84.127 63 9 1 70 131 59 121 2.18e-34 116
MsG0880042186.01.T01 MTR_8g051620 55.072 69 31 0 1 69 1 69 1.89e-25 93.2
MsG0880042186.01.T01 MTR_8g051620 55.072 69 31 0 1 69 1 69 2.35e-25 93.2
MsG0880042186.01.T01 MTR_4g066310 81.633 49 9 0 1 49 151 199 1.89e-23 90.5
MsG0880042186.01.T01 MTR_3g028430 74.074 54 5 1 78 131 15 59 1.75e-20 79.0
MsG0880042186.01.T01 MTR_4g066300 90.625 32 3 0 71 102 7 38 6.99e-15 64.7
MsG0880042186.01.T01 MTR_2g086200 60.000 50 20 0 82 131 185 234 3.54e-14 67.0
MsG0880042186.01.T01 MTR_8g017000 37.838 74 46 0 58 131 616 689 2.00e-11 60.5
MsG0880042186.01.T01 MTR_2g037270 36.486 74 47 0 58 131 616 689 6.88e-11 58.9
MsG0880042186.01.T01 MTR_2g092960 36.066 61 39 0 71 131 1159 1219 8.95e-11 58.5
MsG0880042186.01.T01 MTR_0462s0020 42.105 57 33 0 71 127 235 291 9.74e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCGAAAGTGTTTGGGATTT+TGG 0.107550 8:-5094047 MsG0880042186.01.T01:CDS
TTGCCATTAGGTTGCTTTCT+TGG 0.248489 8:+5093242 None:intergenic
AGAAATAGATCGAAAGTGTT+TGG 0.315223 8:-5094055 MsG0880042186.01.T01:CDS
TATAAGTCATCATCAGTTAA+TGG 0.351177 8:+5093028 None:intergenic
AACTGTCTAATACACTTTGC+TGG 0.367487 8:+5094340 None:intergenic
GAAATAGATCGAAAGTGTTT+GGG 0.378893 8:-5094054 MsG0880042186.01.T01:CDS
TCTTGACTTGTATAAGGCTT+AGG 0.381448 8:-5092975 None:intergenic
GTATTTGGCTCATGTTCTAA+TGG 0.408074 8:+5094379 None:intergenic
TATCCACAATCATTGCCATT+AGG 0.411955 8:+5093230 None:intergenic
GTGTATTAGACAGTTGTTGA+TGG 0.459053 8:-5094332 MsG0880042186.01.T01:CDS
CTGCTAATATTACTAAGTCT+TGG 0.472781 8:-5093175 MsG0880042186.01.T01:CDS
ATATGATTTGCGAAACCAAT+GGG 0.486055 8:-5093008 MsG0880042186.01.T01:CDS
TAGCCAAGAAAGCAACCTAA+TGG 0.495668 8:-5093245 MsG0880042186.01.T01:CDS
CAACCTAATGGCAATGATTG+TGG 0.497368 8:-5093233 MsG0880042186.01.T01:CDS
TCATCATCAGTTAATGGCGT+TGG 0.497730 8:+5093034 None:intergenic
CAAGAAAACAAGTTGCCCAT+TGG 0.504204 8:+5092993 None:intergenic
TGTATTAGACAGTTGTTGAT+GGG 0.546275 8:-5094331 MsG0880042186.01.T01:CDS
TATATGATTTGCGAAACCAA+TGG 0.577102 8:-5093009 MsG0880042186.01.T01:CDS
AGTTGTTGATGGGTAATGCT+TGG 0.594458 8:-5094321 MsG0880042186.01.T01:CDS
TAATATTACTAAGTCTTGGA+TGG 0.604101 8:-5093171 MsG0880042186.01.T01:CDS
AACATGAGCCAAATACCGCA+AGG 0.641032 8:-5094372 MsG0880042186.01.T01:CDS
TATTACTAAGTCTTGGATGG+AGG 0.643493 8:-5093168 MsG0880042186.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTCAAATTATTTAGAAA+GGG - Chr8:5093680-5093699 MsG0880042186.01.T01:intron 15.0%
!! AACTAATCACTTTATAAAAA+TGG - Chr8:5094109-5094128 MsG0880042186.01.T01:intron 15.0%
!! AATAAGGATATGTTTATATT+TGG + Chr8:5094287-5094306 None:intergenic 15.0%
!! ACATTAAATGAAAGAATTAT+TGG + Chr8:5093873-5093892 None:intergenic 15.0%
!! TAAACTCAAATTATTTAGAA+AGG - Chr8:5093679-5093698 MsG0880042186.01.T01:intron 15.0%
!! TATACTTACTTAAATAGATA+TGG + Chr8:5093474-5093493 None:intergenic 15.0%
!!! CTTTTTTACTATTATCAATA+TGG - Chr8:5093135-5093154 MsG0880042186.01.T01:intron 15.0%
!!! GTCATATTTCTTTAAAATAT+GGG + Chr8:5093969-5093988 None:intergenic 15.0%
!!! TGTCATATTTCTTTAAAATA+TGG + Chr8:5093970-5093989 None:intergenic 15.0%
!!! TGTTAATTTTAAATTTGTCT+AGG - Chr8:5093190-5093209 MsG0880042186.01.T01:CDS 15.0%
!! AACACTTAAATATTGAATTG+TGG + Chr8:5093174-5093193 None:intergenic 20.0%
!! ATCGAATACTATTATCAATA+TGG - Chr8:5093231-5093250 MsG0880042186.01.T01:CDS 20.0%
!! CTTAATAATTGTTCTTCTAA+GGG - Chr8:5093538-5093557 MsG0880042186.01.T01:intron 20.0%
!! GGTTAAGTACATTAAATAAA+AGG + Chr8:5093901-5093920 None:intergenic 20.0%
!! TAAAGTAAAAAAATTCACTG+AGG - Chr8:5093711-5093730 MsG0880042186.01.T01:intron 20.0%
!!! TGCTAATTTTAAATTTGTCT+AGG - Chr8:5093286-5093305 MsG0880042186.01.T01:intron 20.0%
! AGCACTTAAATATTGAATTG+TGG + Chr8:5093270-5093289 None:intergenic 25.0%
! CCTTAATAATTGTTCTTCTA+AGG - Chr8:5093537-5093556 MsG0880042186.01.T01:intron 25.0%
! CCTTAGAAGAACAATTATTA+AGG + Chr8:5093540-5093559 None:intergenic 25.0%
! TAATATTACTAAGTCTTGGA+TGG - Chr8:5094217-5094236 MsG0880042186.01.T01:intron 25.0%
! TAGTACTAAAACTAAAGTTC+AGG - Chr8:5093398-5093417 MsG0880042186.01.T01:intron 25.0%
! TATAAGTCATCATCAGTTAA+TGG + Chr8:5094363-5094382 None:intergenic 25.0%
! TATATTAACCTACACATTGT+AGG - Chr8:5094320-5094339 MsG0880042186.01.T01:CDS 25.0%
! TTGGTTAAGTAGTGTAAAAA+AGG + Chr8:5093854-5093873 None:intergenic 25.0%
!! ACTTTTCTATTCTACAACTT+TGG - Chr8:5093094-5093113 MsG0880042186.01.T01:intron 25.0%
!! TAGCTTAATTGATTTAGTAG+TGG + Chr8:5093585-5093604 None:intergenic 25.0%
!!! GTTTTAGTACTATGATCTTT+TGG + Chr8:5093390-5093409 None:intergenic 25.0%
!!! TTGTTTTCTTGACTTGTATA+AGG - Chr8:5094407-5094426 MsG0880042186.01.T01:CDS 25.0%
ATAAAAAACCTTGCGGTATT+TGG + Chr8:5093027-5093046 None:intergenic 30.0%
ATTATTTAGAAAGGGTAGTC+TGG - Chr8:5093688-5093707 MsG0880042186.01.T01:intron 30.0%
ATTGAATACCTACAATGTGT+AGG + Chr8:5094331-5094350 None:intergenic 30.0%
CTGCTAATATTACTAAGTCT+TGG - Chr8:5094213-5094232 MsG0880042186.01.T01:intron 30.0%
GATTAAAATCCAAGCATACT+GGG + Chr8:5093368-5093387 None:intergenic 30.0%
TGTATTAGACAGTTGTTGAT+GGG - Chr8:5093057-5093076 MsG0880042186.01.T01:intron 30.0%
! ATATGATTTGCGAAACCAAT+GGG - Chr8:5094380-5094399 MsG0880042186.01.T01:CDS 30.0%
! TAGACTTAGCTTGATTACAT+TGG - Chr8:5093738-5093757 MsG0880042186.01.T01:intron 30.0%
! TATATGATTTGCGAAACCAA+TGG - Chr8:5094379-5094398 MsG0880042186.01.T01:CDS 30.0%
!! AGAAATAGATCGAAAGTGTT+TGG - Chr8:5093333-5093352 MsG0880042186.01.T01:intron 30.0%
!! GAAATAGATCGAAAGTGTTT+GGG - Chr8:5093334-5093353 MsG0880042186.01.T01:intron 30.0%
AACTGTCTAATACACTTTGC+TGG + Chr8:5093051-5093070 None:intergenic 35.0%
AATATGGGATTTAGCACTCT+AGG + Chr8:5093954-5093973 None:intergenic 35.0%
AGATCTAACTCTGTTCTGTA+TGG + Chr8:5093774-5093793 None:intergenic 35.0%
CTTTCTTGGCTACAAATGAA+TGG + Chr8:5094135-5094154 None:intergenic 35.0%
GATCTAACTCTGTTCTGTAT+GGG + Chr8:5093773-5093792 None:intergenic 35.0%
GCAAACATCGTATTAAAGCT+TGG - Chr8:5094014-5094033 MsG0880042186.01.T01:intron 35.0%
GGATTAAAATCCAAGCATAC+TGG + Chr8:5093369-5093388 None:intergenic 35.0%
GTGTATTAGACAGTTGTTGA+TGG - Chr8:5093056-5093075 MsG0880042186.01.T01:intron 35.0%
TACAGAACAGAGTTAGATCT+AGG - Chr8:5093774-5093793 MsG0880042186.01.T01:intron 35.0%
TATCCACAATCATTGCCATT+AGG + Chr8:5094161-5094180 None:intergenic 35.0%
TATTACTAAGTCTTGGATGG+AGG - Chr8:5094220-5094239 MsG0880042186.01.T01:intron 35.0%
TGCTGGAATAAAAAACCTTG+CGG + Chr8:5093034-5093053 None:intergenic 35.0%
TGCTTCTGCTTATAAAAAGC+TGG - Chr8:5093818-5093837 MsG0880042186.01.T01:intron 35.0%
TGGCTAGCATTGTATTATGA+TGG + Chr8:5093922-5093941 None:intergenic 35.0%
TTCAGGAACACATACAAACT+AGG - Chr8:5093415-5093434 MsG0880042186.01.T01:intron 35.0%
! AGATCTAGGATTCCATTACA+TGG - Chr8:5093788-5093807 MsG0880042186.01.T01:intron 35.0%
! GTATTTGGCTCATGTTCTAA+TGG + Chr8:5093012-5093031 None:intergenic 35.0%
! TGCTCATGTATTAGAAGCAT+TGG + Chr8:5093997-5094016 None:intergenic 35.0%
!!! ATCGAAAGTGTTTGGGATTT+TGG - Chr8:5093341-5093360 MsG0880042186.01.T01:intron 35.0%
AAGCATGTGAGTCCATGTAA+TGG + Chr8:5093803-5093822 None:intergenic 40.0%
CAACCTAATGGCAATGATTG+TGG - Chr8:5094155-5094174 MsG0880042186.01.T01:intron 40.0%
CAAGAAAACAAGTTGCCCAT+TGG + Chr8:5094398-5094417 None:intergenic 40.0%
TAGCCAAGAAAGCAACCTAA+TGG - Chr8:5094143-5094162 MsG0880042186.01.T01:intron 40.0%
TCATCATCAGTTAATGGCGT+TGG + Chr8:5094357-5094376 None:intergenic 40.0%
! AGTTGTTGATGGGTAATGCT+TGG - Chr8:5093067-5093086 MsG0880042186.01.T01:intron 40.0%
! TTGCCATTAGGTTGCTTTCT+TGG + Chr8:5094149-5094168 None:intergenic 40.0%
AACATGAGCCAAATACCGCA+AGG - Chr8:5093016-5093035 MsG0880042186.01.T01:CDS 45.0%
! GATTTTGGACCCAGTATGCT+TGG - Chr8:5093356-5093375 MsG0880042186.01.T01:intron 45.0%
!! ATAAGTAATTAATATTAATA+AGG + Chr8:5094303-5094322 None:intergenic 5.0%
!! AGCACTCTAGGATACGTAGC+TGG + Chr8:5093942-5093961 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
Chr8 gene 5092976 5094434 5092976 ID=MsG0880042186.01;Name=MsG0880042186.01
Chr8 mRNA 5092976 5094434 5092976 ID=MsG0880042186.01.T01;Parent=MsG0880042186.01;Name=MsG0880042186.01.T01;_AED=0.42;_eAED=0.45;_QI=0|0|0|1|1|1|4|0|131
Chr8 exon 5094289 5094434 5094289 ID=MsG0880042186.01.T01:exon:31051;Parent=MsG0880042186.01.T01
Chr8 exon 5094042 5094102 5094042 ID=MsG0880042186.01.T01:exon:31052;Parent=MsG0880042186.01.T01
Chr8 exon 5093169 5093264 5093169 ID=MsG0880042186.01.T01:exon:31053;Parent=MsG0880042186.01.T01
Chr8 exon 5092976 5093068 5092976 ID=MsG0880042186.01.T01:exon:31054;Parent=MsG0880042186.01.T01
Chr8 CDS 5094289 5094434 5094289 ID=MsG0880042186.01.T01:cds;Parent=MsG0880042186.01.T01
Chr8 CDS 5094042 5094102 5094042 ID=MsG0880042186.01.T01:cds;Parent=MsG0880042186.01.T01
Chr8 CDS 5093169 5093264 5093169 ID=MsG0880042186.01.T01:cds;Parent=MsG0880042186.01.T01
Chr8 CDS 5092976 5093068 5092976 ID=MsG0880042186.01.T01:cds;Parent=MsG0880042186.01.T01
Gene Sequence

>MsG0880042186.01.T01

ATGGTTTTGAGAAGTGAAGAAGATATACGCATACCATTAGAACATGAGCCAAATACCGCAAGGTTTTTTATTCCAGCAAAGTGTATTAGACAGTTGTTGATGGGTAATGCTTGGCTTGACTTTTCTATTCTACAACTTTGGTGCACGTGTATGCATCGTCTCTGTATCTCAAGAAATAGATCGAAAGTGTTTGGGATTTTGGACCCACCAAGAAAGCAACCTAATGGCAATGATTGTGGATACTATGTGATGAAGAATATGCTAGATATCATCTCTGCTAATATTACTAAGTCTTGGATGGAGGTATTCAATGATCCAACGCCATTAACTGATGATGACTTATATGATTTGCGAAACCAATGGGCAACTTGTTTTCTTGACTTGTATAAGGCTTAG
Protein sequence

>MsG0880042186.01.T01

MVLRSEEDIRIPLEHEPNTARFFIPAKCIRQLLMGNAWLDFSILQLWCTCMHRLCISRNRSKVFGILDPPRKQPNGNDCGYYVMKNMLDIISANITKSWMEVFNDPTPLTDDDLYDLRNQWATCFLDLYKA*