AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0780040158.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0780040158.01.T01 MTR_7g085490 54.626 227 33 4 1 183 155 355 1.19e-62 197
MsG0780040158.01.T01 MTR_7g085470 90.476 42 4 0 89 130 240 281 1.02e-18 82.0
MsG0780040158.01.T01 MTR_2g104050 63.333 60 22 0 89 148 259 318 4.53e-17 78.2
MsG0780040158.01.T01 MTR_4g010050 85.366 41 6 0 89 129 259 299 2.06e-16 76.6
MsG0780040158.01.T01 MTR_7g085570 88.889 36 4 0 95 130 211 246 7.74e-15 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0780040158.01.T01 AT1G64770 37.054 224 74 4 1 182 150 348 1.39e-31 117
MsG0780040158.01.T01 AT1G64770 41.935 124 30 1 1 82 150 273 1.85e-21 89.4
MsG0780040158.01.T01 AT1G64770 41.935 124 30 1 1 82 150 273 2.99e-21 89.7
MsG0780040158.01.T01 AT1G48900 88.095 42 5 0 89 130 259 300 7.36e-19 83.6
MsG0780040158.01.T01 AT1G48900 88.095 42 5 0 89 130 259 300 7.36e-19 83.6
MsG0780040158.01.T01 AT1G15310 85.714 42 6 0 89 130 259 300 7.04e-18 80.9
MsG0780040158.01.T01 AT5G49500 82.927 41 7 0 89 129 139 179 1.11e-15 74.3
MsG0780040158.01.T01 AT5G49500 80.952 42 8 0 89 130 261 302 1.32e-15 74.3

Find 38 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAAGCCTTTGTTCTTTCTT+TGG 0.192458 7:+73822033 None:intergenic
CTCTTCTCTTAAATCTAAAA+TGG 0.228276 7:+73822278 None:intergenic
CCGTTTGTTAGTCGTCTATT+AGG 0.257109 7:-73821348 MsG0780040158.01.T01:CDS
ATAGCATTGGTTAGAGTAAC+AGG 0.282402 7:+73822307 None:intergenic
CACTGGTCCTGCTTCAATAT+TGG 0.282753 7:-73820588 MsG0780040158.01.T01:CDS
AAAGCCTTTGTTCTTTCTTT+GGG 0.310843 7:+73822034 None:intergenic
TTGGTTAGAGTAACAGGTTT+TGG 0.328743 7:+73822313 None:intergenic
TTATTCTCAAGGAGAGTAAT+AGG 0.341075 7:+73822082 None:intergenic
AGAGGTGGTGCGGCAATTAA+AGG 0.342398 7:-73822259 MsG0780040158.01.T01:intron
AAAATATGAAATCATTGATC+AGG 0.416361 7:-73821994 MsG0780040158.01.T01:intron
GTCTATTAGGCATGGATGAC+TGG 0.428294 7:-73821335 MsG0780040158.01.T01:intron
AAGAGTCCGGTCATATTCAT+AGG 0.428991 7:-73821414 MsG0780040158.01.T01:CDS
CATAGGAACTGGTGAACATA+TGG 0.442484 7:-73821397 MsG0780040158.01.T01:CDS
TATTTCTCTGACATGGAACC+AGG 0.444982 7:+73820630 None:intergenic
CTTTCGATATTTCTCTGACA+TGG 0.457038 7:+73820623 None:intergenic
CCGGTCATATTCATAGGAAC+TGG 0.464779 7:-73821408 MsG0780040158.01.T01:CDS
GCCTTTGTTCTTTCTTTGGG+AGG 0.467470 7:+73822037 None:intergenic
CTGAATTGAAGCCAGGTTCA+TGG 0.470856 7:-73822120 MsG0780040158.01.T01:intron
TTGCCATGCTCACAGGATAG+AGG 0.487005 7:+73822362 None:intergenic
