AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280006699.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006699.01.T01 MTR_2g013130 98.958 96 1 0 17 112 427 522 1.19e-65 206
MsG0280006699.01.T01 MTR_2g013130 98.958 96 1 0 17 112 264 359 1.24e-65 202
MsG0280006699.01.T01 MTR_2g013130 98.958 96 1 0 17 112 412 507 1.63e-65 206
MsG0280006699.01.T01 MTR_2g013130 98.958 96 1 0 17 112 307 402 2.25e-65 202
MsG0280006699.01.T01 MTR_3g005670 59.574 94 38 0 18 111 532 625 1.82e-34 125
MsG0280006699.01.T01 MTR_3g005670 59.574 94 38 0 18 111 530 623 1.90e-34 124
MsG0280006699.01.T01 MTR_4g031680 56.383 94 41 0 18 111 480 573 2.80e-32 118
MsG0280006699.01.T01 MTR_3g005670 66.667 51 17 0 18 68 532 582 6.11e-18 78.2
MsG0280006699.01.T01 MTR_3g005670 66.667 51 17 0 18 68 530 580 6.66e-18 78.2
MsG0280006699.01.T01 MTR_3g005670 66.000 50 17 0 18 67 532 581 2.48e-17 76.3
MsG0280006699.01.T01 MTR_3g005670 66.000 50 17 0 18 67 530 579 2.53e-17 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006699.01.T01 AT1G60830 54.737 95 43 0 17 111 16 110 1.31e-34 115
MsG0280006699.01.T01 AT1G60830 54.737 95 43 0 17 111 16 110 1.31e-34 115
MsG0280006699.01.T01 AT1G60900 56.842 95 41 0 17 111 494 588 6.26e-32 117
MsG0280006699.01.T01 AT4G36690 55.319 94 42 0 17 110 456 549 1.08e-30 114
MsG0280006699.01.T01 AT4G36690 55.319 94 42 0 17 110 478 571 1.18e-30 114

Find 33 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCTAAATGGTAGGAAATT+TGG 0.114660 2:+5141660 MsG0280006699.01.T01:CDS
CTCTAAATGGTAGGAAATTT+GGG 0.201789 2:+5141661 MsG0280006699.01.T01:CDS
GTTTCTCTTGTAGGTGTTCT+TGG 0.203987 2:+5141599 MsG0280006699.01.T01:intron
CGGGATGAATGCCGCAAATT+TGG 0.236754 2:+5140654 MsG0280006699.01.T01:CDS
ACTGAACAATTAACTGATAA+TGG 0.287828 2:+5140603 MsG0280006699.01.T01:CDS
GACAGCTCTCCGTTTGGATT+TGG 0.294715 2:-5141313 None:intergenic
CTCTACCTTATTTCCTTTGA+AGG 0.306648 2:+5140572 MsG0280006699.01.T01:CDS
GAGCAGGTGAGGTGAAAATA+AGG 0.313702 2:-5140552 None:intergenic
GACGGCCTTCAAAGGAAATA+AGG 0.353040 2:-5140577 None:intergenic
TGGAGAATATGAAGAAATAT+TGG 0.357494 2:+5140623 MsG0280006699.01.T01:CDS
GGAGAGCTGTCTACAGGAAT+TGG 0.374888 2:+5141325 MsG0280006699.01.T01:CDS
TATGATTTGTAACCGATTGT+AGG 0.404522 2:+5141738 MsG0280006699.01.T01:exon
CCTGTAGACAGCTCTCCGTT+TGG 0.443182 2:-5141319 None:intergenic
CATTATATATGTAATAAACT+TGG 0.458814 2:-5141836 None:intergenic
