AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280007727.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280007727.01.T01 MTR_2g030630 96.053 76 3 0 1 76 1263 1338 9.22e-47 158
MsG0280007727.01.T01 MTR_8g088370 49.254 67 34 0 1 67 1310 1376 2.44e-18 77.8
MsG0280007727.01.T01 MTR_2g030160 50.746 67 33 0 1 67 775 841 2.96e-18 77.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280007727.01.T01 AT3G16620 67.105 76 23 1 1 74 1014 1089 1.04e-33 121
MsG0280007727.01.T01 AT2G16640 66.667 75 24 1 1 74 1132 1206 1.16e-33 121
MsG0280007727.01.T01 AT2G16640 66.667 75 24 1 1 74 1132 1206 1.16e-33 121
MsG0280007727.01.T01 AT2G16640 66.667 75 24 1 1 74 1132 1206 1.16e-33 121
MsG0280007727.01.T01 AT4G02510 54.386 57 26 0 3 59 1427 1483 1.38e-17 75.5
MsG0280007727.01.T01 AT4G02510 54.386 57 26 0 3 59 1427 1483 1.38e-17 75.5
MsG0280007727.01.T01 AT4G02510 54.386 57 26 0 3 59 1427 1483 1.38e-17 75.5
MsG0280007727.01.T01 AT4G02510 54.386 57 26 0 3 59 1427 1483 1.38e-17 75.5