ATTCTACATGCGTCGAGCCC+TGG 0.497044 7:-73820648 MsG0780040158.01.T01:CDS
GAGCCTGTGACTGTGAATCC+TGG 0.502873 7:-73820566 MsG0780040158.01.T01:CDS
TCACCAGGATTCACAGTCAC+AGG 0.511522 7:+73820563 None:intergenic
TGTTAGTCGTCTATTAGGCA+TGG 0.525929 7:-73821343 MsG0780040158.01.T01:CDS
ACTGCTGTTGCCATGCTCAC+AGG 0.530706 7:+73822355 None:intergenic
AAAATGGCTTAATATAGCAT+TGG 0.535095 7:+73822294 None:intergenic
TGTTGCAGCAACAAAGAGTC+CGG 0.545682 7:-73821427 MsG0780040158.01.T01:CDS
TTTAGATTTAAGAGAAGAGG+TGG 0.556422 7:-73822274 MsG0780040158.01.T01:CDS
ACAGGCTCCAATATTGAAGC+AGG 0.556496 7:+73820581 None:intergenic
CCTAATAGACGACTAACAAA+CGG 0.558547 7:+73821348 None:intergenic
GTCCCTCTATCCTGTGAGCA+TGG 0.565166 7:-73822365 MsG0780040158.01.T01:CDS
CTCTACTCATCTTATTCTCA+AGG 0.565176 7:+73822071 None:intergenic
TGCCATGCTCACAGGATAGA+GGG 0.569663 7:+73822363 None:intergenic
CCAGTTCCTATGAATATGAC+CGG 0.578609 7:+73821408 None:intergenic
CCAGGTTCATGGACTCAACA+AGG 0.611546 7:-73822109 MsG0780040158.01.T01:intron
CATGTCAGAGAAATATCGAA+AGG 0.623193 7:-73820622 MsG0780040158.01.T01:CDS
ACCTCCCAAAGAAAGAACAA+AGG 0.664272 7:-73822038 MsG0780040158.01.T01:CDS
ATTTAAGAGAAGAGGTGGTG+CGG 0.665156 7:-73822269 MsG0780040158.01.T01:CDS
ATTTCTCTGACATGGAACCA+GGG 0.668077 7:+73820631 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATATTTTTTTTATGTGTT+GGG - Chr7:73821413-73821432 MsG0780040158.01.T01:CDS 10.0%
!!! GATATATTTTTTTTATGTGT+TGG - Chr7:73821412-73821431 MsG0780040158.01.T01:CDS 15.0%
!!! TAATCATTCTAGAATTTAAT+TGG + Chr7:73822122-73822141 None:intergenic 15.0%
!! AAAATATGAAATCATTGATC+AGG - Chr7:73820902-73820921 MsG0780040158.01.T01:intron 20.0%
!! ACTTTAATTCTATTTACTCA+AGG - Chr7:73822030-73822049 MsG0780040158.01.T01:CDS 20.0%
!! TGAGTAAATAGAATTAAAGT+CGG + Chr7:73822030-73822049 None:intergenic 20.0%
!!! ATGATTTCATATTTTGAAAG+TGG + Chr7:73821919-73821938 None:intergenic 20.0%
!!! TCAACAATTGAATTTTTTAG+CGG + Chr7:73821348-73821367 None:intergenic 20.0%
!!! TCAATGATTTCATATTTTGA+AGG + Chr7:73820900-73820919 None:intergenic 20.0%
! AAAATGGCTTAATATAGCAT+TGG + Chr7:73820605-73820624 None:intergenic 25.0%
! AAAGTCTTCACTCAATAATA+TGG + Chr7:73822186-73822205 None:intergenic 25.0%
! AACTCATGATGAATTTCATT+TGG - Chr7:73821765-73821784 MsG0780040158.01.T01:intron 25.0%
! CATGAAAAATTCCAAATGTT+TGG + Chr7:73822161-73822180 None:intergenic 25.0%
! CTCTTCTCTTAAATCTAAAA+TGG + Chr7:73820621-73820640 None:intergenic 25.0%
