AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480020651.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020651.01.T01 MTR_4g056300 100.000 136 0 0 1 136 1 136 5.35e-99 280
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020651.01.T01 AT1G08390 64.234 137 46 2 1 135 1 136 5.35e-60 181
MsG0480020651.01.T01 AT1G08390 59.036 83 32 1 1 81 1 83 1.41e-29 103

Find 35 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCAACGCGCTTGGTTAC+AGG 0.187401 4:-45437590 MsG0480020651.01.T01:intron
GTCTTAACCGCAGGGCGTTC+TGG 0.271323 4:-45437500 MsG0480020651.01.T01:intron
CAAGATACCACATTGCTTCT+CGG 0.357532 4:+45435684 None:intergenic
TACCACATTGCTTCTCGGTC+GGG 0.424509 4:+45435689 None:intergenic
CAGCTTTGAATTGACGTTGA+CGG 0.456836 4:+45437398 None:intergenic
TAGTGAGATGGATTACAGTT+TGG 0.458505 4:-45437695 None:intergenic
GGAATGTATGTGATGGTAGT+TGG 0.463985 4:-45437076 MsG0480020651.01.T01:CDS
GCATTCTCTTTCAACGCGCT+TGG 0.476525 4:-45437597 MsG0480020651.01.T01:CDS
ATCATCGAACTCTCTCTTTC+CGG 0.480102 4:-45437427 MsG0480020651.01.T01:CDS
AGGTCCGCTGCCGTCGTTGG+AGG 0.484544 4:+45437474 None:intergenic
CAACATAGCTTCACTCTTGG+CGG 0.489725 4:-45437619 MsG0480020651.01.T01:CDS
ACCACATTGCTTCTCGGTCG+GGG 0.495418 4:+45435690 None:intergenic
CTTCTTCTCGACGATGGAAC+CGG 0.519613 4:-45437451 MsG0480020651.01.T01:CDS
GGGAGAACCTTCTGTGATCA+AGG 0.522819 4:-45437032 MsG0480020651.01.T01:intron
AAGAGGTCCGCTGCCGTCGT+TGG 0.526287 4:+45437471 None:intergenic
GTGTCCTCCAACGACGGCAG+CGG 0.526348 4:-45437478 MsG0480020651.01.T01:CDS
TCTCAACATAGCTTCACTCT+TGG 0.530081 4:-45437622 MsG0480020651.01.T01:CDS
GTTCTGGTGTCCTCCAACGA+CGG 0.536193 4:-45437484 MsG0480020651.01.T01:CDS
AATGTGGTATCTTGAAGTTA+TGG 0.536544 4:-45435675 MsG0480020651.01.T01:CDS
GGGTACGCTACACGTGCGAC+GGG 0.537538 4:-45437052 MsG0480020651.01.T01:CDS
AAGAGAGAGTTCGATGATGC+CGG 0.544037 4:+45437432 None:intergenic
ATACCACATTGCTTCTCGGT+CGG 0.547531 4:+45435688 None:intergenic
CGTCAACGTCAATTCAAAGC+TGG 0.549734 4:-45437397 MsG0480020651.01.T01:intron
CCACATTGCTTCTCGGTCGG+GGG 0.587393 4:+45435691 None:intergenic
GTTCCATCGTCGAGAAGAAG+AGG 0.601711 4:+45437454 None:intergenic
TTGACGTTGACGGAACTCGC+CGG 0.604008 4:+45437408 None:intergenic
AGAGTGAAGCTATGTTGAGA+AGG 0.604560 4:+45437625 None:intergenic
ACACTCACCTTGATCACAGA+AGG 0.611226 4:+45437025 None:intergenic
ACTGTTCTATCAGCCTCTTG+TGG 0.611394 4:-45435642 MsG0480020651.01.T01:CDS
ATGTATGTGATGGTAGTTGG+AGG 0.623456 4:-45437073 MsG0480020651.01.T01:CDS
