AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene013987

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013987.t1 MTR_7g089400 87.200 125 15 1 1 125 1 124 1.35e-74 223
MS.gene013987.t1 MTR_1g093750 49.738 191 89 3 59 243 141 330 5.67e-48 162
MS.gene013987.t1 MTR_3g070970 35.714 252 136 6 14 243 7 254 1.80e-42 145
MS.gene013987.t1 MTR_2g091190 45.810 179 90 3 71 243 54 231 1.48e-33 122
MS.gene013987.t1 MTR_2g015890 38.068 176 100 3 71 241 62 233 2.02e-30 114
MS.gene013987.t1 MTR_4g079760 42.553 188 91 5 68 243 60 242 1.25e-28 109
MS.gene013987.t1 MTR_2g015890 41.880 117 64 1 71 187 62 174 1.06e-24 98.2
MS.gene013987.t1 MTR_5g066080 38.506 174 79 3 59 206 19 190 4.12e-23 94.7
MS.gene013987.t1 MTR_5g032375 32.558 215 117 6 32 233 7 206 2.42e-22 91.7
MS.gene013987.t1 MTR_4g087920 38.415 164 96 4 70 230 69 230 5.73e-22 92.0
MS.gene013987.t1 MTR_2g015890 33.333 138 83 3 109 241 2 135 6.20e-15 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013987.t1 AT2G41130 61.644 219 78 5 18 233 10 225 1.91e-80 242
MS.gene013987.t1 AT3G56770 61.140 193 61 4 70 250 39 229 6.31e-73 222
MS.gene013987.t1 AT1G68810 46.231 199 95 3 57 243 151 349 9.78e-47 159
MS.gene013987.t1 AT3G25710 58.571 140 56 1 72 211 128 265 2.22e-44 152
MS.gene013987.t1 AT2G40200 41.579 190 94 4 71 245 58 245 7.39e-35 125
MS.gene013987.t1 AT4G38070 34.254 181 103 5 26 206 50 214 7.53e-22 91.7

Find 47 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTGTTATTTCGTCGGTTT+CGG 0.235930 7.2:+18992548 None:intergenic
TTTCGATTAGGTCGGGAATT+AGG 0.256589 7.2:+18992448 None:intergenic
CAACAGATTCAGAATAATAT+TGG 0.265015 7.2:-18993940 MS.gene013987:CDS
GTAATAGTTATTGTTGTTAT+CGG 0.378138 7.2:+18993807 None:intergenic
GAATTCACTCAGGTCTTTGT+TGG 0.378871 7.2:-18992298 MS.gene013987:CDS
GAGACTTGAGGATTTCGATT+AGG 0.380801 7.2:+18992436 None:intergenic
AACAGATTCAGAATAATATT+GGG 0.426141 7.2:-18993939 MS.gene013987:CDS
TGTTGCATCATAGTGCTACT+AGG 0.431842 7.2:+18993847 None:intergenic
ATCGAAAAGGCGTCGAGGGT+TGG 0.444038 7.2:-18992250 MS.gene013987:CDS
GCTGAAATGGCCACACTTGG+TGG 0.453567 7.2:-18992393 MS.gene013987:CDS
GTTGAGTATTCAAAGAATGA+AGG 0.456323 7.2:+18993871 None:intergenic
CACTCAGGTCTTTGTTGGAT+AGG 0.462227 7.2:-18992293 MS.gene013987:CDS
AGGAAGCTGAGAAGAGAAGA+AGG 0.471315 7.2:-18993708 MS.gene013987:CDS
GGCAATGACATCTCCGACGA+AGG 0.483297 7.2:-18992516 MS.gene013987:CDS
GTTATTTCGTCGGTTTCGGA+TGG 0.483862 7.2:+18992552 None:intergenic
GTAATTTCAGAAACTTCAAA+GGG 0.483898 7.2:+18993781 None:intergenic
TTGAGGATTTCGATTAGGTC+GGG 0.493776 7.2:+18992441 None:intergenic
AGTAATTTCAGAAACTTCAA+AGG 0.496460 7.2:+18993780 None:intergenic
CTTGAGGATTTCGATTAGGT+CGG 0.504746 7.2:+18992440 None:intergenic
CCTTGGAGTTGCAAGGGAGA+AGG 0.512266 7.2:+18993650 None:intergenic
CTTGGAGTTGCAAGGGAGAA+GGG 0.521866 7.2:+18993651 None:intergenic
TTCGTCGGAGATGTCATTGC+CGG 0.522101 7.2:+18992518 None:intergenic
TTGAGTATTCAAAGAATGAA+GGG 0.546799 7.2:+18993872 None:intergenic
AAAGCTGAAATGGCCACACT+TGG 0.548268 7.2:-18992396 MS.gene013987:CDS
CCTTCTCCCTTGCAACTCCA+AGG 0.549041 7.2:-18993650 MS.gene013987:intron