!! AACAAGATCTAGAACTTAAT+CGG + Chr7:73821139-73821158 None:intergenic 25.0%
!! AGATATGAAGTTGCTATTAA+AGG + Chr7:73821727-73821746 None:intergenic 25.0%
!! CATTTTAGATTTAAGAGAAG+AGG - Chr7:73820619-73820638 MsG0780040158.01.T01:CDS 25.0%
!!! AAATCGTTCTAGAACTTAAT+CGG + Chr7:73821070-73821089 None:intergenic 25.0%
!!! AATTTTTTTGTTTCCCTTTC+AGG - Chr7:73822217-73822236 MsG0780040158.01.T01:intron 25.0%
!!! AGCTGTAATTGTTTCTAAAA+TGG - Chr7:73821251-73821270 MsG0780040158.01.T01:intron 25.0%
!!! AGTTCTAGATCTTGTTATAT+TGG - Chr7:73821143-73821162 MsG0780040158.01.T01:intron 25.0%
!!! ATGATTTCATATTTTGAAGG+CGG + Chr7:73820897-73820916 None:intergenic 25.0%
!!! ATTTTTTTGTTTCCCTTTCA+GGG - Chr7:73822218-73822237 MsG0780040158.01.T01:intron 25.0%
!!! GTAATTGTTTCTAAAATGGA+TGG - Chr7:73821255-73821274 MsG0780040158.01.T01:intron 25.0%
!!! TCTCTTACTTTAAAGTGAAT+TGG + Chr7:73821319-73821338 None:intergenic 25.0%
AAAAGCCTTTGTTCTTTCTT+TGG + Chr7:73820866-73820885 None:intergenic 30.0%
AAAGCCTTTGTTCTTTCTTT+GGG + Chr7:73820865-73820884 None:intergenic 30.0%
AATAAAAAACCGAGTCTCAA+AGG - Chr7:73820731-73820750 MsG0780040158.01.T01:intron 30.0%
ACCTCCTAAAAAAAGATCAA+AGG - Chr7:73821879-73821898 MsG0780040158.01.T01:intron 30.0%
ATGGAGTCAAGATTTGAAAA+GGG + Chr7:73820704-73820723 None:intergenic 30.0%
TGAAAGTGGTGTGTTATAAA+AGG + Chr7:73821905-73821924 None:intergenic 30.0%
TTATTCTCAAGGAGAGTAAT+AGG + Chr7:73820817-73820836 None:intergenic 30.0%
TTTAGATTTAAGAGAAGAGG+TGG - Chr7:73820622-73820641 MsG0780040158.01.T01:CDS 30.0%
TTTATGTGTTGGGTACATAT+TGG - Chr7:73821423-73821442 MsG0780040158.01.T01:CDS 30.0%
! CTTGTTATATTGGTTATCGA+TGG - Chr7:73821153-73821172 MsG0780040158.01.T01:intron 30.0%
! TCTCAAAGGTTGATTTCATT+TGG - Chr7:73820745-73820764 MsG0780040158.01.T01:intron 30.0%
!! TGATTTCATATTTTGAAGGC+GGG + Chr7:73820896-73820915 None:intergenic 30.0%
!! TTCTAGAACGATTTACATTG+TGG - Chr7:73821076-73821095 MsG0780040158.01.T01:intron 30.0%
!! TTTACACATAGTGTTGACAT+TGG - Chr7:73821228-73821247 MsG0780040158.01.T01:intron 30.0%
!!! AAGGCCTTTGATCTTTTTTT+AGG + Chr7:73821886-73821905 None:intergenic 30.0%
AATCCTGGTGAAAAATTCAG+AGG - Chr7:73822345-73822364 MsG0780040158.01.T01:CDS 35.0%
CATGTCAGAGAAATATCGAA+AGG - Chr7:73822274-73822293 MsG0780040158.01.T01:CDS 35.0%
CCTAATAGACGACTAACAAA+CGG + Chr7:73821551-73821570 None:intergenic 35.0%
CTCTACTCATCTTATTCTCA+AGG + Chr7:73820828-73820847 None:intergenic 35.0%
CTTACGACTACAATGATCAA+AGG + Chr7:73821196-73821215 None:intergenic 35.0%