ATGATTTGTAACCGATTGTA+GGG 0.489405 2:+5141739 MsG0280006699.01.T01:exon
CAACATGCATACCAAATTTG+CGG 0.500951 2:-5140665 None:intergenic
TCTCCGTTTGGATTTGGACG+AGG 0.503529 2:-5141307 None:intergenic
AGAAATATTGGAAGACATGC+GGG 0.510930 2:+5140635 MsG0280006699.01.T01:CDS
CCAAACGGAGAGCTGTCTAC+AGG 0.512561 2:+5141319 MsG0280006699.01.T01:CDS
CAAAGGAAATAAGGTAGAGC+AGG 0.515836 2:-5140568 None:intergenic
ATTGGAATGTACAGGGACCT+TGG 0.522185 2:+5141270 MsG0280006699.01.T01:intron
ATTATATCTCTCCCTACAAT+CGG 0.524407 2:-5141750 None:intergenic
CTCCGTTTGGATTTGGACGA+GGG 0.536853 2:-5141306 None:intergenic
ATCCCTCGTCCAAATCCAAA+CGG 0.557458 2:+5141304 MsG0280006699.01.T01:CDS
GAAATAAGGTAGAGCAGGTG+AGG 0.560468 2:-5140563 None:intergenic
AGTTAATTGTTCAGTAGTGA+CGG 0.571985 2:-5140595 None:intergenic
AGCAGGTGAGGTGAAAATAA+GGG 0.573177 2:-5140551 None:intergenic
TCAGTAGTGACGGCCTTCAA+AGG 0.579207 2:-5140585 None:intergenic
AAGAAATATTGGAAGACATG+CGG 0.592315 2:+5140634 MsG0280006699.01.T01:CDS
TCTAAATGGTAGGAAATTTG+GGG 0.622587 2:+5141662 MsG0280006699.01.T01:CDS
GCTGTCTACAGGAATTGGAA+AGG 0.661551 2:+5141330 MsG0280006699.01.T01:CDS
CTAAATGGTAGGAAATTTGG+GGG 0.702819 2:+5141663 MsG0280006699.01.T01:CDS
AGGGATAACAACATTCACCA+AGG 0.737659 2:-5141287 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATTATATATGTAATAAACT+TGG - Chr2:5141839-5141858 None:intergenic 15.0%
!! AGAAGAAAAATATCATAGTA+TGG + Chr2:5141713-5141732 MsG0280006699.01.T01:CDS 20.0%
!! GTTGTAAAACAAAAATTTGT+TGG + Chr2:5140993-5141012 MsG0280006699.01.T01:intron 20.0%
!! TATATAGTTAATTCTCTCTT+GGG + Chr2:5140935-5140954 MsG0280006699.01.T01:intron 20.0%
!! TTAAAAGTTTCAAATCACTA+TGG - Chr2:5141484-5141503 None:intergenic 20.0%
!! TTATATAGTTAATTCTCTCT+TGG + Chr2:5140934-5140953 MsG0280006699.01.T01:intron 20.0%
!!! AGTGATTTGAAACTTTTAAA+TGG + Chr2:5141485-5141504 MsG0280006699.01.T01:intron 20.0%
!!! ATACTATGATATTTTTCTTC+TGG - Chr2:5141714-5141733 None:intergenic 20.0%
!!! GTGATTTGAAACTTTTAAAT+GGG + Chr2:5141486-5141505 MsG0280006699.01.T01:intron 20.0%
! ACTGAACAATTAACTGATAA+TGG + Chr2:5140603-5140622 MsG0280006699.01.T01:CDS 25.0%
! TAGTTGTTTAATTGTGGTTT+CGG + Chr2:5141577-5141596 MsG0280006699.01.T01:intron 25.0%
! TATAATTTCTTGCACCTTAT+TGG + Chr2:5141252-5141271 MsG0280006699.01.T01:intron 25.0%
! TGGAGAATATGAAGAAATAT+TGG + Chr2:5140623-5140642 MsG0280006699.01.T01:CDS 25.0%
