AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0837780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0837780 MtrunA17_Chr5g0404751 96.899 129 4 0 1 129 1 129 9.24e-92 261
Msa0837780 MtrunA17_Chr2g0299021 57.547 106 45 0 21 126 71 176 1.89e-40 133
Msa0837780 MtrunA17_Chr7g0228311 45.556 90 49 0 40 129 10 99 1.78e-24 90.1
Msa0837780 MtrunA17_Chr3g0117411 43.182 88 50 0 42 129 27 114 9.71e-21 80.9
Msa0837780 MtrunA17_Chr1g0182971 41.304 92 53 1 36 126 86 177 5.40e-20 80.9
Msa0837780 MtrunA17_Chr3g0117391 42.353 85 49 0 42 126 30 114 1.75e-19 78.2
Msa0837780 MtrunA17_Chr7g0268761 38.372 86 52 1 45 129 13 98 1.48e-12 59.7
Msa0837780 MtrunA17_Chr7g0224091 38.636 88 53 1 43 129 32 119 4.96e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0837780 AT1G77370.1 67.500 120 39 0 10 129 11 130 2.10e-54 167
Msa0837780 AT1G77370.2 55.479 146 39 1 10 129 11 156 1.76e-48 152
Msa0837780 AT5G20500.1 51.667 120 58 0 7 126 6 125 1.59e-40 132
Msa0837780 AT5G40370.1 45.977 87 47 0 40 126 10 96 1.04e-22 86.3
Msa0837780 AT5G40370.2 48.750 80 41 0 47 126 42 121 2.01e-20 80.9
Msa0837780 AT4G28730.1 44.565 92 50 1 36 126 73 164 2.39e-20 82.0
Msa0837780 AT2G20270.1 41.304 92 53 1 36 126 78 169 6.13e-19 78.2
Msa0837780 AT5G63030.1 42.683 82 47 0 45 126 31 112 6.46e-18 74.3
Msa0837780 AT4G28730.2 45.588 68 36 1 36 102 73 140 4.66e-13 62.0

Find 45 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATCAGTGTCGTGTCAAAT+TGG 0.237203 5_4:-11824848 Msa0837780:five_prime_UTR
TCAAATTCAGGGTGTTCTTC+TGG 0.247136 5_4:-11823868 Msa0837780:CDS
AGATGATGGGTATCAAATTC+AGG 0.269297 5_4:-11823880 Msa0837780:CDS
GTCCCACAAGTGTTTGTCTA+TGG 0.290060 5_4:-11823825 Msa0837780:CDS
GGTTCCGTTCTCAAACAATA+AGG 0.298246 5_4:+11824719 None:intergenic
ATTTGACATTGGTTCTTTGT+AGG 0.328186 5_4:+11822511 None:intergenic
GACACGCGTGGAAAACAATA+AGG 0.342799 5_4:-11824888 None:intergenic
TACGTACGGGCAATAGGATT+TGG 0.352701 5_4:+11824629 None:intergenic
TATATATACGTACGGGCAAT+AGG 0.386425 5_4:+11824623 None:intergenic
GGTGTTCTTCTGGATTTGAT+TGG 0.395517 5_4:-11823858 Msa0837780:CDS
GGAAACTGAATTTGAAGCTT+CGG 0.429054 5_4:+11824698 None:intergenic
AATCAGTGTCGTGTCAAATT+GGG 0.440854 5_4:-11824847 Msa0837780:five_prime_UTR
GTTCCGTTCTCAAACAATAA+GGG 0.444259 5_4:+11824720 None:intergenic
TTTGTGCTTGTTTAGATGAT+GGG 0.450399 5_4:-11823893 Msa0837780:intron
AGCAGTGGAGCTCTAATTGT+TGG 0.456983 5_4:-11822735 Msa0837780:three_prime_UTR
AACAGAACTATTCTATTCAA+TGG 0.462801 5_4:+11822466 None:intergenic
