AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015671

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015671.t1 MTR_8g105110 100.000 154 0 0 1 154 1 154 4.92e-111 312
MS.gene015671.t1 MTR_1g070450 95.455 154 5 1 1 154 1 152 4.61e-104 294
MS.gene015671.t1 MTR_4g075450 92.857 154 9 1 1 154 1 152 4.90e-92 264
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015671.t1 AT5G09500 87.662 154 15 1 1 154 1 150 1.07e-93 268
MS.gene015671.t1 AT5G09510 91.558 154 11 1 1 154 1 152 3.57e-92 264
MS.gene015671.t1 AT1G04270 91.558 154 11 1 1 154 1 152 4.12e-92 264
MS.gene015671.t1 AT1G04270 90.909 154 11 2 1 154 1 151 1.39e-89 258
MS.gene015671.t1 AT5G09490 81.818 154 26 1 1 154 1 152 9.71e-89 255
MS.gene015671.t1 AT5G43640 85.906 149 21 0 6 154 1 149 1.10e-82 240
MS.gene015671.t1 AT5G09510 94.915 118 6 0 37 154 1 118 2.08e-71 210
MS.gene015671.t1 AT5G63070 62.500 160 54 2 1 154 1 160 3.08e-64 194
MS.gene015671.t1 AT1G33850 83.607 61 10 0 12 72 7 67 1.12e-19 78.2

Find 43 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGATTTCAACTTGGTTAA+AGG 0.236449 4.4:-2259236 None:intergenic
GAGATGATTGGGAGCATTAT+TGG 0.247005 4.4:+2259196 MS.gene015671:CDS
CAGTTTCAGAGGAGTTGATT+TGG 0.292075 4.4:+2257958 MS.gene015671:CDS
CCAGGTCTACCATGCTTAAC+AGG 0.341486 4.4:-2259307 None:intergenic
TCAGTGCTCGTGCTCGTAGA+AGG 0.367007 4.4:+2258023 MS.gene015671:CDS
TTCTTGAATGTTCTCTTCTT+CGG 0.377124 4.4:-2257932 None:intergenic
AGATGGGTCCTAACAGGTTC+GGG 0.405557 4.4:-2259151 None:intergenic
GTGAGAAGCCCGAACCTGTT+AGG 0.409377 4.4:+2259143 MS.gene015671:CDS
GATGCAGCAGCCGCCGCCGC+GGG 0.422266 4.4:+2257905 MS.gene015671:CDS
TTACGAAGATGGGTCCTAAC+AGG 0.435557 4.4:-2259157 None:intergenic
AAGATGGGTCCTAACAGGTT+CGG 0.450751 4.4:-2259152 None:intergenic
CAATGATCATGTTACGAAGA+TGG 0.465315 4.4:-2259168 None:intergenic
ATCATTGTACCTGAGATGAT+TGG 0.468347 4.4:+2259184 MS.gene015671:CDS
TTCAAGAAGTTCAGTTTCAG+AGG 0.481387 4.4:+2257947 MS.gene015671:CDS
AGGTAATGACCGATCATCTC+AGG 0.492365 4.4:-2259259 None:intergenic
CCTGTTAAGCATGGTAGACC+TGG 0.509940 4.4:+2259307 MS.gene015671:CDS
AATGATCATGTTACGAAGAT+GGG 0.516658 4.4:-2259167 None:intergenic
GCATTATTGGAGTGTACAAT+GGG 0.517140 4.4:+2259209 MS.gene015671:CDS
ACAGGTTCGGGCTTCTCACC+AGG 0.517899 4.4:-2259139 None:intergenic
CTTCGGTACTCCCGCGGCGG+CGG 0.518043 4.4:-2257915 None:intergenic
TTGGTGCTACTCACTCCTCC+AGG 0.521787 4.4:+2259332 MS.gene015671:CDS