CTTTCGATATTTCTCTGACA+TGG + Chr7:73822276-73822295 None:intergenic 35.0%
GATGGAGTCAAGATTTGAAA+AGG + Chr7:73820705-73820724 None:intergenic 35.0%
TGGAGTCAAGATTTGAAAAG+GGG + Chr7:73820703-73820722 None:intergenic 35.0%
TTGACATGTGACCAAACATT+TGG - Chr7:73822147-73822166 MsG0780040158.01.T01:intron 35.0%
TTGGTTATCGATGGCAATAT+TGG - Chr7:73821162-73821181 MsG0780040158.01.T01:intron 35.0%
TTGTTTGACTGAGACTTCTA+GGG - Chr7:73821692-73821711 MsG0780040158.01.T01:intron 35.0%
! TTGGTTAGAGTAACAGGTTT+TGG + Chr7:73820586-73820605 None:intergenic 35.0%
!! ATAGCATTGGTTAGAGTAAC+AGG + Chr7:73820592-73820611 None:intergenic 35.0%
!! TGAAATCAACCTTTGAGACT+CGG + Chr7:73820743-73820762 None:intergenic 35.0%
!!! CGGTTTTTTATTGCTTCTGA+TGG + Chr7:73820723-73820742 None:intergenic 35.0%
!!! GCCTTTGATCTTTTTTTAGG+AGG + Chr7:73821883-73821902 None:intergenic 35.0%
AAAATGGATGGCTATGCCAT+GGG - Chr7:73821267-73821286 MsG0780040158.01.T01:intron 40.0%
AAGAGTCCGGTCATATTCAT+AGG - Chr7:73821482-73821501 MsG0780040158.01.T01:intron 40.0%
ACCTCCCAAAGAAAGAACAA+AGG - Chr7:73820858-73820877 MsG0780040158.01.T01:intron 40.0%
ACCTGCCAGAAAGAAAAATC+TGG - Chr7:73821630-73821649 MsG0780040158.01.T01:intron 40.0%
AGAAGTCTCAGTCAAACAAG+TGG + Chr7:73821691-73821710 None:intergenic 40.0%
AGAATCTCATGTCCCTGAAA+GGG + Chr7:73822233-73822252 None:intergenic 40.0%
ATTTAAGAGAAGAGGTGGTG+CGG - Chr7:73820627-73820646 MsG0780040158.01.T01:CDS 40.0%
ATTTCTCTGACATGGAACCA+GGG + Chr7:73822268-73822287 None:intergenic 40.0%
ATTTGAAAAGGGGAAGCAAG+AGG + Chr7:73820693-73820712 None:intergenic 40.0%
CATAGGAACTGGTGAACATA+TGG - Chr7:73821499-73821518 MsG0780040158.01.T01:intron 40.0%
CCAGTTCCTATGAATATGAC+CGG + Chr7:73821491-73821510 None:intergenic 40.0%
CTTGTTTGACTGAGACTTCT+AGG - Chr7:73821691-73821710 MsG0780040158.01.T01:intron 40.0%
TAAAATGGATGGCTATGCCA+TGG - Chr7:73821266-73821285 MsG0780040158.01.T01:intron 40.0%
TAGAATCTCATGTCCCTGAA+AGG + Chr7:73822234-73822253 None:intergenic 40.0%
TAGTCTGTGTCCACAATGTT+TGG + Chr7:73821110-73821129 None:intergenic 40.0%
TATTTCTCTGACATGGAACC+AGG + Chr7:73822269-73822288 None:intergenic 40.0%
TGATCATTGTAGTCGTAAGC+AGG - Chr7:73821197-73821216 MsG0780040158.01.T01:intron 40.0%
TGTTAGTCGTCTATTAGGCA+TGG - Chr7:73821553-73821572 MsG0780040158.01.T01:intron 40.0%
! CCGTTTGTTAGTCGTCTATT+AGG - Chr7:73821548-73821567 MsG0780040158.01.T01:intron 40.0%
! GAAAGGACTTTTGTATGCAC+TGG - Chr7:73822291-73822310 MsG0780040158.01.T01:CDS 40.0%