CTCAAACAATAAGGGTAAAA+CGG 0.475865 5_4:+11824728 None:intergenic
TCCCATAGACAAACACTTGT+GGG 0.486540 5_4:+11823823 None:intergenic
GATGATGGGTATCAAATTCA+GGG 0.487362 5_4:-11823879 Msa0837780:CDS
ATCTATAATTTGTATGAATG+TGG 0.490361 5_4:-11822932 Msa0837780:three_prime_UTR
TCTATAATTTGTATGAATGT+GGG 0.491540 5_4:-11822931 Msa0837780:three_prime_UTR
ATTGAATCTATCTCAAGTAA+TGG 0.497398 5_4:-11822563 Msa0837780:three_prime_UTR
TTTGTCTATGGGAAGCATAT+TGG 0.501883 5_4:-11823813 Msa0837780:CDS
CGTGGAAAACAATAAGGGTC+TGG 0.507148 5_4:-11824882 None:intergenic
AAATCAAGCTCAACAACAAA+AGG 0.509148 5_4:+11824477 None:intergenic
GTCTATGGGAAGCATATTGG+TGG 0.513655 5_4:-11823810 Msa0837780:CDS
GGAGAAGATGGTGATTCTGT+TGG 0.515760 5_4:+11824650 None:intergenic
GCAATAGGATTTGGAGAAGA+TGG 0.516584 5_4:+11824638 None:intergenic
TCCCACAAGTGTTTGTCTAT+GGG 0.535106 5_4:-11823824 Msa0837780:CDS
AATCAAAGAAGTAAAACTAC+AGG 0.537670 5_4:-11822534 Msa0837780:three_prime_UTR
ACACGCGTGGAAAACAATAA+GGG 0.548482 5_4:-11824887 None:intergenic
AAGCATATTGGTGGATCAGA+TGG 0.559694 5_4:-11823801 Msa0837780:intron
GTTTCTGCAATTCACCACTC+TGG 0.562376 5_4:+11823001 None:intergenic
AAGACAAGACAATTTGACAT+TGG 0.563313 5_4:+11822500 None:intergenic
CTTCGATATACATGAAAATG+CGG 0.575457 5_4:+11822904 None:intergenic
TTACCCTTATTGTTTGAGAA+CGG 0.579036 5_4:-11824723 Msa0837780:CDS
CTATAATTTGTATGAATGTG+GGG 0.594049 5_4:-11822930 Msa0837780:three_prime_UTR
TTCGATATACATGAAAATGC+GGG 0.595061 5_4:+11822905 None:intergenic
CGAAGGTTTCAAGCTTCTAG+CGG 0.615435 5_4:-11822886 Msa0837780:three_prime_UTR
TTCCCATAGACAAACACTTG+TGG 0.621034 5_4:+11823822 None:intergenic
TGATTGTATACTTGAGACTG+AGG 0.636878 5_4:-11822964 Msa0837780:three_prime_UTR
GAAAGTACGATCATGAGCAG+TGG 0.651793 5_4:-11822750 Msa0837780:three_prime_UTR
GAAGAATGAAGATGTTACAG+TGG 0.663384 5_4:-11824779 Msa0837780:exon
GTTGTTGAGCTTGATTTGCG+AGG 0.668245 5_4:-11824471 Msa0837780:intron
CTCAGTGCTGCAGTCCAGAG+TGG 0.673667 5_4:-11823015 Msa0837780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTATTGTATTTATTTTTTA+TGG + chr5_4:11824857-11824876 None:intergenic 10.0%
!!! TATGTGTTTTGATATTTTTA+AGG - chr5_4:11823006-11823025 Msa0837780:CDS 15.0%
!!! AAGGGAATATTTATTATTTT+CGG + chr5_4:11823996-11824015 None:intergenic 15.0%
!!! TTTTTTTCCATATACTTTAA+AGG - chr5_4:11824087-11824106 Msa0837780:intron 15.0%
!! TATCTATATGTCATTATAAA+AGG - chr5_4:11824169-11824188 Msa0837780:intron 15.0%
!!! AATACTTTTTCATGTTTTTT+AGG - chr5_4:11824411-11824430 Msa0837780:intron 15.0%
!!! ATTAAGTTGTTTATCAAACA+AGG + chr5_4:11822869-11822888 None:intergenic 20.0%