ATAATGCTCCCAATCATCTC+AGG 0.528225 4.4:-2259193 None:intergenic
TCATTGTACCTGAGATGATT+GGG 0.539509 4.4:+2259185 MS.gene015671:CDS
GCTTACGAGTGAGACCTCTC+TGG 0.541580 4.4:-2258048 None:intergenic
TCTCAGGTTTGATTTCAACT+TGG 0.546765 4.4:-2259243 None:intergenic
AGCATTATTGGAGTGTACAA+TGG 0.558872 4.4:+2259208 MS.gene015671:CDS
TAGAAAAGGGAGGCACCACC+TGG 0.561975 4.4:+2259121 MS.gene015671:intron
TCACTTGAGAGGAATGAACC+TGG 0.566509 4.4:-2259350 None:intergenic
AGATGCAGCAGCCGCCGCCG+CGG 0.579389 4.4:+2257904 MS.gene015671:CDS
GAGTGAGTAGCACCAATACC+AGG 0.584094 4.4:-2259325 None:intergenic
GAAATCAAACCTGAGATGAT+CGG 0.585387 4.4:+2259250 MS.gene015671:CDS
AAGCATGGTAGACCTGGTAT+TGG 0.586812 4.4:+2259313 MS.gene015671:CDS
TCATACAAGCCTGTTAAGCA+TGG 0.604339 4.4:+2259298 MS.gene015671:CDS
GAGCTTAACAAGCTCATCAG+TGG 0.607114 4.4:-2257999 None:intergenic
AGGTCTCACTCGTAAGCCCA+TGG 0.623580 4.4:+2258054 MS.gene015671:CDS
AACAAGGTGATTCACTTGAG+AGG 0.631770 4.4:-2259361 None:intergenic
ATGAGATCGAGAATTCAGCT+AGG 0.682732 4.4:-2259279 None:intergenic
GGTTCGGGCTTCTCACCAGG+TGG 0.683492 4.4:-2259136 None:intergenic
TCTCTTCTTCGGTACTCCCG+CGG 0.697626 4.4:-2257921 None:intergenic
CTTCTTCGGTACTCCCGCGG+CGG 0.700206 4.4:-2257918 None:intergenic
GAATTGGTTGTAGAAAAGGG+AGG 0.733330 4.4:+2259111 MS.gene015671:intron
CTTGAGAGGAATGAACCTGG+AGG 0.737810 4.4:-2259347 None:intergenic
GCTCGTAGAAGGTTCCAGAG+AGG 0.763484 4.4:+2258034 MS.gene015671:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATTTGTAAAATAGTAAT+TGG + chr4.4:2258240-2258259 MS.gene015671:intron 10.0%
!!! AACACTTTTTTTTTTTTTTT+TGG + chr4.4:2258591-2258610 MS.gene015671:intron 10.0%
!!! ATTACTATTTTACAAATTTA+AGG - chr4.4:2258240-2258259 None:intergenic 10.0%
!!! TTTGTTATTTTTTTAATTTG+AGG + chr4.4:2258489-2258508 MS.gene015671:intron 10.0%
!! AAATCAAAATCAAATTCAAT+CGG - chr4.4:2257846-2257865 None:intergenic 15.0%
!! ATTACTATTATGCAAATTTA+AGG - chr4.4:2258555-2258574 None:intergenic 15.0%
!!! AAAAAAAAGTGTTCAATTTA+AGG - chr4.4:2258584-2258603 None:intergenic 15.0%
!!! AAAAAAAGTGTTCAATTTAA+GGG - chr4.4:2258583-2258602 None:intergenic 15.0%
!!! ATTGTTATAATTTTGTGAAT+TGG + chr4.4:2259095-2259114 MS.gene015671:intron 15.0%
!!! TTTGATTTTGATTTTGAATT+TGG + chr4.4:2257852-2257871 MS.gene015671:intron 15.0%
!!! TTTGTTATTCTTTTATTTAG+TGG + chr4.4:2258728-2258747 MS.gene015671:intron 15.0%