! TTTGATCGACATTTATAGTT+TGG + Chr2:5140876-5140895 MsG0280006699.01.T01:intron 25.0%
!! CTCATATATTACATTTTCTC+TGG + Chr2:5140742-5140761 MsG0280006699.01.T01:intron 25.0%
!! TATTTTACTGCAAGATCAAT+TGG + Chr2:5141168-5141187 MsG0280006699.01.T01:intron 25.0%
AAACTTAGAGTGACAAAAAG+TGG - Chr2:5141798-5141817 None:intergenic 30.0%
AAGAAATATTGGAAGACATG+CGG + Chr2:5140634-5140653 MsG0280006699.01.T01:CDS 30.0%
AGTTAATTGTTCAGTAGTGA+CGG - Chr2:5140598-5140617 None:intergenic 30.0%
ATTATATCTCTCCCTACAAT+CGG - Chr2:5141753-5141772 None:intergenic 30.0%
CAAACGTAGTTGTTTAATTG+TGG + Chr2:5141571-5141590 MsG0280006699.01.T01:intron 30.0%
CACAATTAAACAACTACGTT+TGG - Chr2:5141573-5141592 None:intergenic 30.0%
CAGAAAATGGCAAAGTAATA+TGG - Chr2:5140702-5140721 None:intergenic 30.0%
CTCTAAATGGTAGGAAATTT+GGG + Chr2:5141661-5141680 MsG0280006699.01.T01:CDS 30.0%
TCTAAATGGTAGGAAATTTG+GGG + Chr2:5141662-5141681 MsG0280006699.01.T01:CDS 30.0%
! AGCATAGTTTTCCAAAAACT+TGG - Chr2:5140822-5140841 None:intergenic 30.0%
! ATGATTTGTAACCGATTGTA+GGG + Chr2:5141739-5141758 MsG0280006699.01.T01:exon 30.0%
! CAAAAAATGCTCTAAATGGT+AGG + Chr2:5141652-5141671 MsG0280006699.01.T01:CDS 30.0%
! CAATATCTCATCCAAGTTTT+TGG + Chr2:5140808-5140827 MsG0280006699.01.T01:intron 30.0%
! TACATTTTCTCTGGTTAAGT+GGG + Chr2:5140751-5140770 MsG0280006699.01.T01:intron 30.0%
! TATGATTTGTAACCGATTGT+AGG + Chr2:5141738-5141757 MsG0280006699.01.T01:exon 30.0%
! TTACATTTTCTCTGGTTAAG+TGG + Chr2:5140750-5140769 MsG0280006699.01.T01:intron 30.0%
AGAAATATTGGAAGACATGC+GGG + Chr2:5140635-5140654 MsG0280006699.01.T01:CDS 35.0%
AGTGTCTTAGACCATTTCAA+CGG + Chr2:5141033-5141052 MsG0280006699.01.T01:intron 35.0%
CAACATGCATACCAAATTTG+CGG - Chr2:5140668-5140687 None:intergenic 35.0%
CCTATAACACCTATAATGAC+TGG - Chr2:5141114-5141133 None:intergenic 35.0%
CTAAATGGTAGGAAATTTGG+GGG + Chr2:5141663-5141682 MsG0280006699.01.T01:CDS 35.0%
CTCTCTTGGGACATATAAAA+TGG + Chr2:5140948-5140967 MsG0280006699.01.T01:intron 35.0%
GCACAACTTTAAGCAGAAAA+TGG - Chr2:5140715-5140734 None:intergenic 35.0%
GTTTCATACGCAAACTAAAG+TGG - Chr2:5141413-5141432 None:intergenic 35.0%
TCCAACAAATAAAGTATGCG+AGG + Chr2:5141536-5141555 MsG0280006699.01.T01:intron 35.0%
! CCAGTCATTATAGGTGTTAT+AGG + Chr2:5141111-5141130 MsG0280006699.01.T01:intron 35.0%
! CTCTACCTTATTTCCTTTGA+AGG + Chr2:5140572-5140591 MsG0280006699.01.T01:CDS 35.0%