!! AATAACCTATATACATAAGA+GGG + chr5_4:11823102-11823121 None:intergenic 20.0%
!! AAATAACCTATATACATAAG+AGG + chr5_4:11823103-11823122 None:intergenic 20.0%
!! ATAAAAAAAAACTGCTTTCA+TGG - chr5_4:11823193-11823212 Msa0837780:intron 20.0%
!! TCATATAGTTTAAGAACTAA+AGG + chr5_4:11823849-11823868 None:intergenic 20.0%
!! TAAACTATATGAAAATAACG+AGG - chr5_4:11823857-11823876 Msa0837780:CDS 20.0%
!!! CTTATATTTTTGGATATAGA+GGG + chr5_4:11823911-11823930 None:intergenic 20.0%
!! CTCTATATCCAAAAATATAA+GGG - chr5_4:11823910-11823929 Msa0837780:intron 20.0%
!!! TGATAGAAATTTTTTATGAG+AGG - chr5_4:11823962-11823981 Msa0837780:intron 20.0%
!!! TATTTAGCCTTTAAAGTATA+TGG + chr5_4:11824097-11824116 None:intergenic 20.0%
!! TATGTCATTATAAAAGGTTA+AGG - chr5_4:11824175-11824194 Msa0837780:intron 20.0%
!!! ATCTATAATTTGTATGAATG+TGG - chr5_4:11824339-11824358 Msa0837780:intron 20.0%
!!! TCTATAATTTGTATGAATGT+GGG - chr5_4:11824340-11824359 Msa0837780:intron 20.0%
!!! ATGTTTTTTAGGTATTTACT+AGG - chr5_4:11824422-11824441 Msa0837780:intron 20.0%
!!! ATGTTTTCATTTTGTTCTAT+AGG - chr5_4:11824499-11824518 Msa0837780:CDS 20.0%
!!! ATTTTGTTGTCATTGTTAAT+TGG - chr5_4:11824564-11824583 Msa0837780:intron 20.0%
!!! AATTGTAGTTTTCAATAATC+TGG - chr5_4:11824592-11824611 Msa0837780:intron 20.0%
! AAGAGAGTTATATATACGTA+CGG + chr5_4:11822659-11822678 None:intergenic 25.0%
! TTCAATTATTATCACGTGTT+AGG - chr5_4:11822684-11822703 Msa0837780:three_prime_UTR 25.0%
! TCAATTATTATCACGTGTTA+GGG - chr5_4:11822685-11822704 Msa0837780:three_prime_UTR 25.0%
! ATGAAATTAATATGCTCTGT+CGG - chr5_4:11822916-11822935 Msa0837780:three_prime_UTR 25.0%
! ATTCAAATAGTATACTCAGT+CGG + chr5_4:11823066-11823085 None:intergenic 25.0%
!! TTTTCATAAGTGTTTATGTC+AGG - chr5_4:11823278-11823297 Msa0837780:intron 25.0%
! AATGATAACAGTTGTCTATT+TGG + chr5_4:11823326-11823345 None:intergenic 25.0%
!! TTAAGTTGTTTATCCAAACA+AGG + chr5_4:11823595-11823614 None:intergenic 25.0%
! TATGAAAATAACGAGGAATT+TGG - chr5_4:11823864-11823883 Msa0837780:CDS 25.0%
!!! CCTTATATTTTTGGATATAG+AGG + chr5_4:11823912-11823931 None:intergenic 25.0%
! CCTCTATATCCAAAAATATA+AGG - chr5_4:11823909-11823928 Msa0837780:intron 25.0%
! TATATCCAAAAATATAAGGG+TGG - chr5_4:11823913-11823932 Msa0837780:intron 25.0%
!! ACAAATTTTCACATACTCAA+GGG + chr5_4:11824014-11824033 None:intergenic 25.0%
!! ATACTTTAAAGGCTAAATAG+AGG - chr5_4:11824098-11824117 Msa0837780:intron 25.0%
! TAATGAAGGGATTAAATTGA+AGG - chr5_4:11824130-11824149 Msa0837780:intron 25.0%