!! ATATGCAAAATACTAACAAT+TGG + chr4.4:2258211-2258230 MS.gene015671:intron 20.0%
!! TATGCAAAATACTAACAATT+GGG + chr4.4:2258212-2258231 MS.gene015671:intron 20.0%
!! TTTAGTACTTAAGATAGTAA+GGG - chr4.4:2259063-2259082 None:intergenic 20.0%
!!! AGGACTAACATTAAAATTTT+TGG - chr4.4:2258766-2258785 None:intergenic 20.0%
!!! ATTTAACACTACCATTTTAA+AGG + chr4.4:2258856-2258875 MS.gene015671:intron 20.0%
!!! GAAGTTTTTATTGATTTTGT+TGG + chr4.4:2258664-2258683 MS.gene015671:intron 20.0%
!!! GTTAGTATTTTGCATATTAA+AGG - chr4.4:2258208-2258227 None:intergenic 20.0%
!!! TGGTGGTTTTTTAAATTTAA+AGG + chr4.4:2258994-2259013 MS.gene015671:intron 20.0%
!!! TTGTTAATTTGTGAATTTGA+GGG + chr4.4:2259023-2259042 MS.gene015671:intron 20.0%
!!! TTTGTTAATTTGTGAATTTG+AGG + chr4.4:2259022-2259041 MS.gene015671:intron 20.0%
!!! TTTTAGTACTTAAGATAGTA+AGG - chr4.4:2259064-2259083 None:intergenic 20.0%
! AAATCGATGTTAGATTCTAT+CGG - chr4.4:2257823-2257842 None:intergenic 25.0%
! AACATGAAACCATTAAAATG+GGG - chr4.4:2258331-2258350 None:intergenic 25.0%
! AAGGAACTAAATTGATATCT+TGG - chr4.4:2258536-2258555 None:intergenic 25.0%
! AATAGCGATATTTAGGTATA+GGG + chr4.4:2258960-2258979 MS.gene015671:intron 25.0%
! ACTTCCATATAAACTTGAAA+AGG - chr4.4:2258649-2258668 None:intergenic 25.0%
! AGTAATTGGATACCAAAAAT+TGG + chr4.4:2258254-2258273 MS.gene015671:intron 25.0%
! GAACATGAAACCATTAAAAT+GGG - chr4.4:2258332-2258351 None:intergenic 25.0%
! TGAACATGAAACCATTAAAA+TGG - chr4.4:2258333-2258352 None:intergenic 25.0%
!! AAACAACAATCTTAGCATTT+TGG + chr4.4:2258165-2258184 MS.gene015671:intron 25.0%
!! AACAACAATCTTAGCATTTT+GGG + chr4.4:2258166-2258185 MS.gene015671:intron 25.0%
!! ATATGACATTGTCCAATTTT+TGG - chr4.4:2258269-2258288 None:intergenic 25.0%
!! GTGCTAATTTGCAAATATAA+AGG - chr4.4:2258786-2258805 None:intergenic 25.0%
!! TTTGATTTCAACTTGGTTAA+AGG - chr4.4:2259239-2259258 None:intergenic 25.0%
!!! AATTTGGAATTGAATTTTGC+AGG + chr4.4:2257868-2257887 MS.gene015671:intron 25.0%
!!! CTCTTGTTGATTATTGATTT+TGG + chr4.4:2258402-2258421 MS.gene015671:intron 25.0%
!!! CTGAAGATATATTTTGATTG+AGG + chr4.4:2258435-2258454 MS.gene015671:intron 25.0%
!!! GAAATTGATTGCTGTTTTTA+GGG + chr4.4:2258461-2258480 MS.gene015671:intron 25.0%
!!! TATGCCTTTTCAAGTTTATA+TGG + chr4.4:2258642-2258661 MS.gene015671:intron 25.0%
!!! TGTTGATTATTGATTTTGGT+GGG + chr4.4:2258406-2258425 MS.gene015671:intron 25.0%
!!! TTGTTGATTATTGATTTTGG+TGG + chr4.4:2258405-2258424 MS.gene015671:intron 25.0%