GTGGTATCTTGAAGTTATGG+AGG 0.631477 4:-45435672 MsG0480020651.01.T01:CDS
AGGGTACGCTACACGTGCGA+CGG 0.641699 4:-45437053 MsG0480020651.01.T01:CDS
GGACCTCTTCTTCTCGACGA+TGG 0.660324 4:-45437457 MsG0480020651.01.T01:CDS
TGTATGTGATGGTAGTTGGA+GGG 0.663704 4:-45437072 MsG0480020651.01.T01:CDS
ATTGGTAGGAATGTATGTGA+TGG 0.690483 4:-45437083 MsG0480020651.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCAACTTATAATATCT+TGG + Chr4:45437130-45437149 None:intergenic 15.0%
!! ATAGAAAATCTTTATCTATT+AGG - Chr4:45436932-45436951 MsG0480020651.01.T01:intron 15.0%
!! ATCAAAACAAAAATGTTTAA+TGG + Chr4:45436199-45436218 None:intergenic 15.0%
!! ATGAAAGTGAAAATATTATT+TGG - Chr4:45437298-45437317 MsG0480020651.01.T01:intron 15.0%
!! GACATTATATAAATAAGAAA+CGG + Chr4:45435799-45435818 None:intergenic 15.0%
!! TAGAAAATCTTTATCTATTA+GGG - Chr4:45436933-45436952 MsG0480020651.01.T01:intron 15.0%
!! TAGCAATATCAATATTATTA+GGG + Chr4:45437519-45437538 None:intergenic 15.0%
!! TGATTATTTACTTGATTTAT+TGG - Chr4:45436215-45436234 MsG0480020651.01.T01:intron 15.0%
!! AATAATATTGATATTGCTAG+CGG - Chr4:45437520-45437539 MsG0480020651.01.T01:intron 20.0%
!! AATAATCTCAAAATGTTGTA+TGG - Chr4:45436379-45436398 MsG0480020651.01.T01:intron 20.0%
!! AGAAAAGAATAAACATGAAA+AGG + Chr4:45437401-45437420 None:intergenic 20.0%
!! AGCAATATCAATATTATTAG+GGG + Chr4:45437518-45437537 None:intergenic 20.0%
!! CTAGCAATATCAATATTATT+AGG + Chr4:45437520-45437539 None:intergenic 20.0%
!! GCTAATTTATATCAAATTGT+AGG + Chr4:45436124-45436143 None:intergenic 20.0%
!! TATTTACTTGATTTATTGGT+AGG - Chr4:45436219-45436238 MsG0480020651.01.T01:intron 20.0%
!!! AATAGTTTCTTAGTTTTTCT+AGG + Chr4:45436720-45436739 None:intergenic 20.0%
!!! TAGATTGTTAATTTAGTTTG+TGG - Chr4:45436066-45436085 MsG0480020651.01.T01:intron 20.0%
!!! TTCATGTTTATTCTTTTCTT+TGG - Chr4:45437402-45437421 MsG0480020651.01.T01:CDS 20.0%
!!! TTTGTTGTTTTAATGCATAT+TGG + Chr4:45436964-45436983 None:intergenic 20.0%
! AATAAGGAAAGTAGATCAAA+TGG - Chr4:45436664-45436683 MsG0480020651.01.T01:intron 25.0%
! AATATTGAAAGTGAAAACGA+CGG + Chr4:45435774-45435793 None:intergenic 25.0%
! AATTATGCATGTGATTAATC+AGG - Chr4:45436170-45436189 MsG0480020651.01.T01:intron 25.0%
! TAATGAGTTTGATCACAATA+TGG - Chr4:45436757-45436776 MsG0480020651.01.T01:intron 25.0%
! TACACAGAACAAAAATTCTT+TGG + Chr4:45435973-45435992 None:intergenic 25.0%
! TGGTTTATGATAGAACATTA+TGG - Chr4:45436777-45436796 MsG0480020651.01.T01:intron 25.0%
