AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680031873.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680031873.01.T01 MTR_6g034190 84.762 315 48 0 1 315 1 315 0.0 542
MsG0680031873.01.T01 MTR_2g070780 53.968 315 138 2 1 314 1 309 6.29e-105 311
MsG0680031873.01.T01 MTR_2g072240 53.846 312 127 5 11 315 4 305 1.29e-102 308
MsG0680031873.01.T01 MTR_2g071700 52.961 304 133 3 18 317 19 316 1.01e-95 287
MsG0680031873.01.T01 MTR_2g070660 38.384 198 87 4 1 196 1 165 4.97e-31 115
MsG0680031873.01.T01 MTR_1g016310 27.106 273 140 9 3 265 7 230 4.90e-14 72.0
MsG0680031873.01.T01 MTR_1g016310 27.106 273 140 9 3 265 7 230 9.70e-14 71.6
MsG0680031873.01.T01 MTR_2g091145 25.373 268 153 7 4 266 8 233 4.85e-13 69.7
MsG0680031873.01.T01 MTR_1g021825 24.812 266 154 7 1 265 1 221 6.30e-12 66.2
MsG0680031873.01.T01 MTR_1g013580 25.000 268 151 9 1 261 1 225 1.19e-11 65.5
MsG0680031873.01.T01 MTR_1g021825 25.591 254 143 7 13 265 84 292 1.49e-11 65.5
MsG0680031873.01.T01 MTR_0743s0010 42.647 68 38 1 7 73 4 71 3.65e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 13 271 6.30e-19 87.4
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 52 310 6.75e-19 87.4
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 52 310 7.76e-19 86.7
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 52 310 8.18e-19 87.0
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 52 310 8.18e-19 87.0
MsG0680031873.01.T01 AT1G80960 28.231 294 172 7 19 308 52 310 8.18e-19 87.0
MsG0680031873.01.T01 AT5G18780 25.424 295 163 13 19 298 13 265 2.30e-11 64.3
MsG0680031873.01.T01 AT5G18780 25.424 295 163 13 19 298 13 265 2.30e-11 64.3
MsG0680031873.01.T01 AT5G18780 25.839 298 158 14 19 298 13 265 3.67e-11 63.9
MsG0680031873.01.T01 AT5G18780 25.839 298 158 14 19 298 13 265 3.67e-11 63.9
MsG0680031873.01.T01 AT3G44810 25.581 258 137 8 19 266 9 221 6.47e-11 63.5

Find 49 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAGAAATCACATTTATTA+AGG 0.192778 6:+28765582 None:intergenic
TCCCTTGCACGGCGAGTTAT+TGG 0.219472 6:+28766420 None:intergenic
AAGCTGTAATATTCGACATT+TGG 0.278791 6:-28765933 MsG0680031873.01.T01:CDS
AATGCTTCAATATTTGTCTT+TGG 0.298181 6:+28766472 None:intergenic
GCACGGAGGATATAAAGTTT+TGG 0.321853 6:+28765410 None:intergenic
AGCTGTAATATTCGACATTT+GGG 0.343909 6:-28765932 MsG0680031873.01.T01:CDS
TCCAACTTTGCATTATCTTC+AGG 0.361121 6:+28766019 None:intergenic
TTTGTCTTTGGTCAAAACTA+AGG 0.374750 6:+28766484 None:intergenic