! GGCATCCAGATTTTTCTTTC+TGG + Chr7:73821638-73821657 None:intergenic 40.0%
! TTTCTTTCTGGCAGGTTTAG+AGG + Chr7:73821626-73821645 None:intergenic 40.0%
!! TCCAGATTTTTCTTTCTGGC+AGG + Chr7:73821634-73821653 None:intergenic 40.0%
ACAGGCTCCAATATTGAAGC+AGG + Chr7:73822318-73822337 None:intergenic 45.0%
CACTGGTCCTGCTTCAATAT+TGG - Chr7:73822308-73822327 MsG0780040158.01.T01:CDS 45.0%
CATGAACCTGGCTTCAATTC+AGG + Chr7:73820778-73820797 None:intergenic 45.0%
CCGGTCATATTCATAGGAAC+TGG - Chr7:73821488-73821507 MsG0780040158.01.T01:intron 45.0%
CTGAAATGAAGCCAGGTTCA+CGG - Chr7:73821796-73821815 MsG0780040158.01.T01:intron 45.0%
CTGAATTGAAGCCAGGTTCA+TGG - Chr7:73820776-73820795 MsG0780040158.01.T01:intron 45.0%
GCCTTTGTTCTTTCTTTGGG+AGG + Chr7:73820862-73820881 None:intergenic 45.0%
GGACAAGTGACCAAACATTG+TGG - Chr7:73821097-73821116 MsG0780040158.01.T01:intron 45.0%
GTCTATTAGGCATGGATGAC+TGG - Chr7:73821561-73821580 MsG0780040158.01.T01:intron 45.0%
TCAAACAAGTGGTGCAACGA+TGG + Chr7:73821680-73821699 None:intergenic 45.0%
TGTTGCAGCAACAAAGAGTC+CGG - Chr7:73821469-73821488 MsG0780040158.01.T01:intron 45.0%
! GCTCCTCTGAATTTTTCACC+AGG + Chr7:73822351-73822370 None:intergenic 45.0%
AACAAGTGGTGCAACGATGG+AGG + Chr7:73821677-73821696 None:intergenic 50.0%
ACAAGTGGTGCAACGATGGA+GGG + Chr7:73821676-73821695 None:intergenic 50.0%
AGAGGTGGTGCGGCAATTAA+AGG - Chr7:73820637-73820656 MsG0780040158.01.T01:CDS 50.0%
CCAGGTTCATGGACTCAACA+AGG - Chr7:73820787-73820806 MsG0780040158.01.T01:intron 50.0%
CCTTGTTGAGTCCATGAACC+TGG + Chr7:73820790-73820809 None:intergenic 50.0%
CGTGAACCTGGCTTCATTTC+AGG + Chr7:73821798-73821817 None:intergenic 50.0%
GGCAGGTTTAGAGGCAATTC+AGG + Chr7:73821617-73821636 None:intergenic 50.0%
TCACCAGGATTCACAGTCAC+AGG + Chr7:73822336-73822355 None:intergenic 50.0%
TGAAAAGGGGAAGCAAGAGG+AGG + Chr7:73820690-73820709 None:intergenic 50.0%
TGCCATGCTCACAGGATAGA+GGG + Chr7:73820536-73820555 None:intergenic 50.0%
TTGCCATGCTCACAGGATAG+AGG + Chr7:73820537-73820556 None:intergenic 50.0%
ACTGCTGTTGCCATGCTCAC+AGG + Chr7:73820544-73820563 None:intergenic 55.0%
ATGGATGGCTATGCCATGGG+TGG - Chr7:73821270-73821289 MsG0780040158.01.T01:intron 55.0%
ATTCTACATGCGTCGAGCCC+TGG - Chr7:73822248-73822267 MsG0780040158.01.T01:intron 55.0%
CCAGGTTCACGGAGTCAACA+AGG - Chr7:73821807-73821826 MsG0780040158.01.T01:intron 55.0%
GAGCCTGTGACTGTGAATCC+TGG - Chr7:73822330-73822349 MsG0780040158.01.T01:CDS 55.0%
GAGGTGTGAGCAGTATGAGC+AGG + Chr7:73820671-73820690 None:intergenic 55.0%
