AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1213340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1213340 MtrunA17_Chr7g0225661 35.714 126 66 3 49 170 55 169 4.70e-17 75.1
Msa1213340 MtrunA17_Chr8g0341311 36.364 121 62 3 54 170 50 159 8.47e-17 74.3
Msa1213340 MtrunA17_Chr7g0220571 42.727 110 59 1 44 149 53 162 4.99e-16 72.4
Msa1213340 MtrunA17_Chr6g0456061 41.441 111 60 1 46 151 57 167 6.46e-16 72.4
Msa1213340 MtrunA17_Chr5g0400901 36.232 138 71 6 43 172 27 155 4.91e-13 63.9
Msa1213340 MtrunA17_Chr4g0035414 37.143 105 56 2 63 157 16 120 2.00e-12 62.0
Msa1213340 MtrunA17_Chr1g0194681 31.624 117 73 1 54 163 7 123 9.35e-12 60.1
Msa1213340 MtrunA17_Chr3g0144941 36.275 102 55 2 63 154 16 117 1.18e-11 60.1
Msa1213340 MtrunA17_Chr4g0054291 33.333 129 72 4 20 142 23 143 2.61e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1213340 AT5G60830.1 54.118 85 39 0 72 156 69 153 6.46e-22 88.6
Msa1213340 AT5G38800.1 41.667 96 54 1 56 149 52 147 3.42e-18 77.8
Msa1213340 AT3G30530.1 43.000 100 57 0 52 151 59 158 6.49e-18 77.4
Msa1213340 AT1G13600.1 42.105 95 50 1 60 149 67 161 2.19e-16 73.9
Msa1213340 AT5G15830.1 36.937 111 64 1 62 166 56 166 1.57e-14 68.9
Msa1213340 AT2G04038.1 40.426 94 50 1 62 149 56 149 1.75e-13 65.5
Msa1213340 AT2G18160.1 33.333 114 69 1 60 166 17 130 5.17e-12 61.6
Msa1213340 AT1G75390.1 40.566 106 55 2 52 149 11 116 9.04e-12 61.2
Msa1213340 AT1G75390.2 40.196 102 53 2 52 145 11 112 7.62e-11 57.4
Msa1213340 AT2G42380.5 39.362 94 55 1 51 142 163 256 8.61e-11 59.7
Msa1213340 AT3G62420.1 33.898 118 69 3 57 166 8 124 8.98e-11 57.8

Find 45 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACAAAATGCTCAACTTAA+AGG 0.201570 8_1:+73496281 Msa1213340:CDS
CCAACAAGTAAATGATCTTT+TGG 0.211603 8_1:-73496238 None:intergenic
ATGAGTTGGGAGAAGATTTA+TGG 0.268120 8_1:-73496040 None:intergenic
AGCCTGCAAAACCTGGAAAA+TGG 0.302202 8_1:+73495903 Msa1213340:CDS
CCAAAAGATCATTTACTTGT+TGG 0.311300 8_1:+73496238 Msa1213340:CDS
GTGAGGTATACCAACATTTC+CGG 0.334411 8_1:-73496351 None:intergenic
TTTATGGTCTGGAATTTGAA+TGG 0.416953 8_1:-73496024 None:intergenic
GAACTCAAGCCTGCAAAACC+TGG 0.431180 8_1:+73495896 Msa1213340:CDS
TTGGGAGAAGATTTATGGTC+TGG 0.437689 8_1:-73496035 None:intergenic
GTTACTGTTTGATGATGAGT+TGG 0.446587 8_1:-73496054 None:intergenic
TGAAGCTGGGAGTAGTGAAA+TGG 0.452683 8_1:-73495978 None:intergenic
TTATGGTCTGGAATTTGAAT+GGG 0.454968 8_1:-73496023 None:intergenic