CTTAATAAATGTGATTTCTC+TGG 0.377879 6:-28765581 MsG0680031873.01.T01:CDS
TATAATGATGTTAAAAGCTT+GGG 0.385851 6:-28765386 MsG0680031873.01.T01:CDS
AGAGAAATCACATTTATTAA+GGG 0.394672 6:+28765583 None:intergenic
TCAAAACCTGGTTGAGATCA+AGG 0.397664 6:+28765690 None:intergenic
CGGGCAAGATAGACGAACTT+TGG 0.404187 6:-28765786 MsG0680031873.01.T01:CDS
TTATAATGATGTTAAAAGCT+TGG 0.440622 6:-28765387 MsG0680031873.01.T01:CDS
ATCTTTATGAATAGAAATGA+TGG 0.441341 6:+28765448 None:intergenic
TCCTGAAGATAATGCAAAGT+TGG 0.447683 6:-28766020 MsG0680031873.01.T01:CDS
AATTGAGAAAGGGGTGGTAA+AGG 0.457097 6:-28765864 MsG0680031873.01.T01:CDS
AAACTAGTGAAAACCTCAAA+AGG 0.471505 6:+28765758 None:intergenic
ATAAAAGTTAGAAGTACATC+AGG 0.475341 6:+28766591 None:intergenic
ATGAAGAAATTAATTGAGAA+AGG 0.477964 6:-28765875 MsG0680031873.01.T01:CDS
GGGGTGGTAAAGGTTTCAAT+TGG 0.478107 6:-28765854 MsG0680031873.01.T01:CDS
TTCAACACACACTTCATTGA+GGG 0.487816 6:+28765658 None:intergenic
TGAAGAAATTAATTGAGAAA+GGG 0.489006 6:-28765874 MsG0680031873.01.T01:CDS
CTAGTGTGCTTTCCAATCGT+TGG 0.489038 6:-28766533 MsG0680031873.01.T01:CDS
TGCACGGCGAGTTATTGGTT+CGG 0.493921 6:+28766425 None:intergenic
AATCACATTTATTAAGGGTG+AGG 0.498335 6:+28765588 None:intergenic
GTTGGTTTCTGCGGCTAACA+TGG 0.503436 6:-28765489 MsG0680031873.01.T01:CDS
TTGGGTATGAGTTGTGTCAA+TGG 0.506616 6:-28765914 MsG0680031873.01.T01:CDS
TATGAAAGTGCAAAAGATGT+TGG 0.507676 6:-28765507 MsG0680031873.01.T01:CDS
CAAAACCTGGTTGAGATCAA+GGG 0.512705 6:+28765691 None:intergenic
AACCAATAACTCGCCGTGCA+AGG 0.516433 6:-28766422 MsG0680031873.01.T01:CDS
ACCAATAACTCGCCGTGCAA+GGG 0.518356 6:-28766421 MsG0680031873.01.T01:CDS
TGCAAGGGATGTTCGTCCTA+AGG 0.524559 6:-28766406 MsG0680031873.01.T01:intron
CAATCATAGATAAACACATT+GGG 0.525328 6:-28765964 MsG0680031873.01.T01:CDS
TTTAATGTGATATAGATTCG+TGG 0.529319 6:-28766049 MsG0680031873.01.T01:intron
GAAGAAATTAATTGAGAAAG+GGG 0.538436 6:-28765873 MsG0680031873.01.T01:CDS
AATAAATGTGATTTCTCTGG+AGG 0.548519 6:-28765578 MsG0680031873.01.T01:CDS
CCAATCGTTGGAAAACATTG+TGG 0.560442 6:-28766521 MsG0680031873.01.T01:CDS
ATTCAACACACACTTCATTG+AGG 0.560971 6:+28765657 None:intergenic
ACCTTCCCTTGATCTCAACC+AGG 0.578543 6:-28765696 MsG0680031873.01.T01:CDS
GCAAAAGATGTTGGTTTCTG+CGG 0.584479 6:-28765498 MsG0680031873.01.T01:CDS
TCAATCATAGATAAACACAT+TGG 0.600536 6:-28765965 MsG0680031873.01.T01:CDS
GAAATTAATTGAGAAAGGGG+TGG 0.635769 6:-28765870 MsG0680031873.01.T01:CDS