! GCTCTAAATGGTAGGAAATT+TGG + Chr2:5141660-5141679 MsG0280006699.01.T01:CDS 35.0%
! GCTGCAAAAAATGCTCTAAA+TGG + Chr2:5141648-5141667 MsG0280006699.01.T01:CDS 35.0%
!! TTTTTGGAAAACTATGCTCG+AGG + Chr2:5140824-5140843 MsG0280006699.01.T01:intron 35.0%
ACACCTATAATGACTGGCAA+AGG - Chr2:5141108-5141127 None:intergenic 40.0%
AGCAGGTGAGGTGAAAATAA+GGG - Chr2:5140554-5140573 None:intergenic 40.0%
AGGGATAACAACATTCACCA+AGG - Chr2:5141290-5141309 None:intergenic 40.0%
ATACAAATTTCACGCACCTC+GGG + Chr2:5141453-5141472 MsG0280006699.01.T01:intron 40.0%
CAAAGGAAATAAGGTAGAGC+AGG - Chr2:5140571-5140590 None:intergenic 40.0%
CACCTATAATGACTGGCAAA+GGG - Chr2:5141107-5141126 None:intergenic 40.0%
CATACAAATTTCACGCACCT+CGG + Chr2:5141452-5141471 MsG0280006699.01.T01:intron 40.0%
CCAGTAACGTCTTTGTTCAT+GGG + Chr2:5141218-5141237 MsG0280006699.01.T01:intron 40.0%
CTGATAGCAATTCAGTACGA+TGG + Chr2:5140971-5140990 MsG0280006699.01.T01:intron 40.0%
GCACCTTATTGGAATGTACA+GGG + Chr2:5141263-5141282 MsG0280006699.01.T01:intron 40.0%
GTGTCTTAGACCATTTCAAC+GGG + Chr2:5141034-5141053 MsG0280006699.01.T01:intron 40.0%
GTTTCTCTTGTAGGTGTTCT+TGG + Chr2:5141599-5141618 MsG0280006699.01.T01:intron 40.0%
TACTCTATGTCCCGTTGAAA+TGG - Chr2:5141047-5141066 None:intergenic 40.0%
TCCAGTAACGTCTTTGTTCA+TGG + Chr2:5141217-5141236 MsG0280006699.01.T01:intron 40.0%
TGCACCTTATTGGAATGTAC+AGG + Chr2:5141262-5141281 MsG0280006699.01.T01:intron 40.0%
TTTAAATGGGTCGAGCTTTG+TGG + Chr2:5141499-5141518 MsG0280006699.01.T01:intron 40.0%
! GCCTCGCATACTTTATTTGT+TGG - Chr2:5141540-5141559 None:intergenic 40.0%
ATCCCTCGTCCAAATCCAAA+CGG + Chr2:5141304-5141323 MsG0280006699.01.T01:CDS 45.0%
ATTGGAATGTACAGGGACCT+TGG + Chr2:5141270-5141289 MsG0280006699.01.T01:intron 45.0%
CCCATGAACAAAGACGTTAC+TGG - Chr2:5141221-5141240 None:intergenic 45.0%
GAAATAAGGTAGAGCAGGTG+AGG - Chr2:5140566-5140585 None:intergenic 45.0%
GACGGCCTTCAAAGGAAATA+AGG - Chr2:5140580-5140599 None:intergenic 45.0%
GAGCAGGTGAGGTGAAAATA+AGG - Chr2:5140555-5140574 None:intergenic 45.0%
GCTGTCTACAGGAATTGGAA+AGG + Chr2:5141330-5141349 MsG0280006699.01.T01:CDS 45.0%
GGTCCCTGTACATTCCAATA+AGG - Chr2:5141269-5141288 None:intergenic 45.0%
GTCCCTTTGCCAGTCATTAT+AGG + Chr2:5141102-5141121 MsG0280006699.01.T01:intron 45.0%
GTGGTTTCGGTTTCTCTTGT+AGG + Chr2:5141590-5141609 MsG0280006699.01.T01:intron 45.0%