Find 20 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTACTTAAGAAGGTTAT+TGG 0.154134 2:+19699687 MsG0280007727.01.T01:CDS
CAGCTTCAAATTGCTTTGAT+TGG 0.306661 2:+19699657 MsG0280007727.01.T01:CDS
AGCCCCACGATTGTTCAAAT+TGG 0.328584 2:-19699601 None:intergenic
CCTTCTTAAGTAGAGGGATT+AGG 0.368598 2:-19699680 None:intergenic
CCTAATCCCTCTACTTAAGA+AGG 0.435437 2:+19699680 MsG0280007727.01.T01:CDS
TTGGGCTTTCTGTTATGGAT+TGG 0.441505 2:+19699502 None:intergenic
AATTTGAACAATCGTGGGGC+TGG 0.464858 2:+19699603 MsG0280007727.01.T01:CDS
TGGCATGGAGATCTTGCTGT+TGG 0.466753 2:+19699522 MsG0280007727.01.T01:CDS
GGCATGGAGATCTTGCTGTT+GGG 0.467831 2:+19699523 MsG0280007727.01.T01:CDS
CTTTCTGTTATGGATTGGCA+TGG 0.513103 2:+19699507 None:intergenic
TTACAATCACAAATTCCCAT+TGG 0.513109 2:+19699552 MsG0280007727.01.T01:CDS
CAATAACCTTCTTAAGTAGA+GGG 0.523046 2:-19699686 None:intergenic
AGGTTTGTATACCGTCCAAT+GGG 0.532753 2:-19699567 None:intergenic
CCAATAACCTTCTTAAGTAG+AGG 0.541542 2:-19699687 None:intergenic
AATCACAAATTCCCATTGGA+CGG 0.544278 2:+19699556 MsG0280007727.01.T01:CDS
CGAGCCAATTTGAACAATCG+TGG 0.556311 2:+19699597 MsG0280007727.01.T01:CDS
AAGGTTTGTATACCGTCCAA+TGG 0.579505 2:-19699568 None:intergenic
GAGCCAATTTGAACAATCGT+GGG 0.581635 2:+19699598 MsG0280007727.01.T01:CDS
TCAAATTGGCTCGTGCAACA+AGG 0.613154 2:-19699587 None:intergenic
AGCCAATTTGAACAATCGTG+GGG 0.683448 2:+19699599 MsG0280007727.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTAAACAATTGCAGTT+TGG + Chr2:19699711-19699730 MsG0280007727.01.T01:CDS 20.0%
CAATAACCTTCTTAAGTAGA+GGG - Chr2:19699689-19699708 None:intergenic 30.0%
TTACAATCACAAATTCCCAT+TGG + Chr2:19699552-19699571 MsG0280007727.01.T01:CDS 30.0%
AATCACAAATTCCCATTGGA+CGG + Chr2:19699556-19699575 MsG0280007727.01.T01:CDS 35.0%
CAGCTTCAAATTGCTTTGAT+TGG + Chr2:19699657-19699676 MsG0280007727.01.T01:CDS 35.0%
CCAATAACCTTCTTAAGTAG+AGG - Chr2:19699690-19699709 None:intergenic 35.0%
CCTCTACTTAAGAAGGTTAT+TGG + Chr2:19699687-19699706 MsG0280007727.01.T01:CDS 35.0%
AAGGTTTGTATACCGTCCAA+TGG - Chr2:19699571-19699590 None:intergenic 40.0%
AGCCAATTTGAACAATCGTG+GGG + Chr2:19699599-19699618 MsG0280007727.01.T01:CDS 40.0%
AGGTTTGTATACCGTCCAAT+GGG - Chr2:19699570-19699589 None:intergenic 40.0%
CCTAATCCCTCTACTTAAGA+AGG + Chr2:19699680-19699699 MsG0280007727.01.T01:CDS 40.0%
CCTTCTTAAGTAGAGGGATT+AGG - Chr2:19699683-19699702 None:intergenic 40.0%
GAGCCAATTTGAACAATCGT+GGG + Chr2:19699598-19699617 MsG0280007727.01.T01:CDS 40.0%
AATTTGAACAATCGTGGGGC+TGG + Chr2:19699603-19699622 MsG0280007727.01.T01:CDS 45.0%
AGCCCCACGATTGTTCAAAT+TGG - Chr2:19699604-19699623 None:intergenic 45.0%
CGAGCCAATTTGAACAATCG+TGG + Chr2:19699597-19699616 MsG0280007727.01.T01:CDS 45.0%
!! TCAAATTGGCTCGTGCAACA+AGG - Chr2:19699590-19699609 None:intergenic 45.0%
! TGGCATGGAGATCTTGCTGT+TGG + Chr2:19699522-19699541 MsG0280007727.01.T01:CDS 50.0%
!! GGCATGGAGATCTTGCTGTT+GGG + Chr2:19699523-19699542 MsG0280007727.01.T01:CDS 50.0%
Chromosome Type Strat End Strand Name
Chr2 gene 19699516 19699746 19699516 ID=MsG0280007727.01;Name=MsG0280007727.01
Chr2 mRNA 19699516 19699746 19699516 ID=MsG0280007727.01.T01;Parent=MsG0280007727.01;Name=MsG0280007727.01.T01;_AED=0.48;_eAED=0.48;_QI=0|-1|0|1|-1|0|1|0|76
Chr2 exon 19699516 19699746 19699516 ID=MsG0280007727.01.T01:exon:1844;Parent=MsG0280007727.01.T01
Chr2 CDS 19699516 19699746 19699516 ID=MsG0280007727.01.T01:cds;Parent=MsG0280007727.01.T01
Gene Sequence

>MsG0280007727.01.T01

ATGGATTGGCATGGAGATCTTGCTGTTGGGTGCAATTTACAATCACAAATTCCCATTGGACGGTATACAAACCTTGTTGCACGAGCCAATTTGAACAATCGTGGGGCTGGACAAATTAGCATTCGATTGAATAGTTCAGAACAGCTTCAAATTGCTTTGATTGGCCTAATCCCTCTACTTAAGAAGGTTATTGGTTATTTTAAACAATTGCAGTTTGGACAAGATTATTGA

Protein sequence

>MsG0280007727.01.T01

MDWHGDLAVGCNLQSQIPIGRYTNLVARANLNNRGAGQISIRLNSSEQLQIALIGLIPLLKKVIGYFKQLQFGQDY*