AAGGCATATAACCTTCAAAA+TGG - chr4.4:2258630-2258649 None:intergenic 30.0%
AATGATCATGTTACGAAGAT+GGG - chr4.4:2259170-2259189 None:intergenic 30.0%
CTTACTGAATAGCGATATTT+AGG + chr4.4:2258953-2258972 MS.gene015671:intron 30.0%
GAATAGCGATATTTAGGTAT+AGG + chr4.4:2258959-2258978 MS.gene015671:intron 30.0%
TGTGAATTGGTTGTAGAAAA+GGG + chr4.4:2259108-2259127 MS.gene015671:intron 30.0%
TTCTTGAATGTTCTCTTCTT+CGG - chr4.4:2257935-2257954 None:intergenic 30.0%
TTGTGAATTGGTTGTAGAAA+AGG + chr4.4:2259107-2259126 MS.gene015671:intron 30.0%
! ACGCATGTAAACCTTTAAAA+TGG - chr4.4:2258870-2258889 None:intergenic 30.0%
! ACTTTAGTACCCCATTTTAA+TGG + chr4.4:2258319-2258338 MS.gene015671:intron 30.0%
! TTAAAATGGGGTACTAAAGT+CGG - chr4.4:2258319-2258338 None:intergenic 30.0%
!!! CGAAATTGATTGCTGTTTTT+AGG + chr4.4:2258460-2258479 MS.gene015671:intron 30.0%
AGCATTATTGGAGTGTACAA+TGG + chr4.4:2259208-2259227 MS.gene015671:CDS 35.0%
ATAGGGACTAAATTGATTGG+TGG + chr4.4:2258977-2258996 MS.gene015671:intron 35.0%
ATCATTGTACCTGAGATGAT+TGG + chr4.4:2259184-2259203 MS.gene015671:CDS 35.0%
CAATGATCATGTTACGAAGA+TGG - chr4.4:2259171-2259190 None:intergenic 35.0%
GAAATCAAACCTGAGATGAT+CGG + chr4.4:2259250-2259269 MS.gene015671:CDS 35.0%
GCATATAACCTTCAAAATGG+TGG - chr4.4:2258627-2258646 None:intergenic 35.0%
GCATTATTGGAGTGTACAAT+GGG + chr4.4:2259209-2259228 MS.gene015671:CDS 35.0%
GGTATAGGGACTAAATTGAT+TGG + chr4.4:2258974-2258993 MS.gene015671:intron 35.0%
GTGACTCAGTGTTCAAATTA+AGG - chr4.4:2258816-2258835 None:intergenic 35.0%
TCATTGTACCTGAGATGATT+GGG + chr4.4:2259185-2259204 MS.gene015671:CDS 35.0%
TTCAAGAAGTTCAGTTTCAG+AGG + chr4.4:2257947-2257966 MS.gene015671:CDS 35.0%
! CAAAGTTACCACCATTTTGA+AGG + chr4.4:2258616-2258635 MS.gene015671:intron 35.0%
! TCTCAGGTTTGATTTCAACT+TGG - chr4.4:2259246-2259265 None:intergenic 35.0%
ATAATGCTCCCAATCATCTC+AGG - chr4.4:2259196-2259215 None:intergenic 40.0%
ATCGGAAATCGAGTTTCAGA+AGG - chr4.4:2257805-2257824 None:intergenic 40.0%
ATGAGATCGAGAATTCAGCT+AGG - chr4.4:2259282-2259301 None:intergenic 40.0%
CATCAAAAAGCTTCGCAAAG+CGG + chr4.4:2258081-2258100 MS.gene015671:CDS 40.0%
GAATTGGTTGTAGAAAAGGG+AGG + chr4.4:2259111-2259130 MS.gene015671:intron 40.0%
TCATACAAGCCTGTTAAGCA+TGG + chr4.4:2259298-2259317 MS.gene015671:CDS 40.0%
! AAGCTTTTTGATGAGAGCCA+TGG - chr4.4:2258074-2258093 None:intergenic 40.0%