GATGGAGGGAAAAACGCACG+TGG + Chr7:73821662-73821681 None:intergenic 55.0%
GCTAAGAGAACCACCACCCA+TGG + Chr7:73821286-73821305 None:intergenic 55.0%
GCTGAGCCTGAAATGAAGCC+AGG - Chr7:73821789-73821808 MsG0780040158.01.T01:intron 55.0%
GCTGAGCCTGAATTGAAGCC+AGG - Chr7:73820769-73820788 MsG0780040158.01.T01:intron 55.0%
GTCCCTCTATCCTGTGAGCA+TGG - Chr7:73820531-73820550 MsG0780040158.01.T01:CDS 55.0%
!! CCTTGTTGACTCCGTGAACC+TGG + Chr7:73821810-73821829 None:intergenic 55.0%
GATGGCTATGCCATGGGTGG+TGG - Chr7:73821273-73821292 MsG0780040158.01.T01:intron 60.0%
GGAGGGAAAAACGCACGTGG+AGG + Chr7:73821659-73821678 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr7 gene 73820517 73822401 73820517 ID=MsG0780040158.01;Name=MsG0780040158.01
Chr7 mRNA 73820517 73822401 73820517 ID=MsG0780040158.01.T01;Parent=MsG0780040158.01;Name=MsG0780040158.01.T01;_AED=0.50;_eAED=0.52;_QI=0|0|0|1|1|1|4|0|183
Chr7 exon 73822260 73822401 73822260 ID=MsG0780040158.01.T01:exon:13313;Parent=MsG0780040158.01.T01
Chr7 exon 73821995 73822127 73821995 ID=MsG0780040158.01.T01:exon:13312;Parent=MsG0780040158.01.T01
Chr7 exon 73821336 73821449 73821336 ID=MsG0780040158.01.T01:exon:13311;Parent=MsG0780040158.01.T01
Chr7 exon 73820517 73820679 73820517 ID=MsG0780040158.01.T01:exon:13310;Parent=MsG0780040158.01.T01
Chr7 CDS 73822260 73822401 73822260 ID=MsG0780040158.01.T01:cds;Parent=MsG0780040158.01.T01
Chr7 CDS 73821995 73822127 73821995 ID=MsG0780040158.01.T01:cds;Parent=MsG0780040158.01.T01
Chr7 CDS 73821336 73821449 73821336 ID=MsG0780040158.01.T01:cds;Parent=MsG0780040158.01.T01
Chr7 CDS 73820517 73820679 73820517 ID=MsG0780040158.01.T01:cds;Parent=MsG0780040158.01.T01
Gene Sequence

>MsG0780040158.01.T01

ATGACTTATATTGTGTCCCTCTATCCTGTGAGCATGGCAACAGCAGTTATAGTTAAGAACAAATCTCCAAAACCTGTTACTCTAACCAATGCTATATTAAGCCATTTTAGATTTAAGAGAAGAGGTGGTGCGGCAATTAAAGGTTCATGGACTCAACAAGGTGTTCCTATTACTCTCCTTGAGAATAAGATGAGTAGAGTTTTTGCTGCACCTCCCAAAGAAAGAACAAAGGCTTTTTATAACACCCGCCTTCAAAATATGAAATCATTGATCAGTGTTGCAGCAACAAAGAGTCCGGTCATATTCATAGGAACTGGTGAACATATGGATGAGTTTGAAGTTTTTGAAGTTAAGCCGTTTGTTAGTCGTCTATTAGGCATGGATGACTGGGACATGAGATTCTACATGCGTCGAGCCCTGGTTCCATGTCAGAGAAATATCGAAAGGACTTTTGTATGCACTGGTCCTGCTTCAATATTGGAGCCTGTGACTGTGAATCCTGGTGAAAAATTCAGAGGAGCACAAGTTATTGAGCATGATGATCTCTCATAA

Protein sequence

>MsG0780040158.01.T01

MTYIVSLYPVSMATAVIVKNKSPKPVTLTNAILSHFRFKRRGGAAIKGSWTQQGVPITLLENKMSRVFAAPPKERTKAFYNTRLQNMKSLISVAATKSPVIFIGTGEHMDEFEVFEVKPFVSRLLGMDDWDMRFYMRRALVPCQRNIERTFVCTGPASILEPVTVNPGEKFRGAQVIEHDDLS*