ATAATAACCTTGGAGTTGCA+AGG 0.549750 7.2:+18993643 None:intergenic
TCTTTGTTGGATAGGTCTAG+TGG 0.556474 7.2:-18992285 MS.gene013987:CDS
AGATATGACTGTTATTTCGT+CGG 0.558305 7.2:+18992542 None:intergenic
TAATAACCTTGGAGTTGCAA+GGG 0.573577 7.2:+18993644 None:intergenic
AAGGGAGAAGGGTACGAAGA+TGG 0.575464 7.2:+18993662 None:intergenic
ACGTGTTCTTCCACCAAGTG+TGG 0.575747 7.2:+18992383 None:intergenic
GAATATGAGTCTGCCTTCGT+CGG 0.576237 7.2:+18992503 None:intergenic
ATAGATCGAAAAGGCGTCGA+GGG 0.576982 7.2:-18992254 MS.gene013987:CDS
AGAGCTCTATCTTGCTGAGA+GGG 0.579252 7.2:+18993751 None:intergenic
TTTCAGAAACTTCAAAGGGG+TGG 0.587837 7.2:+18993785 None:intergenic
GTTGTAACGATAGATCGAAA+AGG 0.589241 7.2:-18992263 MS.gene013987:CDS
GAAATAACAGTCATATCTGC+CGG 0.595239 7.2:-18992537 MS.gene013987:CDS
GATTCAGAATAATATTGGGA+TGG 0.603750 7.2:-18993935 MS.gene013987:CDS
GGAAGCTGAGAAGAGAAGAA+GGG 0.604105 7.2:-18993707 MS.gene013987:CDS
GATTAGGTCGGGAATTAGGT+CGG 0.607145 7.2:+18992452 None:intergenic
GAAGGGTACGAAGATGGTCA+AGG 0.633890 7.2:+18993668 None:intergenic
AGCTGCTTTGAAGAATCACA+AGG 0.645458 7.2:-18993728 MS.gene013987:CDS
TAGAGCTCTATCTTGCTGAG+AGG 0.647696 7.2:+18993750 None:intergenic
ATGAAGGGTTGTTAGCAACA+AGG 0.651347 7.2:+18993887 None:intergenic
GATAGATCGAAAAGGCGTCG+AGG 0.658588 7.2:-18992255 MS.gene013987:CDS
TGATTGATTTCAGACAGACA+AGG 0.674472 7.2:-18992655 MS.gene013987:intron
TAATTTCAGAAACTTCAAAG+GGG 0.757536 7.2:+18993782 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAGATTCAGAATAATATT+GGG - chr7.2:18992240-18992259 MS.gene013987:CDS 20.0%
!! AATGATGAAAATAATAACCT+TGG + chr7.2:18992549-18992568 None:intergenic 20.0%
!! AATTATTTGCAAATTAAGCT+AGG - chr7.2:18993111-18993130 MS.gene013987:intron 20.0%
!! ATTATTTGCAAATTAAGCTA+GGG - chr7.2:18993112-18993131 MS.gene013987:intron 20.0%
!! GATGTTCCAAAAAATAATTA+AGG + chr7.2:18992892-18992911 None:intergenic 20.0%
!! TCATTCTTAATTATTTGTCT+TGG - chr7.2:18992564-18992583 MS.gene013987:CDS 20.0%
!!! CTAGATCCTTAATTATTTTT+TGG - chr7.2:18992883-18992902 MS.gene013987:intron 20.0%
!!! GCTTAATTTGCAAATAATTT+TGG + chr7.2:18993110-18993129 None:intergenic 20.0%
!!! GTAATAGTTATTGTTGTTAT+CGG + chr7.2:18992375-18992394 None:intergenic 20.0%
!!! TTGGATTACATATTTTTTGT+AGG + chr7.2:18993041-18993060 None:intergenic 20.0%
! AGTAATTTCAGAAACTTCAA+AGG + chr7.2:18992402-18992421 None:intergenic 25.0%
! CAACAGATTCAGAATAATAT+TGG - chr7.2:18992239-18992258 MS.gene013987:CDS 25.0%
! CTTAATTACTAAAGTGAGAA+AGG + chr7.2:18992781-18992800 None:intergenic 25.0%
! GTAATTTCAGAAACTTCAAA+GGG + chr7.2:18992401-18992420 None:intergenic 25.0%
! TAATTTCAGAAACTTCAAAG+GGG + chr7.2:18992400-18992419 None:intergenic 25.0%
! TAGTCATGTATAAAACTTGA+TGG + chr7.2:18993201-18993220 None:intergenic 25.0%
! TTGAGTATTCAAAGAATGAA+GGG + chr7.2:18992310-18992329 None:intergenic 25.0%
!! ACATGTTTTCACTCTTTTTT+TGG + chr7.2:18992726-18992745 None:intergenic 25.0%
!! TCAATTTTACAAAACCTACA+AGG - chr7.2:18993319-18993338 MS.gene013987:intron 25.0%
!! TTTTGTTCTTTTGTTCTCAA+AGG - chr7.2:18992624-18992643 MS.gene013987:CDS 25.0%
