AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1073720


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1073720 MtrunA17_Chr7g0256741 93.125 160 11 0 3 162 50 209 1.93e-108 311
Msa1073720 MtrunA17_Chr4g0004071 39.375 160 95 2 3 162 49 206 3.78e-36 127
Msa1073720 MtrunA17_Chr4g0004061 37.500 160 98 2 3 162 49 206 1.35e-34 123
Msa1073720 MtrunA17_Chr1g0148781 29.448 163 110 4 3 162 54 214 3.60e-19 82.4
Msa1073720 MtrunA17_Chr3g0138351 28.395 162 113 3 3 162 50 210 2.48e-15 71.6
Msa1073720 MtrunA17_Chr4g0009541 32.468 154 94 6 15 162 59 208 8.60e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1073720 AT1G52820.2 42.949 156 87 2 7 162 56 209 2.38e-39 134
Msa1073720 AT1G52820.1 42.675 157 88 2 7 163 56 210 1.38e-38 134
Msa1073720 AT1G52800.1 38.994 159 95 2 4 162 52 208 2.48e-37 130
Msa1073720 AT1G52790.1 39.375 160 95 2 3 162 46 203 6.54e-36 126
Msa1073720 AT1G80320.1 36.646 161 99 3 4 162 50 209 2.35e-31 115
Msa1073720 AT4G03070.1 37.725 167 91 5 3 162 54 214 5.24e-26 100
Msa1073720 AT1G52810.1 40.000 105 63 0 3 107 52 156 1.55e-21 88.6
Msa1073720 AT4G03050.2 32.051 156 92 3 3 158 48 189 6.77e-18 79.7
Msa1073720 AT4G03050.1 32.051 156 92 3 3 158 48 189 6.77e-18 79.7
Msa1073720 AT1G15540.3 34.591 159 98 4 8 162 61 217 9.26e-18 79.0
Msa1073720 AT1G15540.2 34.591 159 98 4 8 162 57 213 9.90e-18 79.0
Msa1073720 AT1G15540.1 34.591 159 98 4 8 162 54 210 1.09e-17 78.6
Msa1073720 AT1G15540.4 34.591 159 98 4 8 162 54 210 1.09e-17 78.6

Find 34 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTGACAATGTTATATT+TGG 0.130973 7_2:-71341034 Msa1073720:CDS
GTCTAATTCTCCCAACAATT+TGG 0.196750 7_2:+71340507 None:intergenic
TCCTTGAGGCCATATGATTT+TGG 0.205239 7_2:+71340856 None:intergenic
CTCAAGGAAATGATCGTTTC+TGG 0.227781 7_2:-71340841 Msa1073720:intron
ACTTCCCTTATATGAATCTT+TGG 0.231965 7_2:-71340921 Msa1073720:CDS
TGACATCCAAGCATAGTTAA+TGG 0.255056 7_2:+71340887 None:intergenic
AGAGATGGATGAGAAGGATT+TGG 0.277633 7_2:-71340374 Msa1073720:CDS
GATATCCAAAGATTCATATA+AGG 0.300354 7_2:+71340916 None:intergenic
AACATTGTCAGAAAGTTCTT+TGG 0.308306 7_2:+71341042 None:intergenic
GAGATGGATGAGAAGGATTT+GGG 0.312045 7_2:-71340373 Msa1073720:CDS
CATCAGCTAAATAATGTAAA+TGG 0.321665 7_2:-71340310 Msa1073720:CDS
ATACCATCCTCTTTGCTATA+TGG 0.351908 7_2:+71340485 None:intergenic
TAATTTCTTGATTCTATCAA+TGG 0.386845 7_2:+71340427 None:intergenic
CAAGCATAGTTAATGGATCT+TGG 0.392821 7_2:+71340894 None:intergenic
AGAATTCTTCAAGCTCCCTT+TGG 0.396656 7_2:-71341005 Msa1073720:CDS
AATGAGTACTCCAAATTGTT+GGG 0.403546 7_2:-71340517 Msa1073720:CDS