! AGCTTTTTGATGAGAGCCAT+GGG - chr4.4:2258073-2258092 None:intergenic 40.0%
! CAGTTTCAGAGGAGTTGATT+TGG + chr4.4:2257958-2257977 MS.gene015671:CDS 40.0%
!! GAGATGATTGGGAGCATTAT+TGG + chr4.4:2259196-2259215 MS.gene015671:CDS 40.0%
AAGATGGGTCCTAACAGGTT+CGG - chr4.4:2259155-2259174 None:intergenic 45.0%
AAGCATGGTAGACCTGGTAT+TGG + chr4.4:2259313-2259332 MS.gene015671:CDS 45.0%
AGGTAATGACCGATCATCTC+AGG - chr4.4:2259262-2259281 None:intergenic 45.0%
GAGCTTAACAAGCTCATCAG+TGG - chr4.4:2258002-2258021 None:intergenic 45.0%
TCACTTGAGAGGAATGAACC+TGG - chr4.4:2259353-2259372 None:intergenic 45.0%
TTACGAAGATGGGTCCTAAC+AGG - chr4.4:2259160-2259179 None:intergenic 45.0%
! AATTTTGCAGGCAGACGTTG+AGG + chr4.4:2257880-2257899 MS.gene015671:intron 45.0%
!! ATAAATAAAAGAAATAAAAA+TGG - chr4.4:2258122-2258141 None:intergenic 5.0%
!! TAAATAAAAGAAATAAAAAT+GGG - chr4.4:2258121-2258140 None:intergenic 5.0%
AGATGGGTCCTAACAGGTTC+GGG - chr4.4:2259154-2259173 None:intergenic 50.0%
CCAGGTCTACCATGCTTAAC+AGG - chr4.4:2259310-2259329 None:intergenic 50.0%
CCTGTTAAGCATGGTAGACC+TGG + chr4.4:2259307-2259326 MS.gene015671:CDS 50.0%
CTTGAGAGGAATGAACCTGG+AGG - chr4.4:2259350-2259369 None:intergenic 50.0%
GAGTGAGTAGCACCAATACC+AGG - chr4.4:2259328-2259347 None:intergenic 50.0%
AGGTCTCACTCGTAAGCCCA+TGG + chr4.4:2258054-2258073 MS.gene015671:CDS 55.0%
GCTCGTAGAAGGTTCCAGAG+AGG + chr4.4:2258034-2258053 MS.gene015671:CDS 55.0%
GCTTACGAGTGAGACCTCTC+TGG - chr4.4:2258051-2258070 None:intergenic 55.0%
GTGAGAAGCCCGAACCTGTT+AGG + chr4.4:2259143-2259162 MS.gene015671:CDS 55.0%
TCAGTGCTCGTGCTCGTAGA+AGG + chr4.4:2258023-2258042 MS.gene015671:CDS 55.0%
TCTCTTCTTCGGTACTCCCG+CGG - chr4.4:2257924-2257943 None:intergenic 55.0%
!! TAGAAAAGGGAGGCACCACC+TGG + chr4.4:2259121-2259140 MS.gene015671:intron 55.0%
!! TTGGTGCTACTCACTCCTCC+AGG + chr4.4:2259332-2259351 MS.gene015671:CDS 55.0%
ACAGGTTCGGGCTTCTCACC+AGG - chr4.4:2259142-2259161 None:intergenic 60.0%
CTTCTTCGGTACTCCCGCGG+CGG - chr4.4:2257921-2257940 None:intergenic 65.0%
GGTTCGGGCTTCTCACCAGG+TGG - chr4.4:2259139-2259158 None:intergenic 65.0%
AGATGCAGCAGCCGCCGCCG+CGG + chr4.4:2257904-2257923 MS.gene015671:CDS 75.0%
CTTCGGTACTCCCGCGGCGG+CGG - chr4.4:2257918-2257937 None:intergenic 75.0%
! GATGCAGCAGCCGCCGCCGC+GGG + chr4.4:2257905-2257924 MS.gene015671:CDS 80.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 2257786 2259372 2257786 ID=MS.gene015671
