AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1449770


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1449770 MtrunA17_Chr3g0126341 98.413 63 1 0 1 63 1 63 3.12e-38 120
Msa1449770 MtrunA17_Chr1g0159001 76.271 59 12 1 7 63 4 62 1.81e-18 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1449770 AT2G46330.1 63.462 52 19 0 12 63 11 62 1.02e-18 72.4
Msa1449770 AT3G61640.1 56.667 60 26 0 4 63 3 62 1.41e-17 69.3
Msa1449770 AT5G53250.1 58.182 55 23 0 9 63 9 63 2.33e-15 63.5
Msa1449770 AT5G24105.1 63.492 63 23 0 1 63 1 63 5.03e-11 52.4

Find 20 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTTCATGTGCTTCATTC+AGG 0.175879 tig0032701:-13585 Msa1449770:CDS
TGTTCTAATGCTTGTGGCTT+TGG 0.292333 tig0032701:-12747 Msa1449770:CDS
TTCAGGGTGGTTGCCTTCCT+TGG 0.296499 tig0032701:-13568 Msa1449770:CDS
GATAAATTAATGAATGATAT+AGG 0.396044 tig0032701:+12718 None:intergenic
GAATATTTACCATCGCTTGT+AGG 0.408971 tig0032701:+13484 None:intergenic
TGTTTCATGTGCTTCATTCA+GGG 0.448362 tig0032701:-13584 Msa1449770:CDS
TTACCATCGCTTGTAGGAGC+AGG 0.455603 tig0032701:+13490 None:intergenic
AGGAGCAGGGGCAGGTGCAA+TGG 0.532358 tig0032701:+13504 None:intergenic
TTATGCAACACTTATTTCTG+TGG 0.538882 tig0032701:-13539 Msa1449770:CDS
TACCATCGCTTGTAGGAGCA+GGG 0.542274 tig0032701:+13491 None:intergenic
AAATAAGTGTTGCATAAATG+AGG 0.548157 tig0032701:+13545 None:intergenic
TGCATGTGTTCTAATGCTTG+TGG 0.551000 tig0032701:-12753 Msa1449770:CDS
TCGCTTGTAGGAGCAGGGGC+AGG 0.566771 tig0032701:+13496 None:intergenic
TGCATAAATGAGGCCAAGGA+AGG 0.567934 tig0032701:+13555 None:intergenic
TTAGAACACATGCAATCGCT+TGG 0.574241 tig0032701:+12762 None:intergenic
TGCAATCGCTTGGTCAATTG+TGG 0.581446 tig0032701:+12772 None:intergenic
GTGTTGCATAAATGAGGCCA+AGG 0.582795 tig0032701:+13551 None:intergenic
GCCCCTGCTCCTACAAGCGA+TGG 0.595947 tig0032701:-13493 Msa1449770:intron
ACCATCGCTTGTAGGAGCAG+GGG 0.636251 tig0032701:+13492 None:intergenic
TTCATGTGCTTCATTCAGGG+TGG 0.668781 tig0032701:-13581 Msa1449770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAAATAAATTAAAATGG+AGG + tig0032701:12945-12964 None:intergenic 15.0%
!!! TTTATTTTCAGAGATTAAAT+TGG + tig0032701:12985-13004 None:intergenic 15.0%
!!! AATCATTTCATAAATCTTTT+TGG - tig0032701:13139-13158 Msa1449770:intron 15.0%
!! TAATGATTATAAAACAAATG+TGG - tig0032701:13264-13283 Msa1449770:intron 15.0%
!! AACAAATTGAAAATCAAATA+TGG + tig0032701:13429-13448 None:intergenic 15.0%
!! TGAAAAATAAATTAAAATGG+AGG + tig0032701:12945-12964 None:intergenic 15.0%
!!! TTTATTTTCAGAGATTAAAT+TGG + tig0032701:12985-13004 None:intergenic 15.0%
!!! AATCATTTCATAAATCTTTT+TGG - tig0032701:13139-13158 Msa1449770:intron 15.0%
!! TAATGATTATAAAACAAATG+TGG - tig0032701:13264-13283 Msa1449770:intron 15.0%
!! AACAAATTGAAAATCAAATA+TGG + tig0032701:13429-13448 None:intergenic 15.0%
!! AAGTGATGAAACATTAATAA+GGG + tig0032701:12884-12903 None:intergenic 20.0%
!! AAAGTGATGAAACATTAATA+AGG + tig0032701:12885-12904 None:intergenic 20.0%
!!! AAAACACCTTATACTTTTTA+AGG - tig0032701:13181-13200 Msa1449770:intron 20.0%
!!! ATTTAGCCTTAAAAAGTATA+AGG + tig0032701:13190-13209 None:intergenic 20.0%
!! GCTAAAAGTTAAGTAAAATT+TGG + tig0032701:13346-13365 None:intergenic 20.0%
!!! AATTGTTGTTTATAATATGC+AGG - tig0032701:13516-13535 Msa1449770:CDS 20.0%
!! AAGTGATGAAACATTAATAA+GGG + tig0032701:12884-12903 None:intergenic 20.0%
!! AAAGTGATGAAACATTAATA+AGG + tig0032701:12885-12904 None:intergenic 20.0%
!!! AAAACACCTTATACTTTTTA+AGG - tig0032701:13181-13200 Msa1449770:intron 20.0%
!!! ATTTAGCCTTAAAAAGTATA+AGG + tig0032701:13190-13209 None:intergenic 20.0%
!! GCTAAAAGTTAAGTAAAATT+TGG + tig0032701:13346-13365 None:intergenic 20.0%
!!! AATTGTTGTTTATAATATGC+AGG - tig0032701:13516-13535 Msa1449770:CDS 20.0%
!! AAATAAGTGTTGCATAAATG+AGG + tig0032701:12771-12790 None:intergenic 25.0%
!! GATTAAATTGGTGATTCATT+TGG + tig0032701:12973-12992 None:intergenic 25.0%
!!! CTTTCAATCACATTAGTTTT+CGG + tig0032701:13110-13129 None:intergenic 25.0%
!!! AAACTCACATATATTTTGAG+AGG + tig0032701:13222-13241 None:intergenic 25.0%
! TGGACTAATATCCATATAAA+CGG - tig0032701:13284-13303 Msa1449770:intron 25.0%
! TAATATCCATATAAACGGTT+AGG - tig0032701:13289-13308 Msa1449770:intron 25.0%
!! ATCAAATATGGAGATGTTTT+TGG + tig0032701:13417-13436 None:intergenic 25.0%
! TCTTTATGAGCATTATTGAT+AGG - tig0032701:13467-13486 Msa1449770:intron 25.0%
!! AAATAAGTGTTGCATAAATG+AGG + tig0032701:12771-12790 None:intergenic 25.0%
!! GATTAAATTGGTGATTCATT+TGG + tig0032701:12973-12992 None:intergenic 25.0%
!!! CTTTCAATCACATTAGTTTT+CGG + tig0032701:13110-13129 None:intergenic 25.0%
!!! AAACTCACATATATTTTGAG+AGG + tig0032701:13222-13241 None:intergenic 25.0%
! TGGACTAATATCCATATAAA+CGG - tig0032701:13284-13303 Msa1449770:intron 25.0%
! TAATATCCATATAAACGGTT+AGG - tig0032701:13289-13308 Msa1449770:intron 25.0%
!! ATCAAATATGGAGATGTTTT+TGG + tig0032701:13417-13436 None:intergenic 25.0%
! TCTTTATGAGCATTATTGAT+AGG - tig0032701:13467-13486 Msa1449770:intron 25.0%
!! TTATGCAACACTTATTTCTG+TGG - tig0032701:12774-12793 Msa1449770:CDS 30.0%
GCTCATAAAGAATAATAGCA+TGG + tig0032701:13458-13477 None:intergenic 30.0%
!! TTATGCAACACTTATTTCTG+TGG - tig0032701:12774-12793 Msa1449770:CDS 30.0%
GCTCATAAAGAATAATAGCA+TGG + tig0032701:13458-13477 None:intergenic 30.0%
TGTTTCATGTGCTTCATTCA+GGG - tig0032701:12729-12748 Msa1449770:CDS 35.0%
GAATATTTACCATCGCTTGT+AGG + tig0032701:12832-12851 None:intergenic 35.0%
GTTCTTCCTAACCGTTTATA+TGG + tig0032701:13298-13317 None:intergenic 35.0%
TGTTTCATGTGCTTCATTCA+GGG - tig0032701:12729-12748 Msa1449770:CDS 35.0%
GAATATTTACCATCGCTTGT+AGG + tig0032701:12832-12851 None:intergenic 35.0%
GTTCTTCCTAACCGTTTATA+TGG + tig0032701:13298-13317 None:intergenic 35.0%
CTGTTTCATGTGCTTCATTC+AGG - tig0032701:12728-12747 Msa1449770:CDS 40.0%
ATAAACGGTTAGGAAGAACC+TGG - tig0032701:13299-13318 Msa1449770:intron 40.0%
TAAACGGTTAGGAAGAACCT+GGG - tig0032701:13300-13319 Msa1449770:intron 40.0%
AAGATTGTTCGTACAAACCC+AGG + tig0032701:13320-13339 None:intergenic 40.0%
TCCCATTCCCTAGAACTAAA+GGG - tig0032701:13385-13404 Msa1449770:intron 40.0%
!! ACCCTTTAGTTCTAGGGAAT+GGG + tig0032701:13389-13408 None:intergenic 40.0%
!! AACCCTTTAGTTCTAGGGAA+TGG + tig0032701:13390-13409 None:intergenic 40.0%
TTAGAACACATGCAATCGCT+TGG + tig0032701:13554-13573 None:intergenic 40.0%
TGCATGTGTTCTAATGCTTG+TGG - tig0032701:13560-13579 Msa1449770:CDS 40.0%
TGTTCTAATGCTTGTGGCTT+TGG - tig0032701:13566-13585 Msa1449770:CDS 40.0%
CTGTTTCATGTGCTTCATTC+AGG - tig0032701:12728-12747 Msa1449770:CDS 40.0%
ATAAACGGTTAGGAAGAACC+TGG - tig0032701:13299-13318 Msa1449770:intron 40.0%
TAAACGGTTAGGAAGAACCT+GGG - tig0032701:13300-13319 Msa1449770:intron 40.0%
AAGATTGTTCGTACAAACCC+AGG + tig0032701:13320-13339 None:intergenic 40.0%
TCCCATTCCCTAGAACTAAA+GGG - tig0032701:13385-13404 Msa1449770:intron 40.0%
!! ACCCTTTAGTTCTAGGGAAT+GGG + tig0032701:13389-13408 None:intergenic 40.0%
!! AACCCTTTAGTTCTAGGGAA+TGG + tig0032701:13390-13409 None:intergenic 40.0%
TTAGAACACATGCAATCGCT+TGG + tig0032701:13554-13573 None:intergenic 40.0%
TGCATGTGTTCTAATGCTTG+TGG - tig0032701:13560-13579 Msa1449770:CDS 40.0%
TGTTCTAATGCTTGTGGCTT+TGG - tig0032701:13566-13585 Msa1449770:CDS 40.0%
TTCATGTGCTTCATTCAGGG+TGG - tig0032701:12732-12751 Msa1449770:CDS 45.0%
TGCATAAATGAGGCCAAGGA+AGG + tig0032701:12761-12780 None:intergenic 45.0%
GTGTTGCATAAATGAGGCCA+AGG + tig0032701:12765-12784 None:intergenic 45.0%
!! TAGTTCTAGGGAATGGGACA+TGG + tig0032701:13383-13402 None:intergenic 45.0%
GTCCCATTCCCTAGAACTAA+AGG - tig0032701:13384-13403 Msa1449770:intron 45.0%
TCCCTAGAACTAAAGGGTTG+TGG - tig0032701:13391-13410 Msa1449770:intron 45.0%
!! GCCACAACCCTTTAGTTCTA+GGG + tig0032701:13395-13414 None:intergenic 45.0%
TGCAATCGCTTGGTCAATTG+TGG + tig0032701:13544-13563 None:intergenic 45.0%
TTCATGTGCTTCATTCAGGG+TGG - tig0032701:12732-12751 Msa1449770:CDS 45.0%
TGCATAAATGAGGCCAAGGA+AGG + tig0032701:12761-12780 None:intergenic 45.0%
GTGTTGCATAAATGAGGCCA+AGG + tig0032701:12765-12784 None:intergenic 45.0%
!! TAGTTCTAGGGAATGGGACA+TGG + tig0032701:13383-13402 None:intergenic 45.0%
GTCCCATTCCCTAGAACTAA+AGG - tig0032701:13384-13403 Msa1449770:intron 45.0%
TCCCTAGAACTAAAGGGTTG+TGG - tig0032701:13391-13410 Msa1449770:intron 45.0%
!! GCCACAACCCTTTAGTTCTA+GGG + tig0032701:13395-13414 None:intergenic 45.0%
TGCAATCGCTTGGTCAATTG+TGG + tig0032701:13544-13563 None:intergenic 45.0%
!! TATTGAAAAATAAATTAAAA+TGG + tig0032701:12948-12967 None:intergenic 5.0%
!! TATTGAAAAATAAATTAAAA+TGG + tig0032701:12948-12967 None:intergenic 5.0%
TACCATCGCTTGTAGGAGCA+GGG + tig0032701:12825-12844 None:intergenic 50.0%
TTACCATCGCTTGTAGGAGC+AGG + tig0032701:12826-12845 None:intergenic 50.0%
!! GGCCACAACCCTTTAGTTCT+AGG + tig0032701:13396-13415 None:intergenic 50.0%
TACCATCGCTTGTAGGAGCA+GGG + tig0032701:12825-12844 None:intergenic 50.0%
TTACCATCGCTTGTAGGAGC+AGG + tig0032701:12826-12845 None:intergenic 50.0%
!! GGCCACAACCCTTTAGTTCT+AGG + tig0032701:13396-13415 None:intergenic 50.0%
TTCAGGGTGGTTGCCTTCCT+TGG - tig0032701:12745-12764 Msa1449770:CDS 55.0%
ACCATCGCTTGTAGGAGCAG+GGG + tig0032701:12824-12843 None:intergenic 55.0%
TTCAGGGTGGTTGCCTTCCT+TGG - tig0032701:12745-12764 Msa1449770:CDS 55.0%
ACCATCGCTTGTAGGAGCAG+GGG + tig0032701:12824-12843 None:intergenic 55.0%
AGGAGCAGGGGCAGGTGCAA+TGG + tig0032701:12812-12831 None:intergenic 65.0%
TCGCTTGTAGGAGCAGGGGC+AGG + tig0032701:12820-12839 None:intergenic 65.0%
GCCCCTGCTCCTACAAGCGA+TGG - tig0032701:12820-12839 Msa1449770:intron 65.0%
AGGAGCAGGGGCAGGTGCAA+TGG + tig0032701:12812-12831 None:intergenic 65.0%
TCGCTTGTAGGAGCAGGGGC+AGG + tig0032701:12820-12839 None:intergenic 65.0%
GCCCCTGCTCCTACAAGCGA+TGG - tig0032701:12820-12839 Msa1449770:intron 65.0%
Chromosome Type Strat End Strand Name
tig0032701 gene 12724 13611 12724 ID=Msa1449770;Name=Msa1449770
tig0032701 mRNA 12724 13611 12724 ID=Msa1449770-mRNA-1;Parent=Msa1449770;Name=Msa1449770-mRNA-1;_AED=0.20;_eAED=0.20;_QI=0|0|0|0.5|1|1|2|0|63
tig0032701 exon 13494 13611 13494 ID=Msa1449770-mRNA-1:exon:17129;Parent=Msa1449770-mRNA-1
tig0032701 exon 12724 12797 12724 ID=Msa1449770-mRNA-1:exon:17128;Parent=Msa1449770-mRNA-1
tig0032701 CDS 13494 13611 13494 ID=Msa1449770-mRNA-1:cds;Parent=Msa1449770-mRNA-1
tig0032701 CDS 12724 12797 12724 ID=Msa1449770-mRNA-1:cds;Parent=Msa1449770-mRNA-1
Gene Sequence

>Msa1449770

ATGGCTGTTTCATGTGCTTCATTCAGGGTGGTTGCCTTCCTTGGCCTCATTTATGCAACACTTATTTCTGTGGCTTGTTCACAATCCATTGCACCTGCCCCTGCTCCTACAAGCGATGGCACCACAATTGACCAAGCGATTGCATGTGTTCTAATGCTTGTGGCTTTGGTGTTGACCTATATCATTCATTAA

Protein sequence

>Msa1449770

MAVSCASFRVVAFLGLIYATLISVACSQSIAPAPAPTSDGTTIDQAIACVLMLVALVLTYIIH*