!! AGTGAAAATATTATTTGGTG+TGG - Chr4:45437303-45437322 MsG0480020651.01.T01:intron 25.0%
!! GTTTTTATAATTCATCTTGC+TGG - Chr4:45437370-45437389 MsG0480020651.01.T01:intron 25.0%
!! TAATCACATGCATAATTTTG+TGG + Chr4:45436167-45436186 None:intergenic 25.0%
!! TATATAAAGTTTTCCACAAG+AGG + Chr4:45437690-45437709 None:intergenic 25.0%
!!! TCAGATTTTTCAACATTCAA+TGG + Chr4:45436010-45436029 None:intergenic 25.0%
!!! TTAGTTTGTGGTTAAAATTG+CGG - Chr4:45436078-45436097 MsG0480020651.01.T01:intron 25.0%
AATGTGGTATCTTGAAGTTA+TGG - Chr4:45437641-45437660 MsG0480020651.01.T01:CDS 30.0%
CAACTGTAGATTCTGTAATA+AGG - Chr4:45436648-45436667 MsG0480020651.01.T01:intron 30.0%
GAAACTAGAATTAAGTGGTT+CGG - Chr4:45436535-45436554 MsG0480020651.01.T01:intron 30.0%
TATATAATGTCTTAACCGCA+GGG - Chr4:45435808-45435827 MsG0480020651.01.T01:intron 30.0%
TTATATAATGTCTTAACCGC+AGG - Chr4:45435807-45435826 MsG0480020651.01.T01:intron 30.0%
TTGCTCAACATAACAAGTTT+AGG + Chr4:45437484-45437503 None:intergenic 30.0%
! AGTTGAATTTGTTCTTCACT+AGG - Chr4:45437140-45437159 MsG0480020651.01.T01:intron 30.0%
!! TTTTGTTGATGAAATCCAAC+TGG - Chr4:45437205-45437224 MsG0480020651.01.T01:intron 30.0%
AAAGCACAACATGTTCTTAG+GGG - Chr4:45437243-45437262 MsG0480020651.01.T01:intron 35.0%
AACAATGTCTTGATGTCAGA+AGG - Chr4:45437088-45437107 MsG0480020651.01.T01:intron 35.0%
AAGGAAAGTAGATCAAATGG+AGG - Chr4:45436667-45436686 MsG0480020651.01.T01:intron 35.0%
ACCTATAGTAGAAAAGATGG+TGG - Chr4:45436513-45436532 MsG0480020651.01.T01:intron 35.0%
ATTGGTAGGAATGTATGTGA+TGG - Chr4:45436233-45436252 MsG0480020651.01.T01:intron 35.0%
CTCAACATAACAAGTTTAGG+CGG + Chr4:45437481-45437500 None:intergenic 35.0%
GTAATGTAGATGAGGATGTT+GGG - Chr4:45436444-45436463 MsG0480020651.01.T01:intron 35.0%
TAGATCAAATGGAGGATAGT+TGG - Chr4:45436675-45436694 MsG0480020651.01.T01:intron 35.0%
TAGCGGAAATAATGAACGTT+GGG - Chr4:45437537-45437556 MsG0480020651.01.T01:intron 35.0%
TATCGTTGAGCGAAACTATA+CGG + Chr4:45437005-45437024 None:intergenic 35.0%
TCAATGAGCAAAACTACTTG+AGG + Chr4:45437330-45437349 None:intergenic 35.0%
TGGTGGAAACTAGAATTAAG+TGG - Chr4:45436530-45436549 MsG0480020651.01.T01:intron 35.0%
TTCATTCTTTGTGAGAAGTG+AGG + Chr4:45437283-45437302 None:intergenic 35.0%
! AGAAAGCACAACATGTTCTT+AGG - Chr4:45437241-45437260 MsG0480020651.01.T01:intron 35.0%
! CTATCTTTAGAGAGAGAGTT+GGG - Chr4:45436484-45436503 MsG0480020651.01.T01:intron 35.0%
! GAAAGCACAACATGTTCTTA+GGG - Chr4:45437242-45437261 MsG0480020651.01.T01:intron 35.0%
! GAATCATATTGACTGCTAAG+TGG + Chr4:45437062-45437081 None:intergenic 35.0%
! TATCTTTAGAGAGAGAGTTG+GGG - Chr4:45436485-45436504 MsG0480020651.01.T01:intron 35.0%
! TCCACCATCTTTTCTACTAT+AGG + Chr4:45436517-45436536 None:intergenic 35.0%
! TGAAATCCAACTGGTTTCTT+TGG - Chr4:45437214-45437233 MsG0480020651.01.T01:intron 35.0%
AGAGTGAAGCTATGTTGAGA+AGG + Chr4:45435694-45435713 None:intergenic 40.0%
AGGATGTTGGGTTTAATGTG+TGG - Chr4:45436456-45436475 MsG0480020651.01.T01:intron 40.0%
ATAGTTGGATCACTAGAGGT+AGG - Chr4:45436690-45436709 MsG0480020651.01.T01:intron 40.0%
ATCATCGAACTCTCTCTTTC+CGG - Chr4:45435889-45435908 MsG0480020651.01.T01:intron 40.0%
ATCTACATTACGCTTTCCTC+AGG + Chr4:45436435-45436454 None:intergenic 40.0%
ATGTATGTGATGGTAGTTGG+AGG - Chr4:45436243-45436262 MsG0480020651.01.T01:intron 40.0%
CAAGATACCACATTGCTTCT+CGG + Chr4:45437635-45437654 None:intergenic 40.0%
CGTAATGTAGATGAGGATGT+TGG - Chr4:45436443-45436462 MsG0480020651.01.T01:intron 40.0%
CTAGCGGAAATAATGAACGT+TGG - Chr4:45437536-45437555 MsG0480020651.01.T01:intron 40.0%
GGAATGTATGTGATGGTAGT+TGG - Chr4:45436240-45436259 MsG0480020651.01.T01:intron 40.0%
GGCACCTATAGTAGAAAAGA+TGG - Chr4:45436510-45436529 MsG0480020651.01.T01:intron 40.0%
GTGGTATCTTGAAGTTATGG+AGG - Chr4:45437644-45437663 MsG0480020651.01.T01:CDS 40.0%
GTTCGCTTGTTTGTCAGTTA+AGG - Chr4:45436314-45436333 MsG0480020651.01.T01:intron 40.0%
TCTCAACATAGCTTCACTCT+TGG - Chr4:45435694-45435713 MsG0480020651.01.T01:CDS 40.0%
TGTATGTGATGGTAGTTGGA+GGG - Chr4:45436244-45436263 MsG0480020651.01.T01:intron 40.0%
TGTTGTATGGAACAGAGTGT+TGG - Chr4:45436392-45436411 MsG0480020651.01.T01:intron 40.0%
! AGGAAAGCGTAATGTAGATG+AGG - Chr4:45436436-45436455 MsG0480020651.01.T01:intron 40.0%
! ATGTCTTTAGAGGGAGAGTT+GGG - Chr4:45436560-45436579 MsG0480020651.01.T01:intron 40.0%
! CCAACTCTCTCTCTAAAGAT+AGG + Chr4:45436486-45436505 None:intergenic 40.0%
! CCTATCTTTAGAGAGAGAGT+TGG - Chr4:45436483-45436502 MsG0480020651.01.T01:intron 40.0%
! CTGTATTGACATGTTGTGAC+AGG - Chr4:45437575-45437594 MsG0480020651.01.T01:intron 40.0%
! GTTGTATGGAACAGAGTGTT+GGG - Chr4:45436393-45436412 MsG0480020651.01.T01:intron 40.0%
!! CAGCTTTGAATTGACGTTGA+CGG + Chr4:45435921-45435940 None:intergenic 40.0%
AAGAGAGAGTTCGATGATGC+CGG + Chr4:45435887-45435906 None:intergenic 45.0%
ACACTCACCTTGATCACAGA+AGG + Chr4:45436294-45436313 None:intergenic 45.0%
ACTGTTCTATCAGCCTCTTG+TGG - Chr4:45437674-45437693 MsG0480020651.01.T01:CDS 45.0%
ATACCACATTGCTTCTCGGT+CGG + Chr4:45437631-45437650 None:intergenic 45.0%
ATTACGCTTTCCTCAGGTGT+TGG + Chr4:45436429-45436448 None:intergenic 45.0%
CAACATAGCTTCACTCTTGG+CGG - Chr4:45435697-45435716 MsG0480020651.01.T01:CDS 45.0%
CAGTAAAGAACCAACACCTG+AGG - Chr4:45436416-45436435 MsG0480020651.01.T01:intron 45.0%
CGTCAACGTCAATTCAAAGC+TGG - Chr4:45435919-45435938 MsG0480020651.01.T01:intron 45.0%
CTGCTTCCAAAGAAACCAGT+TGG + Chr4:45437223-45437242 None:intergenic 45.0%
CTTATCCCACTAAGTGGGAT+CGG + Chr4:45436822-45436841 None:intergenic 45.0%
GAGGATAGTTGGATCACTAG+AGG - Chr4:45436686-45436705 MsG0480020651.01.T01:intron 45.0%
GCGAAACTATACGGTTAGAG+AGG + Chr4:45436996-45437015 None:intergenic 45.0%
GGTTCGGACATGTCTTTAGA+GGG - Chr4:45436551-45436570 MsG0480020651.01.T01:intron 45.0%
TTTAGAGAGAGAGTTGGGGT+AGG - Chr4:45436489-45436508 MsG0480020651.01.T01:intron 45.0%
! AACGACGGCGTTTTTGAACA+AGG + Chr4:45435759-45435778 None:intergenic 45.0%
! CAAGCCTTATCCCACTAAGT+GGG + Chr4:45436827-45436846 None:intergenic 45.0%
! CATGTCTTTAGAGGGAGAGT+TGG - Chr4:45436559-45436578 MsG0480020651.01.T01:intron 45.0%
! TGGTTCGGACATGTCTTTAG+AGG - Chr4:45436550-45436569 MsG0480020651.01.T01:intron 45.0%
! TGTCTTTAGAGGGAGAGTTG+GGG - Chr4:45436561-45436580 MsG0480020651.01.T01:intron 45.0%
ATGTAGCCGATCCCACTTAG+TGG - Chr4:45436813-45436832 MsG0480020651.01.T01:intron 50.0%
CCACTTAGTGGGATAAGGCT+TGG - Chr4:45436825-45436844 MsG0480020651.01.T01:intron 50.0%
CGATCCCACTTAGTGGGATA+AGG - Chr4:45436820-45436839 MsG0480020651.01.T01:intron 50.0%
CTTCTTCTCGACGATGGAAC+CGG - Chr4:45435865-45435884 MsG0480020651.01.T01:intron 50.0%
CTTTCAACGCGCTTGGTTAC+AGG - Chr4:45435726-45435745 MsG0480020651.01.T01:intron 50.0%
GCATTCTCTTTCAACGCGCT+TGG - Chr4:45435719-45435738 MsG0480020651.01.T01:CDS 50.0%
GGGAGAACCTTCTGTGATCA+AGG - Chr4:45436284-45436303 MsG0480020651.01.T01:intron 50.0%
GTTCCATCGTCGAGAAGAAG+AGG + Chr4:45435865-45435884 None:intergenic 50.0%
TACCACATTGCTTCTCGGTC+GGG + Chr4:45437630-45437649 None:intergenic 50.0%
TGTAGCCGATCCCACTTAGT+GGG - Chr4:45436814-45436833 MsG0480020651.01.T01:intron 50.0%
TTTAGAGGGAGAGTTGGGGT+AGG - Chr4:45436565-45436584 MsG0480020651.01.T01:intron 50.0%
! CCAAGCCTTATCCCACTAAG+TGG + Chr4:45436828-45436847 None:intergenic 50.0%
ACCACATTGCTTCTCGGTCG+GGG + Chr4:45437629-45437648 None:intergenic 55.0%
GGACCTCTTCTTCTCGACGA+TGG - Chr4:45435859-45435878 MsG0480020651.01.T01:intron 55.0%
GTTCTGGTGTCCTCCAACGA+CGG - Chr4:45435832-45435851 MsG0480020651.01.T01:intron 55.0%
TTGACGTTGACGGAACTCGC+CGG + Chr4:45435911-45435930 None:intergenic 55.0%
AGGGTACGCTACACGTGCGA+CGG - Chr4:45436263-45436282 MsG0480020651.01.T01:intron 60.0%
CCACATTGCTTCTCGGTCGG+GGG + Chr4:45437628-45437647 None:intergenic 60.0%
! GTCTTAACCGCAGGGCGTTC+TGG - Chr4:45435816-45435835 MsG0480020651.01.T01:intron 60.0%
AAGAGGTCCGCTGCCGTCGT+TGG + Chr4:45435848-45435867 None:intergenic 65.0%
CCCCCGACCGAGAAGCAATG+TGG - Chr4:45437625-45437644 MsG0480020651.01.T01:CDS 65.0%
GAGGACACCAGAACGCCCTG+CGG + Chr4:45435826-45435845 None:intergenic 65.0%
GGGTACGCTACACGTGCGAC+GGG - Chr4:45436264-45436283 MsG0480020651.01.T01:intron 65.0%
GTGTCCTCCAACGACGGCAG+CGG - Chr4:45435838-45435857 MsG0480020651.01.T01:intron 65.0%
AGGTCCGCTGCCGTCGTTGG+AGG + Chr4:45435845-45435864 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr4 gene 45435628 45437710 45435628 ID=MsG0480020651.01;Name=MsG0480020651.01
Chr4 mRNA 45435628 45437710 45435628 ID=MsG0480020651.01.T01;Parent=MsG0480020651.01;Name=MsG0480020651.01.T01;_AED=0.42;_eAED=0.42;_QI=0|0|0|1|1|1|4|0|136
Chr4 exon 45437591 45437710 45437591 ID=MsG0480020651.01.T01:exon:19174;Parent=MsG0480020651.01.T01
Chr4 exon 45437398 45437509 45437398 ID=MsG0480020651.01.T01:exon:19173;Parent=MsG0480020651.01.T01
Chr4 exon 45437033 45437097 45437033 ID=MsG0480020651.01.T01:exon:19172;Parent=MsG0480020651.01.T01
Chr4 exon 45435628 45435741 45435628 ID=MsG0480020651.01.T01:exon:19171;Parent=MsG0480020651.01.T01
Chr4 CDS 45437591 45437710 45437591 ID=MsG0480020651.01.T01:cds;Parent=MsG0480020651.01.T01
Chr4 CDS 45437398 45437509 45437398 ID=MsG0480020651.01.T01:cds;Parent=MsG0480020651.01.T01
Chr4 CDS 45437033 45437097 45437033 ID=MsG0480020651.01.T01:cds;Parent=MsG0480020651.01.T01
Chr4 CDS 45435628 45435741 45435628 ID=MsG0480020651.01.T01:cds;Parent=MsG0480020651.01.T01
Gene Sequence

>MsG0480020651.01.T01

ATGGATTACAGTTTGGCAGCGTTGAAGCTATTTTGCTCACAACTGAAACTCGCTCGTGAAGTTCCTTCTCAACATAGCTTCACTCTTGGCGGCATTCTCTTTCAACGCGCTTGGTTACAGGGCGTTCTGGTGTCCTCCAACGACGGCAGCGGACCTCTTCTTCTCGACGATGGAACCGGCATCATCGAACTCTCTCTTTCCGGCGAGTTCCGTCAACGTCAATTCAAAGCTGGAATGTATGTGATGGTAGTTGGAGGGTACGCTACACGTGCGACGGGAGAACCTTCTGTGATCAAGGTTCACAAGATTGTTGATCTTTCATCATCCCCCGACCGAGAAGCAATGTGGTATCTTGAAGTTATGGAGGCATACAAACTGTTCTATCAGCCTCTTGTGGAAAACTTTATATAG
Protein sequence

>MsG0480020651.01.T01

MDYSLAALKLFCSQLKLAREVPSQHSFTLGGILFQRAWLQGVLVSSNDGSGPLLLDDGTGIIELSLSGEFRQRQFKAGMYVMVVGGYATRATGEPSVIKVHKIVDLSSSPDREAMWYLEVMEAYKLFYQPLVENFI*