AGCGGTACTATCTACTTTGT+TGG 0.466162 8_1:+73496322 Msa1213340:CDS
TTGATGATCGAAAGAAGAAA+AGG 0.480340 8_1:+73496105 Msa1213340:CDS
AGACGAGTTGAAAGGTTGGC+TGG 0.483172 8_1:-73496392 None:intergenic
TGTCGTTAGAGAGGTGAAGC+TGG 0.483487 8_1:-73495992 None:intergenic
ACCCATCTGTATCCATCTCA+AGG 0.506932 8_1:+73495942 Msa1213340:CDS
CTACTCAAAATCGCTATGCT+CGG 0.512535 8_1:-73496435 None:intergenic
TCTACTTTGTTGGTTACGAC+CGG 0.517483 8_1:+73496332 Msa1213340:CDS
TACTCAAAATCGCTATGCTC+GGG 0.518651 8_1:-73496434 None:intergenic
TTACTGTTTGATGATGAGTT+GGG 0.525916 8_1:-73496053 None:intergenic
ATTGATGGTTCAGCGCCTGC+AGG 0.527456 8_1:-73496211 None:intergenic
AGGTTGGCTGGGAAGCCACT+AGG 0.529008 8_1:-73496380 None:intergenic
GATACAGATGGGTCAAAGAA+TGG 0.534656 8_1:-73495932 None:intergenic
CTGGGAAGCCACTAGGGATG+TGG 0.538645 8_1:-73496373 None:intergenic
GTATCAAGTGAATCACCTGC+AGG 0.567327 8_1:+73496196 Msa1213340:CDS
ATATCATGTAAACCTTGAGA+TGG 0.573761 8_1:-73495954 None:intergenic
TCAAACAGTAACAACAACTC+TGG 0.574952 8_1:+73496065 Msa1213340:CDS
GTCGTTAGAGAGGTGAAGCT+GGG 0.575441 8_1:-73495991 None:intergenic
GACGAGTTGAAAGGTTGGCT+GGG 0.575767 8_1:-73496391 None:intergenic
AACCTTGAGATGGATACAGA+TGG 0.576394 8_1:-73495944 None:intergenic
GGTTGGCTGGGAAGCCACTA+GGG 0.587937 8_1:-73496379 None:intergenic
TTGTAACTAGACGAGTTGAA+AGG 0.591340 8_1:-73496400 None:intergenic
TTGGTTACGACCGGAAATGT+TGG 0.596096 8_1:+73496341 Msa1213340:CDS
AGATAGTACCGCTTGAAGAG+AGG 0.597446 8_1:-73496312 None:intergenic
CAAAACCTGGAAAATGGAGA+AGG 0.605645 8_1:+73495909 Msa1213340:CDS
CAAAGTTTCCTCTCTTCAAG+CGG 0.609354 8_1:+73496304 Msa1213340:CDS
CAACAACTCTGGTAAAGCAA+AGG 0.613348 8_1:+73496076 Msa1213340:CDS
GGTGATTCACTTGATACCAC+AGG 0.615500 8_1:-73496190 None:intergenic
AACTAGACGAGTTGAAAGGT+TGG 0.615858 8_1:-73496396 None:intergenic
ACCTTGAGATGGATACAGAT+GGG 0.616103 8_1:-73495943 None:intergenic
CTAACAGAGAATCTGCTCGT+CGG 0.675721 8_1:+73496135 Msa1213340:CDS
ATACCTCACCACATCCCTAG+TGG 0.679014 8_1:+73496365 Msa1213340:CDS
AGCAGCGAATTGAAGTCCTG+TGG 0.703639 8_1:+73496174 Msa1213340:CDS
AAGCCACTAGGGATGTGGTG+AGG 0.721984 8_1:-73496368 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAACAAGTAAATGATCTTTT+GGG - chr8_1:73496240-73496259 None:intergenic 25.0%
ATATCATGTAAACCTTGAGA+TGG - chr8_1:73495957-73495976 None:intergenic 30.0%
! TTATGGTCTGGAATTTGAAT+GGG - chr8_1:73496026-73496045 None:intergenic 30.0%
! TTTATGGTCTGGAATTTGAA+TGG - chr8_1:73496027-73496046 None:intergenic 30.0%