CTGATGTACTACAGATATAA+TGG 0.431408 7_2:+71340327 None:intergenic
CAATGAGTACTCCAAATTGT+TGG 0.439455 7_2:-71340518 Msa1073720:CDS
CAAGATCCATTAACTATGCT+TGG 0.444301 7_2:-71340893 Msa1073720:CDS
AAATATTCACCAAAATCATA+TGG 0.463691 7_2:-71340865 Msa1073720:CDS
ATATCCAAAGATTCATATAA+GGG 0.472934 7_2:+71340917 None:intergenic
AACAAGAGAGATGGATGAGA+AGG 0.485145 7_2:-71340380 Msa1073720:CDS
AGACCTTTCCATGGCTACTC+AGG 0.493237 7_2:-71340956 Msa1073720:CDS
GTAGCACACTATGATAAAGT+TGG 0.526616 7_2:-71341065 None:intergenic
ACCAAAATCATATGGCCTCA+AGG 0.544014 7_2:-71340857 Msa1073720:CDS
AGAGTTGTCCTGAGTAGCCA+TGG 0.568925 7_2:+71340948 None:intergenic
GAAATATAGAACAAGAGAGA+TGG 0.576102 7_2:-71340389 Msa1073720:CDS
AGGATGGTATTTGAAAGCTA+TGG 0.598356 7_2:-71340472 Msa1073720:CDS
ATAATGGTCAAGTCTGAATG+AGG 0.623723 7_2:+71340343 None:intergenic
TGTCCTGAGTAGCCATGGAA+AGG 0.627328 7_2:+71340953 None:intergenic
ATAAGTGATAGACCTTTCCA+TGG 0.632144 7_2:-71340965 Msa1073720:CDS
AGACCATATAGCAAAGAGGA+TGG 0.638381 7_2:-71340488 Msa1073720:CDS
CAGAAACGATCATTTCCTTG+AGG 0.669988 7_2:+71340842 None:intergenic
AATTAGACCATATAGCAAAG+AGG 0.678010 7_2:-71340492 Msa1073720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAATAAATATATATTTTGA+TGG + chr7_2:71340769-71340788 None:intergenic 10.0%
!!! TCAATAAATATATATTTTGA+TGG + chr7_2:71340769-71340788 None:intergenic 10.0%
!! ATATCCAAAGATTCATATAA+GGG + chr7_2:71340435-71340454 None:intergenic 20.0%
!! AAATATTCACCAAAATCATA+TGG - chr7_2:71340484-71340503 Msa1073720:CDS 20.0%
!! TAATTTCTTGATTCTATCAA+TGG + chr7_2:71340925-71340944 None:intergenic 20.0%
!! ATATCCAAAGATTCATATAA+GGG + chr7_2:71340435-71340454 None:intergenic 20.0%
!! AAATATTCACCAAAATCATA+TGG - chr7_2:71340484-71340503 Msa1073720:CDS 20.0%
!! TAATTTCTTGATTCTATCAA+TGG + chr7_2:71340925-71340944 None:intergenic 20.0%
! CTTTCTGACAATGTTATATT+TGG - chr7_2:71340315-71340334 Msa1073720:CDS 25.0%
! GATATCCAAAGATTCATATA+AGG + chr7_2:71340436-71340455 None:intergenic 25.0%
! TGCTTCATGAATCTATATTA+TGG + chr7_2:71340548-71340567 None:intergenic 25.0%
! TCTCAAATTATTAGTGATGT+CGG - chr7_2:71340668-71340687 Msa1073720:intron 25.0%
! CATCAGCTAAATAATGTAAA+TGG - chr7_2:71341039-71341058 Msa1073720:CDS 25.0%
! CTTTCTGACAATGTTATATT+TGG - chr7_2:71340315-71340334 Msa1073720:CDS 25.0%
! GATATCCAAAGATTCATATA+AGG + chr7_2:71340436-71340455 None:intergenic 25.0%
! TGCTTCATGAATCTATATTA+TGG + chr7_2:71340548-71340567 None:intergenic 25.0%
! TCTCAAATTATTAGTGATGT+CGG - chr7_2:71340668-71340687 Msa1073720:intron 25.0%
! CATCAGCTAAATAATGTAAA+TGG - chr7_2:71341039-71341058 Msa1073720:CDS 25.0%