chr4.4 mRNA 2257786 2259372 2257786 ID=MS.gene015671.t1;Parent=MS.gene015671
chr4.4 exon 2257786 2257788 2257786 ID=MS.gene015671.t1.exon1;Parent=MS.gene015671.t1
chr4.4 CDS 2257786 2257788 2257786 ID=cds.MS.gene015671.t1;Parent=MS.gene015671.t1
chr4.4 exon 2257890 2258102 2257890 ID=MS.gene015671.t1.exon2;Parent=MS.gene015671.t1
chr4.4 CDS 2257890 2258102 2257890 ID=cds.MS.gene015671.t1;Parent=MS.gene015671.t1
chr4.4 exon 2259124 2259372 2259124 ID=MS.gene015671.t1.exon3;Parent=MS.gene015671.t1
chr4.4 CDS 2259124 2259372 2259124 ID=cds.MS.gene015671.t1;Parent=MS.gene015671.t1
Gene Sequence

>MS.gene015671

ATGGTGAGTTAACAATCCTTCTGAAACTCGATTTCCGATAGAATCTAACATCGATTTCCGATTGAATTTGATTTTGATTTTGAATTTGGAATTGAATTTTGCAGGCAGACGTTGAGGTAGATGCAGCAGCCGCCGCCGCGGGAGTACCGAAGAAGAGAACATTCAAGAAGTTCAGTTTCAGAGGAGTTGATTTGGATGCACTTCTTGACATGTCCACTGATGAGCTTGTTAAGCTCTTCAGTGCTCGTGCTCGTAGAAGGTTCCAGAGAGGTCTCACTCGTAAGCCCATGGCTCTCATCAAAAAGCTTCGCAAAGCGGTACAATTTTATTTTCCCATTTTTATTTCTTTTATTTATCTGAAAATTAAATAGTAAAATTAAAACAACAATCTTAGCATTTTGGGCGTGCTCAATTTAGTTCCTTTAATATGCAAAATACTAACAATTGGGTTCCTTAAATTTGTAAAATAGTAATTGGATACCAAAAATTGGACAATGTCATATCAGTCATTAGTATTTTTGTGTTTTTGTCCGACTTTAGTACCCCATTTTAATGGTTTCATGTTCATTTTGATGCAATAATTGCTTCTAGAACATATTCAAGTTACTATTCAAGTCTCTTGTTGATTATTGATTTTGGTGGGTTTGTTCTGAAGATATATTTTGATTGAGGTGCGAAATTGATTGCTGTTTTTAGGGATTAATTTGTTATTTTTTTAATTTGAGGCATTAAATTGCTCAAACTTTACCAAGATATCAATTTAGTTCCTTAAATTTGCATAATAGTAATTTAGTCCCTTAAATTGAACACTTTTTTTTTTTTTTTTGGTGCAAAGTTACCACCATTTTGAAGGTTATATGCCTTTTCAAGTTTATATGGAAGTTTTTATTGATTTTGTTGGATCTTTACTAAAGTTATATTTTGCTTGAAGAACTTAGTTATTTTGTTATTCTTTTATTTAGTGGTTAATTGAATTTCCAAAAATTTTAATGTTAGTCCTTTATATTTGCAAATTAGCACTTTAGTACCTTAATTTGAACACTGAGTCACTTTTTTTTTTTTTGCTTTAAATTTAACACTACCATTTTAAAGGTTTACATGCGTCAAATGCATCAAGAGACTAGTTAAGTTAATATTTAAACAATTTTATTGCTTTTTTGATGAATGCTTACTGAATAGCGATATTTAGGTATAGGGACTAAATTGATTGGTGGTTTTTTAAATTTAAAGGACTACTTTGTTAATTTGTGAATTTGAGGGACTAAATTACTTGACCCTTACTATCTTAAGTACTAAAATGCTGATTCATATTGTTATAATTTTGTGAATTGGTTGTAGAAAAGGGAGGCACCACCTGGTGAGAAGCCCGAACCTGTTAGGACCCATCTTCGTAACATGATCATTGTACCTGAGATGATTGGGAGCATTATTGGAGTGTACAATGGGAAGACCTTTAACCAAGTTGAAATCAAACCTGAGATGATCGGTCATTACCTAGCTGAATTCTCGATCTCATACAAGCCTGTTAAGCATGGTAGACCTGGTATTGGTGCTACTCACTCCTCCAGGTTCATTCCTCTCAAGTGA
Protein sequence

>MS.gene015671.t1

MADVEVDAAAAAAGVPKKRTFKKFSFRGVDLDALLDMSTDELVKLFSARARRRFQRGLTRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK