AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880042616.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042616.01.T01 MTR_8g018320 87.963 108 9 1 1 108 1 104 1.45e-63 188
MsG0880042616.01.T01 MTR_8g018360 87.850 107 9 1 1 107 1 103 5.31e-61 184
MsG0880042616.01.T01 MTR_2g099630 62.963 108 32 5 1 106 1 102 3.14e-35 117
MsG0880042616.01.T01 MTR_4g125990 50.847 118 45 3 2 107 3 119 8.17e-28 98.6
MsG0880042616.01.T01 MTR_3g104640 55.238 105 42 2 4 107 6 106 2.89e-20 79.0
MsG0880042616.01.T01 MTR_7g109290 44.318 88 40 2 28 107 1 87 6.87e-17 69.7
MsG0880042616.01.T01 MTR_1g087730 56.250 48 21 0 60 107 55 102 5.73e-15 65.5
MsG0880042616.01.T01 MTR_1g015810 42.857 98 47 2 11 102 15 109 1.52e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042616.01.T01 AT5G11970 45.192 104 48 2 4 107 6 100 3.60e-20 78.6
MsG0880042616.01.T01 AT2G19460 42.105 114 56 4 2 107 3 114 2.04e-19 77.0
MsG0880042616.01.T01 AT2G19460 42.105 114 56 4 2 107 55 166 4.54e-19 77.4
MsG0880042616.01.T01 AT1G72720 38.095 126 58 5 3 108 2 127 3.15e-14 63.9
MsG0880042616.01.T01 AT3G13910 55.738 61 24 1 47 104 39 99 8.33e-14 62.4
MsG0880042616.01.T01 AT3G13910 53.125 64 27 1 47 107 39 102 1.06e-13 62.4
MsG0880042616.01.T01 AT2G47480 45.000 60 33 0 48 107 47 106 8.11e-12 57.4

Find 15 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCAATCATCACCATAAT+TGG 0.249026 8:+11512858 None:intergenic
ACTTTGATCCCTGCATGATT+TGG 0.293039 8:+11513159 None:intergenic
CTCAGGTCTTGCATGCTTGA+TGG 0.298734 8:+11513100 None:intergenic
AGAACACATGCAGCCAATTA+TGG 0.342449 8:-11512871 MsG0880042616.01.T01:CDS
AATTTGTACTATAACTTCTC+AGG 0.430942 8:+11513083 None:intergenic
CAGAGAAAGAAAAGAGTAGC+TGG 0.442245 8:-11512959 MsG0880042616.01.T01:CDS
TTGCAGATTGAAAGCTATAG+TGG 0.472998 8:-11513136 MsG0880042616.01.T01:CDS
CTTTCAAGAAGAGTTTAAGA+TGG 0.490246 8:-11512898 MsG0880042616.01.T01:CDS
GATGTTGAAGGAAAAGTGAA+AGG 0.521803 8:-11512923 MsG0880042616.01.T01:CDS
TATAAAGTATATGATGTTGA+AGG 0.535495 8:-11512935 MsG0880042616.01.T01:CDS
AGTTATAGTACAAATTATGA+TGG 0.547941 8:-11513076 MsG0880042616.01.T01:CDS
ATGTTGAAGGAAAAGTGAAA+GGG 0.557577 8:-11512922 MsG0880042616.01.T01:CDS
AATTCAGATCCAAATCATGC+AGG 0.564800 8:-11513168 MsG0880042616.01.T01:CDS
CAGATTGAAAGCTATAGTGG+TGG 0.602253 8:-11513133 MsG0880042616.01.T01:CDS
ATTCAGATCCAAATCATGCA+GGG 0.608352 8:-11513167 MsG0880042616.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTATAGTACAAATTATGA+TGG - Chr8:11512964-11512983 MsG0880042616.01.T01:CDS 20.0%
!! GAAAAAAGTAAGAGTAAATT+TGG - Chr8:11513018-11513037 MsG0880042616.01.T01:CDS 20.0%
!! TATAAAGTATATGATGTTGA+AGG - Chr8:11513105-11513124 MsG0880042616.01.T01:CDS 20.0%
! AATTTGTACTATAACTTCTC+AGG + Chr8:11512960-11512979 None:intergenic 25.0%
ATGTTGAAGGAAAAGTGAAA+GGG - Chr8:11513118-11513137 MsG0880042616.01.T01:CDS 30.0%
CTTTCAAGAAGAGTTTAAGA+TGG - Chr8:11513142-11513161 MsG0880042616.01.T01:CDS 30.0%
! TTGGCAAAGCATCAAAAATT+TGG - Chr8:11513037-11513056 MsG0880042616.01.T01:CDS 30.0%
!! ATCTGCTTTTGATCAAAACA+AGG - Chr8:11512993-11513012 MsG0880042616.01.T01:CDS 30.0%
AATTCAGATCCAAATCATGC+AGG - Chr8:11512872-11512891 MsG0880042616.01.T01:CDS 35.0%
ATTCAGATCCAAATCATGCA+GGG - Chr8:11512873-11512892 MsG0880042616.01.T01:CDS 35.0%
GATGTTGAAGGAAAAGTGAA+AGG - Chr8:11513117-11513136 MsG0880042616.01.T01:CDS 35.0%
TTGCAGATTGAAAGCTATAG+TGG - Chr8:11512904-11512923 MsG0880042616.01.T01:CDS 35.0%
ACTTTGATCCCTGCATGATT+TGG + Chr8:11512884-11512903 None:intergenic 40.0%
AGAACACATGCAGCCAATTA+TGG - Chr8:11513169-11513188 MsG0880042616.01.T01:CDS 40.0%
CAGAGAAAGAAAAGAGTAGC+TGG - Chr8:11513081-11513100 MsG0880042616.01.T01:CDS 40.0%
CAGATTGAAAGCTATAGTGG+TGG - Chr8:11512907-11512926 MsG0880042616.01.T01:CDS 40.0%
! CTTTTCTTTCTCTGCAACTC+TGG + Chr8:11513075-11513094 None:intergenic 40.0%
CTCAGGTCTTGCATGCTTGA+TGG + Chr8:11512943-11512962 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
Chr8 gene 11512868 11513194 11512868 ID=MsG0880042616.01;Name=MsG0880042616.01
Chr8 mRNA 11512868 11513194 11512868 ID=MsG0880042616.01.T01;Parent=MsG0880042616.01;Name=MsG0880042616.01.T01;_AED=0.05;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|108
Chr8 exon 11512868 11513194 11512868 ID=MsG0880042616.01.T01:exon:3527;Parent=MsG0880042616.01.T01
Chr8 CDS 11512868 11513194 11512868 ID=MsG0880042616.01.T01:cds;Parent=MsG0880042616.01.T01
Gene Sequence

>MsG0880042616.01.T01

ATGGAATTCAGATCCAAATCATGCAGGGATCAAAGTTTGCAGATTGAAAGCTATAGTGGTGGAAGAGTAGCTCCATCAAGCATGCAAGACCTGAGAAGTTATAGTACAAATTATGATGGTAATTCATCTGCTTTTGATCAAAACAAGGTAGAAAAAAGTAAGAGTAAATTTGGCAAAGCATCAAAAATTTGGAGCTTCAATGATCCAGAGTTGCAGAGAAAGAAAAGAGTAGCTGGATATAAAGTATATGATGTTGAAGGAAAAGTGAAAGGGTCTTTCAAGAAGAGTTTAAGATGGAACAAGAACACATGCAGCCAATTATGGTGA

Protein sequence

>MsG0880042616.01.T01

MEFRSKSCRDQSLQIESYSGGRVAPSSMQDLRSYSTNYDGNSSAFDQNKVEKSKSKFGKASKIWSFNDPELQRKKRVAGYKVYDVEGKVKGSFKKSLRWNKNTCSQLW*