AACATTGTCAGAAAGTTCTT+TGG + chr7_2:71340310-71340329 None:intergenic 30.0%
ACTTCCCTTATATGAATCTT+TGG - chr7_2:71340428-71340447 Msa1073720:CDS 30.0%
CTCAAATTATTAGTGATGTC+GGG - chr7_2:71340669-71340688 Msa1073720:intron 30.0%
AGATAAGAGAATATGAAGCA+CGG + chr7_2:71340739-71340758 None:intergenic 30.0%
AATGAGTACTCCAAATTGTT+GGG - chr7_2:71340832-71340851 Msa1073720:intron 30.0%
AATTAGACCATATAGCAAAG+AGG - chr7_2:71340857-71340876 Msa1073720:CDS 30.0%
GAAATATAGAACAAGAGAGA+TGG - chr7_2:71340960-71340979 Msa1073720:CDS 30.0%
CTGATGTACTACAGATATAA+TGG + chr7_2:71341025-71341044 None:intergenic 30.0%
AACATTGTCAGAAAGTTCTT+TGG + chr7_2:71340310-71340329 None:intergenic 30.0%
ACTTCCCTTATATGAATCTT+TGG - chr7_2:71340428-71340447 Msa1073720:CDS 30.0%
CTCAAATTATTAGTGATGTC+GGG - chr7_2:71340669-71340688 Msa1073720:intron 30.0%
AGATAAGAGAATATGAAGCA+CGG + chr7_2:71340739-71340758 None:intergenic 30.0%
AATGAGTACTCCAAATTGTT+GGG - chr7_2:71340832-71340851 Msa1073720:intron 30.0%
AATTAGACCATATAGCAAAG+AGG - chr7_2:71340857-71340876 Msa1073720:CDS 30.0%
GAAATATAGAACAAGAGAGA+TGG - chr7_2:71340960-71340979 Msa1073720:CDS 30.0%
CTGATGTACTACAGATATAA+TGG + chr7_2:71341025-71341044 None:intergenic 30.0%
!! TTTGCGCTTTTGTTTCCAAA+GGG + chr7_2:71340362-71340381 None:intergenic 35.0%
!! TTTTGCGCTTTTGTTTCCAA+AGG + chr7_2:71340363-71340382 None:intergenic 35.0%
ATAAGTGATAGACCTTTCCA+TGG - chr7_2:71340384-71340403 Msa1073720:CDS 35.0%
! CAAGCATAGTTAATGGATCT+TGG + chr7_2:71340458-71340477 None:intergenic 35.0%
CAAGATCCATTAACTATGCT+TGG - chr7_2:71340456-71340475 Msa1073720:CDS 35.0%
TGACATCCAAGCATAGTTAA+TGG + chr7_2:71340465-71340484 None:intergenic 35.0%
AAATTATTAGTGATGTCGGG+CGG - chr7_2:71340672-71340691 Msa1073720:intron 35.0%
CAATGAGTACTCCAAATTGT+TGG - chr7_2:71340831-71340850 Msa1073720:intron 35.0%
GTCTAATTCTCCCAACAATT+TGG + chr7_2:71340845-71340864 None:intergenic 35.0%
! ATACCATCCTCTTTGCTATA+TGG + chr7_2:71340867-71340886 None:intergenic 35.0%
AGGATGGTATTTGAAAGCTA+TGG - chr7_2:71340877-71340896 Msa1073720:CDS 35.0%
ATAATGGTCAAGTCTGAATG+AGG + chr7_2:71341009-71341028 None:intergenic 35.0%
!! TTTGCGCTTTTGTTTCCAAA+GGG + chr7_2:71340362-71340381 None:intergenic 35.0%
!! TTTTGCGCTTTTGTTTCCAA+AGG + chr7_2:71340363-71340382 None:intergenic 35.0%
ATAAGTGATAGACCTTTCCA+TGG - chr7_2:71340384-71340403 Msa1073720:CDS 35.0%
! CAAGCATAGTTAATGGATCT+TGG + chr7_2:71340458-71340477 None:intergenic 35.0%
CAAGATCCATTAACTATGCT+TGG - chr7_2:71340456-71340475 Msa1073720:CDS 35.0%
TGACATCCAAGCATAGTTAA+TGG + chr7_2:71340465-71340484 None:intergenic 35.0%
AAATTATTAGTGATGTCGGG+CGG - chr7_2:71340672-71340691 Msa1073720:intron 35.0%
CAATGAGTACTCCAAATTGT+TGG - chr7_2:71340831-71340850 Msa1073720:intron 35.0%
GTCTAATTCTCCCAACAATT+TGG + chr7_2:71340845-71340864 None:intergenic 35.0%
! ATACCATCCTCTTTGCTATA+TGG + chr7_2:71340867-71340886 None:intergenic 35.0%
AGGATGGTATTTGAAAGCTA+TGG - chr7_2:71340877-71340896 Msa1073720:CDS 35.0%
ATAATGGTCAAGTCTGAATG+AGG + chr7_2:71341009-71341028 None:intergenic 35.0%
AGAATTCTTCAAGCTCCCTT+TGG - chr7_2:71340344-71340363 Msa1073720:CDS 40.0%
ACCAAAATCATATGGCCTCA+AGG - chr7_2:71340492-71340511 Msa1073720:CDS 40.0%
! TCCTTGAGGCCATATGATTT+TGG + chr7_2:71340496-71340515 None:intergenic 40.0%
CAGAAACGATCATTTCCTTG+AGG + chr7_2:71340510-71340529 None:intergenic 40.0%
CTCAAGGAAATGATCGTTTC+TGG - chr7_2:71340508-71340527 Msa1073720:CDS 40.0%
!! AGGAAATGATCGTTTCTGGT+TGG - chr7_2:71340512-71340531 Msa1073720:CDS 40.0%
TATCAGTGTCGTGTTTGTGT+CGG + chr7_2:71340620-71340639 None:intergenic 40.0%
GAGAATATGAAGCACGGATA+TGG + chr7_2:71340733-71340752 None:intergenic 40.0%
AGACCATATAGCAAAGAGGA+TGG - chr7_2:71340861-71340880 Msa1073720:CDS 40.0%
AACAAGAGAGATGGATGAGA+AGG - chr7_2:71340969-71340988 Msa1073720:CDS 40.0%
AGAGATGGATGAGAAGGATT+TGG - chr7_2:71340975-71340994 Msa1073720:CDS 40.0%
GAGATGGATGAGAAGGATTT+GGG - chr7_2:71340976-71340995 Msa1073720:CDS 40.0%
AGAATTCTTCAAGCTCCCTT+TGG - chr7_2:71340344-71340363 Msa1073720:CDS 40.0%
ACCAAAATCATATGGCCTCA+AGG - chr7_2:71340492-71340511 Msa1073720:CDS 40.0%
! TCCTTGAGGCCATATGATTT+TGG + chr7_2:71340496-71340515 None:intergenic 40.0%
CAGAAACGATCATTTCCTTG+AGG + chr7_2:71340510-71340529 None:intergenic 40.0%
CTCAAGGAAATGATCGTTTC+TGG - chr7_2:71340508-71340527 Msa1073720:CDS 40.0%
!! AGGAAATGATCGTTTCTGGT+TGG - chr7_2:71340512-71340531 Msa1073720:CDS 40.0%
TATCAGTGTCGTGTTTGTGT+CGG + chr7_2:71340620-71340639 None:intergenic 40.0%
GAGAATATGAAGCACGGATA+TGG + chr7_2:71340733-71340752 None:intergenic 40.0%
AGACCATATAGCAAAGAGGA+TGG - chr7_2:71340861-71340880 Msa1073720:CDS 40.0%
AACAAGAGAGATGGATGAGA+AGG - chr7_2:71340969-71340988 Msa1073720:CDS 40.0%
AGAGATGGATGAGAAGGATT+TGG - chr7_2:71340975-71340994 Msa1073720:CDS 40.0%
GAGATGGATGAGAAGGATTT+GGG - chr7_2:71340976-71340995 Msa1073720:CDS 40.0%
! TCCACGGATTAAACATGTCC+CGG - chr7_2:71340575-71340594 Msa1073720:intron 45.0%
ACACAACACATGTCTGACAC+CGG + chr7_2:71340597-71340616 None:intergenic 45.0%
ACGGATATGGATACAGACAC+CGG + chr7_2:71340720-71340739 None:intergenic 45.0%
! TCCACGGATTAAACATGTCC+CGG - chr7_2:71340575-71340594 Msa1073720:intron 45.0%
ACACAACACATGTCTGACAC+CGG + chr7_2:71340597-71340616 None:intergenic 45.0%
ACGGATATGGATACAGACAC+CGG + chr7_2:71340720-71340739 None:intergenic 45.0%
AGACCTTTCCATGGCTACTC+AGG - chr7_2:71340393-71340412 Msa1073720:CDS 50.0%
TGTCCTGAGTAGCCATGGAA+AGG + chr7_2:71340399-71340418 None:intergenic 50.0%
AGAGTTGTCCTGAGTAGCCA+TGG + chr7_2:71340404-71340423 None:intergenic 50.0%
CATGAAGCACAGACACTCCA+CGG - chr7_2:71340559-71340578 Msa1073720:intron 50.0%
ACCGGGACATGTTTAATCCG+TGG + chr7_2:71340579-71340598 None:intergenic 50.0%
CACAACACATGTCTGACACC+GGG + chr7_2:71340596-71340615 None:intergenic 50.0%
AGACCTTTCCATGGCTACTC+AGG - chr7_2:71340393-71340412 Msa1073720:CDS 50.0%
TGTCCTGAGTAGCCATGGAA+AGG + chr7_2:71340399-71340418 None:intergenic 50.0%
AGAGTTGTCCTGAGTAGCCA+TGG + chr7_2:71340404-71340423 None:intergenic 50.0%
CATGAAGCACAGACACTCCA+CGG - chr7_2:71340559-71340578 Msa1073720:intron 50.0%
ACCGGGACATGTTTAATCCG+TGG + chr7_2:71340579-71340598 None:intergenic 50.0%
CACAACACATGTCTGACACC+GGG + chr7_2:71340596-71340615 None:intergenic 50.0%
TACAGACACCGGACGCGACA+CGG + chr7_2:71340709-71340728 None:intergenic 60.0%
TACAGACACCGGACGCGACA+CGG + chr7_2:71340709-71340728 None:intergenic 60.0%
GTCAGTGTCCGTGTCGCGTC+CGG - chr7_2:71340698-71340717 Msa1073720:intron 65.0%
GTCAGTGTCCGTGTCGCGTC+CGG - chr7_2:71340698-71340717 Msa1073720:intron 65.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 71340294 71341077 71340294 ID=Msa1073720;Name=Msa1073720
chr7_2 mRNA 71340294 71341077 71340294 ID=Msa1073720-mRNA-1;Parent=Msa1073720;Name=Msa1073720-mRNA-1;_AED=0.40;_eAED=0.41;_QI=0|0|0|1|1|1|2|0|163
chr7_2 exon 71340842 71341077 71340842 ID=Msa1073720-mRNA-1:exon:16166;Parent=Msa1073720-mRNA-1
chr7_2 exon 71340294 71340549 71340294 ID=Msa1073720-mRNA-1:exon:16165;Parent=Msa1073720-mRNA-1
chr7_2 CDS 71340842 71341077 71340842 ID=Msa1073720-mRNA-1:cds;Parent=Msa1073720-mRNA-1
chr7_2 CDS 71340294 71340549 71340294 ID=Msa1073720-mRNA-1:cds;Parent=Msa1073720-mRNA-1
Gene Sequence

>Msa1073720

ATGATAAAGTTGGCCAAAGAACTTTCTGACAATGTTATATTTGGAATTGAAGAATTCTTCAAGCTCCCTTTGGAAACAAAAGCGCAAAAGATAAGTGATAGACCTTTCCATGGCTACTCAGGACAACTCTCAACACTTCCCTTATATGAATCTTTGGATATCCAAGATCCATTAACTATGCTTGGATGTCAAATATTCACCAAAATCATATGGCCTCAAGGAAATGATCGTTTCTGCGAAAGTTTCAATGAGTACTCCAAATTGTTGGGAGAATTAGACCATATAGCAAAGAGGATGGTATTTGAAAGCTATGGTGTTGATATGAAAATATGTGAACCATTGATAGAATCAAGAAATTATCTCATTCGATGCTTGAAATATAGAACAAGAGAGATGGATGAGAAGGATTTGGGATTAACACCTCATTCAGACTTGACCATTATATCTGTAGTACATCAGCTAAATAATGTAAATGGCTTGCAAATCAATTGA

Protein sequence

>Msa1073720

MIKLAKELSDNVIFGIEEFFKLPLETKAQKISDRPFHGYSGQLSTLPLYESLDIQDPLTMLGCQIFTKIIWPQGNDRFCESFNEYSKLLGELDHIAKRMVFESYGVDMKICEPLIESRNYLIRCLKYRTREMDEKDLGLTPHSDLTIISVVHQLNNVNGLQIN*