TATGATTGACATGATTAACA+TGG 0.651938 6:+28765979 None:intergenic
ACCTGGTTGAGATCAAGGGA+AGG 0.653409 6:+28765695 None:intergenic
TAGGACGAACATCCCTTGCA+CGG 0.661668 6:+28766409 None:intergenic
TCAATGGAGATGTTGTGCGG+TGG 0.696201 6:-28765898 MsG0680031873.01.T01:CDS
TAACATCATTATAAGCACGG+AGG 0.721649 6:+28765396 None:intergenic
GTGTCAATGGAGATGTTGTG+CGG 0.728030 6:-28765901 MsG0680031873.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAATAATTAGATTAATTAAA+TGG - Chr6:28765853-28765872 MsG0680031873.01.T01:CDS 10.0%
!!! AAACTAAGTTATATTATTTT+CGG - Chr6:28766227-28766246 MsG0680031873.01.T01:intron 10.0%
!!! ATTTATGATTTGATTTTTTT+GGG - Chr6:28765755-28765774 MsG0680031873.01.T01:CDS 10.0%
!!! TCTCAAATATTTTAAAATTT+TGG - Chr6:28766502-28766521 MsG0680031873.01.T01:CDS 10.0%
!!! AACTAAGTTATATTATTTTC+GGG - Chr6:28766228-28766247 MsG0680031873.01.T01:intron 15.0%
!!! AATTTTATCTTATAGGTTTT+AGG - Chr6:28765678-28765697 MsG0680031873.01.T01:CDS 15.0%
!!! ATATTTTTTTGAGATTCATT+TGG - Chr6:28765881-28765900 MsG0680031873.01.T01:CDS 15.0%
!!! GATTTATGATTTGATTTTTT+TGG - Chr6:28765754-28765773 MsG0680031873.01.T01:CDS 15.0%
!!! TAGTTTTTCAAAATAATCAT+GGG + Chr6:28766213-28766232 None:intergenic 15.0%
!!! TTAGTTTTTCAAAATAATCA+TGG + Chr6:28766214-28766233 None:intergenic 15.0%
!! AGAAAAATTGAAACAAAATC+TGG + Chr6:28765931-28765950 None:intergenic 20.0%
!! AGAGAAATCACATTTATTAA+GGG + Chr6:28766453-28766472 None:intergenic 20.0%
!! ATCTTTATGAATAGAAATGA+TGG + Chr6:28766588-28766607 None:intergenic 20.0%
!! ATGAAGAAATTAATTGAGAA+AGG - Chr6:28766158-28766177 MsG0680031873.01.T01:intron 20.0%
!! GAATCTATATCACATTAAAA+AGG + Chr6:28765983-28766002 None:intergenic 20.0%
!! TATAATGATGTTAAAAGCTT+GGG - Chr6:28766647-28766666 MsG0680031873.01.T01:CDS 20.0%
!! TGAAGAAATTAATTGAGAAA+GGG - Chr6:28766159-28766178 MsG0680031873.01.T01:intron 20.0%
!! TTATAATGATGTTAAAAGCT+TGG - Chr6:28766646-28766665 MsG0680031873.01.T01:CDS 20.0%
!!! ATCTACGAATTTTATCTTAT+AGG - Chr6:28765671-28765690 MsG0680031873.01.T01:CDS 20.0%
!!! TTTTAACATCATTATAAGCA+CGG + Chr6:28766643-28766662 None:intergenic 20.0%
! AATGCTTCAATATTTGTCTT+TGG + Chr6:28765564-28765583 None:intergenic 25.0%
! CAATCATAGATAAACACATT+GGG - Chr6:28766069-28766088 MsG0680031873.01.T01:intron 25.0%
! CAGAGAAATCACATTTATTA+AGG + Chr6:28766454-28766473 None:intergenic 25.0%
! CTTAATAAATGTGATTTCTC+TGG - Chr6:28766452-28766471 MsG0680031873.01.T01:CDS 25.0%