!! CTATAATTTGTATGAATGTG+GGG - chr5_4:11824341-11824360 Msa0837780:intron 25.0%
! ATTGAATCTATCTCAAGTAA+TGG - chr5_4:11824708-11824727 Msa0837780:CDS 25.0%
! AATCAAAGAAGTAAAACTAC+AGG - chr5_4:11824737-11824756 Msa0837780:CDS 25.0%
! AACAGAACTATTCTATTCAA+TGG + chr5_4:11824808-11824827 None:intergenic 25.0%
!!! TGTTTTTGTACCAAACAAAA+TGG - chr5_4:11824824-11824843 Msa0837780:five_prime_UTR 25.0%
CTCAAACAATAAGGGTAAAA+CGG + chr5_4:11822546-11822565 None:intergenic 30.0%
TTACCCTTATTGTTTGAGAA+CGG - chr5_4:11822548-11822567 Msa0837780:three_prime_UTR 30.0%
AGAGAGTTATATATACGTAC+GGG + chr5_4:11822658-11822677 None:intergenic 30.0%
! AATGTTTCTCTGATTTTCGT+AGG - chr5_4:11822726-11822745 Msa0837780:three_prime_UTR 30.0%
AAATCAAGCTCAACAACAAA+AGG + chr5_4:11822797-11822816 None:intergenic 30.0%
!! TATATACATAAGAGGGTATC+AGG + chr5_4:11823095-11823114 None:intergenic 30.0%
TGATACCCTCTTATGTATAT+AGG - chr5_4:11823094-11823113 Msa0837780:intron 30.0%
TAACAGTTGTCTATTTGGAT+TGG + chr5_4:11823321-11823340 None:intergenic 30.0%
! TTTTGTGCTTGTTTAGATGA+TGG - chr5_4:11823377-11823396 Msa0837780:intron 30.0%
TTTGTGCTTGTTTAGATGAT+GGG - chr5_4:11823378-11823397 Msa0837780:intron 30.0%
!! TTCTTAGACTTTTGCTTTTC+TGG - chr5_4:11823504-11823523 Msa0837780:intron 30.0%
!! TCTTAGACTTTTGCTTTTCT+GGG - chr5_4:11823505-11823524 Msa0837780:intron 30.0%
TTTCATACTTAGTCCTTGTT+TGG - chr5_4:11823579-11823598 Msa0837780:intron 30.0%
! ACTTTCCACCCTTATATTTT+TGG + chr5_4:11823921-11823940 None:intergenic 30.0%
! GACAAATTTTCACATACTCA+AGG + chr5_4:11824015-11824034 None:intergenic 30.0%
CATTAGTACTTAAGATGCTA+GGG + chr5_4:11824046-11824065 None:intergenic 30.0%
TCATTAGTACTTAAGATGCT+AGG + chr5_4:11824047-11824066 None:intergenic 30.0%
TCTTAAGTACTAATGAGACA+AGG - chr5_4:11824051-11824070 Msa0837780:intron 30.0%
CTTAAGTACTAATGAGACAA+GGG - chr5_4:11824052-11824071 Msa0837780:intron 30.0%
TTAAGTACTAATGAGACAAG+GGG - chr5_4:11824053-11824072 Msa0837780:intron 30.0%
! AGAGGAGATAATGATAATGA+AGG - chr5_4:11824116-11824135 Msa0837780:intron 30.0%
! GAGGAGATAATGATAATGAA+GGG - chr5_4:11824117-11824136 Msa0837780:intron 30.0%
ATGAGCAAACTTTGTAAGAA+TGG + chr5_4:11824222-11824241 None:intergenic 30.0%
TTCGATATACATGAAAATGC+GGG + chr5_4:11824369-11824388 None:intergenic 30.0%
CTTCGATATACATGAAAATG+CGG + chr5_4:11824370-11824389 None:intergenic 30.0%
!! ATTTGACATTGGTTCTTTGT+AGG + chr5_4:11824763-11824782 None:intergenic 30.0%
AAGACAAGACAATTTGACAT+TGG + chr5_4:11824774-11824793 None:intergenic 30.0%