!! TTACTGTTTGATGATGAGTT+GGG - chr8_1:73496056-73496075 None:intergenic 30.0%
! TTTTCTTCTTTCGATCATCA+AGG - chr8_1:73496106-73496125 None:intergenic 30.0%
! TTGATGATCGAAAGAAGAAA+AGG + chr8_1:73496105-73496124 Msa1213340:CDS 30.0%
! CCAACAAGTAAATGATCTTT+TGG - chr8_1:73496241-73496260 None:intergenic 30.0%
CCAAAAGATCATTTACTTGT+TGG + chr8_1:73496238-73496257 Msa1213340:CDS 30.0%
!! CATTTTGTTGGTTGATTAGT+TGG - chr8_1:73496271-73496290 None:intergenic 30.0%
!!! CTTTAAGTTGAGCATTTTGT+TGG - chr8_1:73496283-73496302 None:intergenic 30.0%
CAACAAAATGCTCAACTTAA+AGG + chr8_1:73496281-73496300 Msa1213340:CDS 30.0%
! ATGAGTTGGGAGAAGATTTA+TGG - chr8_1:73496043-73496062 None:intergenic 35.0%
!! GTTACTGTTTGATGATGAGT+TGG - chr8_1:73496057-73496076 None:intergenic 35.0%
TCAAACAGTAACAACAACTC+TGG + chr8_1:73496065-73496084 Msa1213340:CDS 35.0%
!!! TGATCTTTTGGGACAATTGA+TGG - chr8_1:73496229-73496248 None:intergenic 35.0%
! TTGTAACTAGACGAGTTGAA+AGG - chr8_1:73496403-73496422 None:intergenic 35.0%
CAAAACCTGGAAAATGGAGA+AGG + chr8_1:73495909-73495928 Msa1213340:CDS 40.0%
GATACAGATGGGTCAAAGAA+TGG - chr8_1:73495935-73495954 None:intergenic 40.0%
ACCTTGAGATGGATACAGAT+GGG - chr8_1:73495946-73495965 None:intergenic 40.0%
AACCTTGAGATGGATACAGA+TGG - chr8_1:73495947-73495966 None:intergenic 40.0%
TTGGGAGAAGATTTATGGTC+TGG - chr8_1:73496038-73496057 None:intergenic 40.0%
CAACAACTCTGGTAAAGCAA+AGG + chr8_1:73496076-73496095 Msa1213340:CDS 40.0%
CAAAGTTTCCTCTCTTCAAG+CGG + chr8_1:73496304-73496323 Msa1213340:CDS 40.0%
AGCGGTACTATCTACTTTGT+TGG + chr8_1:73496322-73496341 Msa1213340:CDS 40.0%
! TCTACTTTGTTGGTTACGAC+CGG + chr8_1:73496332-73496351 Msa1213340:CDS 40.0%
GTGAGGTATACCAACATTTC+CGG - chr8_1:73496354-73496373 None:intergenic 40.0%
! AACTAGACGAGTTGAAAGGT+TGG - chr8_1:73496399-73496418 None:intergenic 40.0%
TACTCAAAATCGCTATGCTC+GGG - chr8_1:73496437-73496456 None:intergenic 40.0%
CTACTCAAAATCGCTATGCT+CGG - chr8_1:73496438-73496457 None:intergenic 40.0%
AGCCTGCAAAACCTGGAAAA+TGG + chr8_1:73495903-73495922 Msa1213340:CDS 45.0%
! CTCCATTTTCCAGGTTTTGC+AGG - chr8_1:73495908-73495927 None:intergenic 45.0%
! AATGGCCTTCTCCATTTTCC+AGG - chr8_1:73495917-73495936 None:intergenic 45.0%
ACCCATCTGTATCCATCTCA+AGG + chr8_1:73495942-73495961 Msa1213340:CDS 45.0%
TGAAGCTGGGAGTAGTGAAA+TGG - chr8_1:73495981-73496000 None:intergenic 45.0%
CTAACAGAGAATCTGCTCGT+CGG + chr8_1:73496135-73496154 Msa1213340:CDS 45.0%
GGTGATTCACTTGATACCAC+AGG - chr8_1:73496193-73496212 None:intergenic 45.0%
GTATCAAGTGAATCACCTGC+AGG + chr8_1:73496196-73496215 Msa1213340:CDS 45.0%
AGATAGTACCGCTTGAAGAG+AGG - chr8_1:73496315-73496334 None:intergenic 45.0%
TTGGTTACGACCGGAAATGT+TGG + chr8_1:73496341-73496360 Msa1213340:CDS 45.0%
GAACTCAAGCCTGCAAAACC+TGG + chr8_1:73495896-73495915 Msa1213340:CDS 50.0%
GTCGTTAGAGAGGTGAAGCT+GGG - chr8_1:73495994-73496013 None:intergenic 50.0%
TGTCGTTAGAGAGGTGAAGC+TGG - chr8_1:73495995-73496014 None:intergenic 50.0%
AGCAGCGAATTGAAGTCCTG+TGG + chr8_1:73496174-73496193 Msa1213340:CDS 50.0%
ATACCTCACCACATCCCTAG+TGG + chr8_1:73496365-73496384 Msa1213340:CDS 50.0%
! GACGAGTTGAAAGGTTGGCT+GGG - chr8_1:73496394-73496413 None:intergenic 50.0%
! AGACGAGTTGAAAGGTTGGC+TGG - chr8_1:73496395-73496414 None:intergenic 50.0%
GACTGTCGCTGTCGTTAGAG+AGG - chr8_1:73496004-73496023 None:intergenic 55.0%
! ATTGATGGTTCAGCGCCTGC+AGG - chr8_1:73496214-73496233 None:intergenic 55.0%
AAGCCACTAGGGATGTGGTG+AGG - chr8_1:73496371-73496390 None:intergenic 55.0%
CTGGGAAGCCACTAGGGATG+TGG - chr8_1:73496376-73496395 None:intergenic 60.0%
! GGTTGGCTGGGAAGCCACTA+GGG - chr8_1:73496382-73496401 None:intergenic 60.0%
! AGGTTGGCTGGGAAGCCACT+AGG - chr8_1:73496383-73496402 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 73495894 73496457 73495894 ID=Msa1213340;Name=Msa1213340
chr8_1 mRNA 73495894 73496457 73495894 ID=Msa1213340-mRNA-1;Parent=Msa1213340;Name=Msa1213340-mRNA-1;_AED=0.05;_eAED=0.32;_QI=0|-1|0|1|-1|1|1|0|187
chr8_1 exon 73495894 73496457 73495894 ID=Msa1213340-mRNA-1:exon:24994;Parent=Msa1213340-mRNA-1
chr8_1 CDS 73495894 73496457 73495894 ID=Msa1213340-mRNA-1:cds;Parent=Msa1213340-mRNA-1
Gene Sequence

>Msa1213340

ATGAACTCAAGCCTGCAAAACCTGGAAAATGGAGAAGGCCATTCTTTGACCCATCTGTATCCATCTCAAGGTTTACATGATATTCCATTTCACTACTCCCAGCTTCACCTCTCTAACGACAGCGACAGTCCCATTCAAATTCCAGACCATAAATCTTCTCCCAACTCATCATCAAACAGTAACAACAACTCTGGTAAAGCAAAGGATCTCCTTGATGATCGAAAGAAGAAAAGGATGTTCTCTAACAGAGAATCTGCTCGTCGGTCGCGAATGAGAAAGAAGCAGCGAATTGAAGTCCTGTGGTATCAAGTGAATCACCTGCAGGCGCTGAACCATCAATTGTCCCAAAAGATCATTTACTTGTTGGAATGTAACCAACTAATCAACCAACAAAATGCTCAACTTAAAGGCAAAGTTTCCTCTCTTCAAGCGGTACTATCTACTTTGTTGGTTACGACCGGAAATGTTGGTATACCTCACCACATCCCTAGTGGCTTCCCAGCCAACCTTTCAACTCGTCTAGTTACAAACTTACAATTTCCCGAGCATAGCGATTTTGAGTAG
Protein sequence

>Msa1213340

MNSSLQNLENGEGHSLTHLYPSQGLHDIPFHYSQLHLSNDSDSPIQIPDHKSSPNSSSNSNNNSGKAKDLLDDRKKKRMFSNRESARRSRMRKKQRIEVLWYQVNHLQALNHQLSQKIIYLLECNQLINQQNAQLKGKVSSLQAVLSTLLVTTGNVGIPHHIPSGFPANLSTRLVTNLQFPEHSDFE*