! GAAGAAATTAATTGAGAAAG+GGG - Chr6:28766160-28766179 MsG0680031873.01.T01:intron 25.0%
! TACAAGCCATTAAATTAATC+TGG - Chr6:28765811-28765830 MsG0680031873.01.T01:CDS 25.0%
! TATGATTGACATGATTAACA+TGG + Chr6:28766057-28766076 None:intergenic 25.0%
! TCAATCATAGATAAACACAT+TGG - Chr6:28766068-28766087 MsG0680031873.01.T01:intron 25.0%
! TTTAATGTGATATAGATTCG+TGG - Chr6:28765984-28766003 MsG0680031873.01.T01:CDS 25.0%
!! ATAAAAGTTAGAAGTACATC+AGG + Chr6:28765445-28765464 None:intergenic 25.0%
!! CGAATATTACAGCTTTTTAA+AGG + Chr6:28766095-28766114 None:intergenic 25.0%
!! GATTAATTTAATGGCTTGTA+CGG + Chr6:28765811-28765830 None:intergenic 25.0%
!!! GTTTTAGGATCTATGATTTT+TGG - Chr6:28765693-28765712 MsG0680031873.01.T01:CDS 25.0%
AAACTAGTGAAAACCTCAAA+AGG + Chr6:28766278-28766297 None:intergenic 30.0%
AAAGAAAAAAATGCGAGCTA+TGG - Chr6:28765390-28765409 MsG0680031873.01.T01:CDS 30.0%
AAGCTGTAATATTCGACATT+TGG - Chr6:28766100-28766119 MsG0680031873.01.T01:intron 30.0%
AATAAATGTGATTTCTCTGG+AGG - Chr6:28766455-28766474 MsG0680031873.01.T01:CDS 30.0%
AATCACATTTATTAAGGGTG+AGG + Chr6:28766448-28766467 None:intergenic 30.0%
AGCTGTAATATTCGACATTT+GGG - Chr6:28766101-28766120 MsG0680031873.01.T01:intron 30.0%
CTCGATCCAGATTAATTTAA+TGG + Chr6:28765820-28765839 None:intergenic 30.0%
TCTGGAAATTCGATTCTTTA+TGG + Chr6:28765913-28765932 None:intergenic 30.0%
TTTGTCTTTGGTCAAAACTA+AGG + Chr6:28765552-28765571 None:intergenic 30.0%
! AACTTTGGATTTACCTTTTG+AGG - Chr6:28766262-28766281 MsG0680031873.01.T01:intron 30.0%
! TACATCTAAGATTGTACCTT+AGG + Chr6:28765646-28765665 None:intergenic 30.0%
! TATGAAAGTGCAAAAGATGT+TGG - Chr6:28766526-28766545 MsG0680031873.01.T01:CDS 30.0%
!!! GATTTGATTTTTTTGGGATC+TGG - Chr6:28765761-28765780 MsG0680031873.01.T01:CDS 30.0%
!!! TTTTTGAGATTCATTTGGAG+AGG - Chr6:28765886-28765905 MsG0680031873.01.T01:CDS 30.0%
AAAAAAATGCGAGCTATGGA+GGG - Chr6:28765394-28765413 MsG0680031873.01.T01:CDS 35.0%
ATTCAACACACACTTCATTG+AGG + Chr6:28766379-28766398 None:intergenic 35.0%
GAAATTAATTGAGAAAGGGG+TGG - Chr6:28766163-28766182 MsG0680031873.01.T01:intron 35.0%
TAACATCATTATAAGCACGG+AGG + Chr6:28766640-28766659 None:intergenic 35.0%
TCCAACTTTGCATTATCTTC+AGG + Chr6:28766017-28766036 None:intergenic 35.0%
TCCTGAAGATAATGCAAAGT+TGG - Chr6:28766013-28766032 MsG0680031873.01.T01:CDS 35.0%
TTCAACACACACTTCATTGA+GGG + Chr6:28766378-28766397 None:intergenic 35.0%
! AATTTAATGGCTTGTACGGA+GGG + Chr6:28765807-28765826 None:intergenic 35.0%
! AATTTCTTTTCTGTCAGTCG+AGG - Chr6:28765465-28765484 MsG0680031873.01.T01:CDS 35.0%
! ACGGAGGATATAAAGTTTTG+GGG + Chr6:28766624-28766643 None:intergenic 35.0%
! CACGGAGGATATAAAGTTTT+GGG + Chr6:28766625-28766644 None:intergenic 35.0%
! TAATTTAATGGCTTGTACGG+AGG + Chr6:28765808-28765827 None:intergenic 35.0%
!!! TGAGGTTTTCACTAGTTTTG+AGG - Chr6:28766280-28766299 MsG0680031873.01.T01:intron 35.0%
AATTGAGAAAGGGGTGGTAA+AGG - Chr6:28766169-28766188 MsG0680031873.01.T01:intron 40.0%
CAAAACCTGGTTGAGATCAA+GGG + Chr6:28766345-28766364 None:intergenic 40.0%
CCAATCGTTGGAAAACATTG+TGG - Chr6:28765512-28765531 MsG0680031873.01.T01:CDS 40.0%
GAAAAAAATGCGAGCTATGG+AGG - Chr6:28765393-28765412 MsG0680031873.01.T01:CDS 40.0%
TCAAAACCTGGTTGAGATCA+AGG + Chr6:28766346-28766365 None:intergenic 40.0%
TTGGGTATGAGTTGTGTCAA+TGG - Chr6:28766119-28766138 MsG0680031873.01.T01:intron 40.0%
! ATTTAATGGCTTGTACGGAG+GGG + Chr6:28765806-28765825 None:intergenic 40.0%
! CCACAATGTTTTCCAACGAT+TGG + Chr6:28765515-28765534 None:intergenic 40.0%
! GCACGGAGGATATAAAGTTT+TGG + Chr6:28766626-28766645 None:intergenic 40.0%
! GGGTAAGAGTTTTCAAAACC+TGG + Chr6:28766358-28766377 None:intergenic 40.0%
!! GCAAAAGATGTTGGTTTCTG+CGG - Chr6:28766535-28766554 MsG0680031873.01.T01:CDS 40.0%
!!! TTTTGGGATCTGGTCCTTTT+TGG - Chr6:28765771-28765790 MsG0680031873.01.T01:CDS 40.0%
CTAGTGTGCTTTCCAATCGT+TGG - Chr6:28765500-28765519 MsG0680031873.01.T01:CDS 45.0%
GGGGTGGTAAAGGTTTCAAT+TGG - Chr6:28766179-28766198 MsG0680031873.01.T01:intron 45.0%
GTGTCAATGGAGATGTTGTG+CGG - Chr6:28766132-28766151 MsG0680031873.01.T01:intron 45.0%
! TTTAATGGCTTGTACGGAGG+GGG + Chr6:28765805-28765824 None:intergenic 45.0%
AACCAATAACTCGCCGTGCA+AGG - Chr6:28765611-28765630 MsG0680031873.01.T01:CDS 50.0%
ACCAATAACTCGCCGTGCAA+GGG - Chr6:28765612-28765631 MsG0680031873.01.T01:CDS 50.0%
ACCTGGTTGAGATCAAGGGA+AGG + Chr6:28766341-28766360 None:intergenic 50.0%
ACCTTCCCTTGATCTCAACC+AGG - Chr6:28766337-28766356 MsG0680031873.01.T01:intron 50.0%
CGGGCAAGATAGACGAACTT+TGG - Chr6:28766247-28766266 MsG0680031873.01.T01:intron 50.0%
TAGGACGAACATCCCTTGCA+CGG + Chr6:28765627-28765646 None:intergenic 50.0%
TCAATGGAGATGTTGTGCGG+TGG - Chr6:28766135-28766154 MsG0680031873.01.T01:intron 50.0%
TGCAAGGGATGTTCGTCCTA+AGG - Chr6:28765627-28765646 MsG0680031873.01.T01:CDS 50.0%
! GTTGGTTTCTGCGGCTAACA+TGG - Chr6:28766544-28766563 MsG0680031873.01.T01:CDS 50.0%
! TGCACGGCGAGTTATTGGTT+CGG + Chr6:28765611-28765630 None:intergenic 50.0%
TCCCTTGCACGGCGAGTTAT+TGG + Chr6:28765616-28765635 None:intergenic 55.0%
AGGGGGTGGAGGGACCAAAA+AGG + Chr6:28765788-28765807 None:intergenic 60.0%
! AATGGCTTGTACGGAGGGGG+TGG + Chr6:28765802-28765821 None:intergenic 60.0%
GCTTGTACGGAGGGGGTGGA+GGG + Chr6:28765798-28765817 None:intergenic 65.0%
GGCTTGTACGGAGGGGGTGG+AGG + Chr6:28765799-28765818 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr6 gene 28765376 28766679 28765376 ID=MsG0680031873.01;Name=MsG0680031873.01
Chr6 mRNA 28765376 28766679 28765376 ID=MsG0680031873.01.T01;Parent=MsG0680031873.01;Name=MsG0680031873.01.T01;_AED=0.31;_eAED=0.31;_QI=0|0|0|1|1|1|2|0|317
Chr6 exon 28766407 28766679 28766407 ID=MsG0680031873.01.T01:exon:14714;Parent=MsG0680031873.01.T01
Chr6 exon 28765376 28766056 28765376 ID=MsG0680031873.01.T01:exon:14713;Parent=MsG0680031873.01.T01
Chr6 CDS 28766407 28766679 28766407 ID=MsG0680031873.01.T01:cds;Parent=MsG0680031873.01.T01
Chr6 CDS 28765376 28766056 28765376 ID=MsG0680031873.01.T01:cds;Parent=MsG0680031873.01.T01
Gene Sequence

>MsG0680031873.01.T01

ATGGCGGAAAGAAAAAAGAAAAAAATGCGAGCTATGGAGGGAGAAGCATATATGATCAATAGTCTTCCTGATGTACTTCTAACTTTTATAATTTCTTTTCTGTCAGTCGAGGAAGCTGTGAGAACTAGTGTGCTTTCCAATCGTTGGAAAACATTGTGGAAGTACTCTTTTCACCTTAGTTTTGACCAAAGACAAATATTGAAGCATTTGATCAAAATTGACAATCAAAATTCCGAACCAATAACTCGCCGTGCAAGGGATGTTCGTCCTAAGATTCGTGGAATTTATCCTGAAGATAATGCAAAGTTGGATACAGTTGTTGAAGCGTCCATGTTAATCATGTCAATCATAGATAAACACATTGGGCCTTTAAAAAGCTGTAATATTCGACATTTGGGTATGAGTTGTGTCAATGGAGATGTTGTGCGGTGGATGAAGAAATTAATTGAGAAAGGGGTGGTAAAGGTTTCAATTGGACTTGAGTCCCATGATTATTTTGAAAAACTAAGTTATATTATTTTCGGGCAAGATAGACGAACTTTGGATTTACCTTTTGAGGTTTTCACTAGTTTTGAGGTTCTTGAGTTGAATCATTATTATTTTATAACTACACCTTCCCTTGATCTCAACCAGGTTTTGAAAACTCTTACCCTCAATGAAGTGTGTGTTGAATCAAACAATTTTCAAGAGATTATTTCTCACTGTTCATTTCTTGAAAACCTCACCCTTAATAAATGTGATTTCTCTGGAGGTGAAGTTAACATTAATAGTTCAAGTCTCAAATATTTTAAAATTTTGGATATGAAAGTGCAAAAGATGTTGGTTTCTGCGGCTAACATGGAAGTCATAGAGATTGAATCCATCATTTCTATTCATAAAGATCTAGCATTTGAGACCCCAAAACTTTATATCCTCCGTGCTTATAATGATGTTAAAAGCTTGGGCAATATTTGA
Protein sequence

>MsG0680031873.01.T01

MAERKKKKMRAMEGEAYMINSLPDVLLTFIISFLSVEEAVRTSVLSNRWKTLWKYSFHLSFDQRQILKHLIKIDNQNSEPITRRARDVRPKIRGIYPEDNAKLDTVVEASMLIMSIIDKHIGPLKSCNIRHLGMSCVNGDVVRWMKKLIEKGVVKVSIGLESHDYFEKLSYIIFGQDRRTLDLPFEVFTSFEVLELNHYYFITTPSLDLNQVLKTLTLNEVCVESNNFQEIISHCSFLENLTLNKCDFSGGEVNINSSSLKYFKILDMKVQKMLVSAANMEVIEIESIISIHKDLAFETPKLYILRAYNDVKSLGNI*