AAATCAGTGTCGTGTCAAAT+TGG - chr5_4:11822423-11822442 Msa0837780:three_prime_UTR 35.0%
AATCAGTGTCGTGTCAAATT+GGG - chr5_4:11822424-11822443 Msa0837780:three_prime_UTR 35.0%
GAAGAATGAAGATGTTACAG+TGG - chr5_4:11822492-11822511 Msa0837780:three_prime_UTR 35.0%
GTTCCGTTCTCAAACAATAA+GGG + chr5_4:11822554-11822573 None:intergenic 35.0%
! GGAAACTGAATTTGAAGCTT+CGG + chr5_4:11822576-11822595 None:intergenic 35.0%
!! GATTGCGTTTTGAACAAAAG+CGG + chr5_4:11822597-11822616 None:intergenic 35.0%
TATATATACGTACGGGCAAT+AGG + chr5_4:11822651-11822670 None:intergenic 35.0%
TAACGAGACAACACAATCAT+CGG + chr5_4:11822965-11822984 None:intergenic 35.0%
! AAAGTTTTCGCGTAAGCTAT+AGG - chr5_4:11823131-11823150 Msa0837780:intron 35.0%
!! AGATGATGGGTATCAAATTC+AGG - chr5_4:11823391-11823410 Msa0837780:intron 35.0%
!! GATGATGGGTATCAAATTCA+GGG - chr5_4:11823392-11823411 Msa0837780:intron 35.0%
! TTTGTCTATGGGAAGCATAT+TGG - chr5_4:11823458-11823477 Msa0837780:intron 35.0%
TTAAGATGCTAGGGATTAAC+AGG + chr5_4:11824037-11824056 None:intergenic 35.0%
TGGATAGAGAAACACAAAGA+GGG + chr5_4:11824202-11824221 None:intergenic 35.0%
ATGGATAGAGAAACACAAAG+AGG + chr5_4:11824203-11824222 None:intergenic 35.0%
TGATTGTATACTTGAGACTG+AGG - chr5_4:11824307-11824326 Msa0837780:intron 35.0%
! CGCATTTTCATGTATATCGA+AGG - chr5_4:11824368-11824387 Msa0837780:intron 35.0%
!!! ACATGTACTTTTAGCTTGTC+TGG - chr5_4:11824451-11824470 Msa0837780:intron 35.0%
!! TGGTACAAAGCCATTTTGTT+TGG + chr5_4:11824837-11824856 None:intergenic 35.0%
GGTTCCGTTCTCAAACAATA+AGG + chr5_4:11822555-11822574 None:intergenic 40.0%
GCAATAGGATTTGGAGAAGA+TGG + chr5_4:11822636-11822655 None:intergenic 40.0%
! TCAAATTCAGGGTGTTCTTC+TGG - chr5_4:11823403-11823422 Msa0837780:intron 40.0%
GGTGTTCTTCTGGATTTGAT+TGG - chr5_4:11823413-11823432 Msa0837780:intron 40.0%
TCCCACAAGTGTTTGTCTAT+GGG - chr5_4:11823447-11823466 Msa0837780:intron 40.0%
TCCCATAGACAAACACTTGT+GGG + chr5_4:11823451-11823470 None:intergenic 40.0%
TTCCCATAGACAAACACTTG+TGG + chr5_4:11823452-11823471 None:intergenic 40.0%
! AAGCATATTGGTGGATCAGA+TGG - chr5_4:11823470-11823489 Msa0837780:intron 40.0%
GTGGAAAGTGAGAGAAGATA+GGG - chr5_4:11823932-11823951 Msa0837780:intron 40.0%
GGAGAAGATGGTGATTCTGT+TGG + chr5_4:11822624-11822643 None:intergenic 45.0%
TACGTACGGGCAATAGGATT+TGG + chr5_4:11822645-11822664 None:intergenic 45.0%
!! GTTGTTGAGCTTGATTTGCG+AGG - chr5_4:11822800-11822819 Msa0837780:three_prime_UTR 45.0%
ACTGCTTTCATGGTCTGTCA+TGG - chr5_4:11823203-11823222 Msa0837780:intron 45.0%
GTCCCACAAGTGTTTGTCTA+TGG - chr5_4:11823446-11823465 Msa0837780:intron 45.0%
! GTCTATGGGAAGCATATTGG+TGG - chr5_4:11823461-11823480 Msa0837780:intron 45.0%
AGGGATGCATGTTTGAGAGA+GGG + chr5_4:11823892-11823911 None:intergenic 45.0%
GGTGGAAAGTGAGAGAAGAT+AGG - chr5_4:11823931-11823950 Msa0837780:intron 45.0%
GTTTCTGCAATTCACCACTC+TGG + chr5_4:11824273-11824292 None:intergenic 45.0%
CGAAGGTTTCAAGCTTCTAG+CGG - chr5_4:11824385-11824404 Msa0837780:intron 45.0%
! GAAAGTACGATCATGAGCAG+TGG - chr5_4:11824521-11824540 Msa0837780:CDS 45.0%
! AGCAGTGGAGCTCTAATTGT+TGG - chr5_4:11824536-11824555 Msa0837780:intron 45.0%
GAGGGATGCATGTTTGAGAG+AGG + chr5_4:11823893-11823912 None:intergenic 50.0%
CTCAGTGCTGCAGTCCAGAG+TGG - chr5_4:11824256-11824275 Msa0837780:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 11822395 11824898 11822395 ID=Msa0837780;Name=Msa0837780
chr5_4 mRNA 11822395 11824898 11822395 ID=Msa0837780-mRNA-1;Parent=Msa0837780;Name=Msa0837780-mRNA-1;_AED=0.17;_eAED=0.17;_QI=102|1|1|1|1|1|4|589|129
chr5_4 exon 11822395 11823039 11822395 ID=Msa0837780-mRNA-1:exon:5230;Parent=Msa0837780-mRNA-1
chr5_4 exon 11823802 11823900 11823802 ID=Msa0837780-mRNA-1:exon:5229;Parent=Msa0837780-mRNA-1
chr5_4 exon 11824472 11824545 11824472 ID=Msa0837780-mRNA-1:exon:5228;Parent=Msa0837780-mRNA-1
chr5_4 exon 11824636 11824898 11824636 ID=Msa0837780-mRNA-1:exon:5227;Parent=Msa0837780-mRNA-1
chr5_4 five_prime_UTR 11824797 11824898 11824797 ID=Msa0837780-mRNA-1:five_prime_utr;Parent=Msa0837780-mRNA-1
chr5_4 CDS 11824636 11824796 11824636 ID=Msa0837780-mRNA-1:cds;Parent=Msa0837780-mRNA-1
chr5_4 CDS 11824472 11824545 11824472 ID=Msa0837780-mRNA-1:cds;Parent=Msa0837780-mRNA-1
chr5_4 CDS 11823802 11823900 11823802 ID=Msa0837780-mRNA-1:cds;Parent=Msa0837780-mRNA-1
chr5_4 CDS 11822984 11823039 11822984 ID=Msa0837780-mRNA-1:cds;Parent=Msa0837780-mRNA-1
chr5_4 three_prime_UTR 11822395 11822983 11822395 ID=Msa0837780-mRNA-1:three_prime_utr;Parent=Msa0837780-mRNA-1
Gene Sequence

>Msa0837780

ATGAAGATGTTACAGTGGAGCATGTTCATAACTCTCACGTTATTGACCGTTTTACCCTTATTGTTTGAGAACGGAACCGAAGCTTCAAATTCAGTTTCCGCTTTTGTTCAAAACGCAATCTACTCCAACAGAATCACCATCTTCTCCAAATCCTATTGCCCGTATTGTTTACGTGCTAAACGTGTTTTTGTTGAACTAAATGAGCAACCTTTTGTTGTTGAGCTTGATTTGCGAGATGATGGGTATCAAATTCAGGGTGTTCTTCTGGATTTGATTGGTAGAAGAACAGTCCCACAAGTGTTTGTCTATGGGAAGCATATTGGTGGATCAGATGATCTCAGTGCTGCAGTCCAGAGTGGTGAATTGCAGAAACTTCTCAAATCAAGTTGA

Protein sequence

>Msa0837780

MKMLQWSMFITLTLLTVLPLLFENGTEASNSVSAFVQNAIYSNRITIFSKSYCPYCLRAKRVFVELNEQPFVVELDLRDDGYQIQGVLLDLIGRRTVPQVFVYGKHIGGSDDLSAAVQSGELQKLLKSS*