CGGGATGAATGCCGCAAATT+TGG + Chr2:5140654-5140673 MsG0280006699.01.T01:CDS 50.0%
CTCCGTTTGGATTTGGACGA+GGG - Chr2:5141309-5141328 None:intergenic 50.0%
CTCTGGTTAAGTGGGTGAGT+TGG + Chr2:5140759-5140778 MsG0280006699.01.T01:intron 50.0%
GACAGCTCTCCGTTTGGATT+TGG - Chr2:5141316-5141335 None:intergenic 50.0%
GGAGAGCTGTCTACAGGAAT+TGG + Chr2:5141325-5141344 MsG0280006699.01.T01:CDS 50.0%
TCAGTAGTGACGGCCTTCAA+AGG - Chr2:5140588-5140607 None:intergenic 50.0%
TCTCCGTTTGGATTTGGACG+AGG - Chr2:5141310-5141329 None:intergenic 50.0%
AAATTTCACGCACCTCGGGC+TGG + Chr2:5141457-5141476 MsG0280006699.01.T01:intron 55.0%
AATTTCACGCACCTCGGGCT+GGG + Chr2:5141458-5141477 MsG0280006699.01.T01:intron 55.0%
CCAAACGGAGAGCTGTCTAC+AGG + Chr2:5141319-5141338 MsG0280006699.01.T01:CDS 55.0%
CCTGTAGACAGCTCTCCGTT+TGG - Chr2:5141322-5141341 None:intergenic 55.0%
AATCACTATGGCCCAGCCCG+AGG - Chr2:5141472-5141491 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 5140543 5141870 5140543 ID=MsG0280006699.01;Name=MsG0280006699.01
Chr2 mRNA 5140543 5141870 5140543 ID=MsG0280006699.01.T01;Parent=MsG0280006699.01;Name=MsG0280006699.01.T01;_AED=0.49;_eAED=0.55;_QI=0|1|0.66|1|1|1|3|121|112
Chr2 exon 5140543 5140675 5140543 ID=MsG0280006699.01.T01:exon:1965;Parent=MsG0280006699.01.T01
Chr2 exon 5141284 5141351 5141284 ID=MsG0280006699.01.T01:exon:1966;Parent=MsG0280006699.01.T01
Chr2 exon 5141612 5141870 5141612 ID=MsG0280006699.01.T01:exon:1967;Parent=MsG0280006699.01.T01
Chr2 CDS 5140543 5140675 5140543 ID=MsG0280006699.01.T01:cds;Parent=MsG0280006699.01.T01
Chr2 CDS 5141284 5141351 5141284 ID=MsG0280006699.01.T01:cds;Parent=MsG0280006699.01.T01
Chr2 CDS 5141612 5141749 5141612 ID=MsG0280006699.01.T01:cds;Parent=MsG0280006699.01.T01
Chr2 three_prime_UTR 5141750 5141870 5141750 ID=MsG0280006699.01.T01:three_prime_utr;Parent=MsG0280006699.01.T01
Gene Sequence

>MsG0280006699.01.T01

TTGACTGACCCTTATTTTCACCTCACCTGCTCTACCTTATTTCCTTTGAAGGCCGTCACTACTGAACAATTAACTGATAATGGAGAATATGAAGAAATATTGGAAGACATGCGGGATGAATGCCGCAAATTTGGGACCTTGGTGAATGTTGTTATCCCTCGTCCAAATCCAAACGGAGAGCTGTCTACAGGAATTGGAAAGGTGTTCTTGGAATACTCTGATTGTACTGCTTGTTTAGCTGCAAAAAATGCTCTAAATGGTAGGAAATTTGGGGGTAGTATTGTGACTGCATTTTATTATCCAGAAGAAAAATATCATAGTATGGATTATGATTTGTAA
Protein sequence

>MsG0280006699.01.T01

LTDPYFHLTCSTLFPLKAVTTEQLTDNGEYEEILEDMRDECRKFGTLVNVVIPRPNPNGELSTGIGKVFLEYSDCTACLAAKNALNGRKFGGSIVTAFYYPEEKYHSMDYDL*