!!! TTGTAGGTTTTGTAAAATTG+AGG + chr7.2:18993320-18993339 None:intergenic 25.0%
AAAAACTCTCAAAGCTGAAA+TGG - chr7.2:18993773-18993792 MS.gene013987:CDS 30.0%
AAACCATTGTGATTTAGAAG+AGG + chr7.2:18993347-18993366 None:intergenic 30.0%
GATTCAGAATAATATTGGGA+TGG - chr7.2:18992244-18992263 MS.gene013987:CDS 30.0%
GTTGAGTATTCAAAGAATGA+AGG + chr7.2:18992311-18992330 None:intergenic 30.0%
TGATGAGTGATTAAGTTCAT+TGG + chr7.2:18993060-18993079 None:intergenic 30.0%
! ATTTTCTTCAGAATTCACTC+AGG - chr7.2:18993871-18993890 MS.gene013987:CDS 30.0%
! CTTTAGTAATTAAGTTGCCA+TGG - chr7.2:18992787-18992806 MS.gene013987:intron 30.0%
!! AGATATGACTGTTATTTCGT+CGG + chr7.2:18993640-18993659 None:intergenic 30.0%
!! TCATTTTTGTCTCAAAACCT+AGG + chr7.2:18993424-18993443 None:intergenic 30.0%
!!! GTTTTCACTCTTTTTTTGGA+TGG + chr7.2:18992722-18992741 None:intergenic 30.0%
!!! TTTCAGCTTTGAGAGTTTTT+AGG + chr7.2:18993773-18993792 None:intergenic 30.0%
ACACACACAATTATCTTTGC+TGG + chr7.2:18992665-18992684 None:intergenic 35.0%
ATAATAACCTTGGAGTTGCA+AGG + chr7.2:18992539-18992558 None:intergenic 35.0%
CTAGTACATGTTTGCATATG+TGG + chr7.2:18993382-18993401 None:intergenic 35.0%
GAAATAACAGTCATATCTGC+CGG - chr7.2:18993642-18993661 MS.gene013987:intron 35.0%
GTTGTAACGATAGATCGAAA+AGG - chr7.2:18993916-18993935 MS.gene013987:CDS 35.0%
TAATAACCTTGGAGTTGCAA+GGG + chr7.2:18992538-18992557 None:intergenic 35.0%
TCAATCTTGTCACAAAACCT+AGG + chr7.2:18993461-18993480 None:intergenic 35.0%
TCTTATGAGTTTAGCACAAG+TGG - chr7.2:18992956-18992975 MS.gene013987:intron 35.0%
TGATGAAGAAAGCAAAACCT+AGG - chr7.2:18993441-18993460 MS.gene013987:intron 35.0%
! AGGCATATTTTCACTCATTC+TGG + chr7.2:18992761-18992780 None:intergenic 35.0%
! AGTATCGAACTCAAAACATC+CGG + chr7.2:18993016-18993035 None:intergenic 35.0%
! GTAAAGTACTACATGTTCCA+TGG + chr7.2:18992807-18992826 None:intergenic 35.0%
! TGATTGATTTCAGACAGACA+AGG - chr7.2:18993524-18993543 MS.gene013987:intron 35.0%
!!! TTTTTAGGTGAAGAGACTTG+AGG + chr7.2:18993758-18993777 None:intergenic 35.0%
ATGAAGGGTTGTTAGCAACA+AGG + chr7.2:18992295-18992314 None:intergenic 40.0%
ATGAGTTTAGCACAAGTGGT+CGG - chr7.2:18992960-18992979 MS.gene013987:intron 40.0%
ATTTAGAAGAGGCTCCTTGT+AGG + chr7.2:18993336-18993355 None:intergenic 40.0%
CTTGAGGATTTCGATTAGGT+CGG + chr7.2:18993742-18993761 None:intergenic 40.0%
GAATTCACTCAGGTCTTTGT+TGG - chr7.2:18993881-18993900 MS.gene013987:CDS 40.0%
GAGACTTGAGGATTTCGATT+AGG + chr7.2:18993746-18993765 None:intergenic 40.0%
GAGCCTCTTCTAAATCACAA+TGG - chr7.2:18993341-18993360 MS.gene013987:intron 40.0%
TCTTTGTTGGATAGGTCTAG+TGG - chr7.2:18993894-18993913 MS.gene013987:CDS 40.0%
TGATGAAGAAAGCAAAGCCT+AGG - chr7.2:18993404-18993423 MS.gene013987:intron 40.0%
TTAAGCTAGGGAAGTCACTT+AGG - chr7.2:18993124-18993143 MS.gene013987:intron 40.0%
TTGAGGATTTCGATTAGGTC+GGG + chr7.2:18993741-18993760 None:intergenic 40.0%
TTTCAGAAACTTCAAAGGGG+TGG + chr7.2:18992397-18992416 None:intergenic 40.0%
TTTCGATTAGGTCGGGAATT+AGG + chr7.2:18993734-18993753 None:intergenic 40.0%
! AGGGAAGTCACTTAGGTTTT+AGG - chr7.2:18993131-18993150 MS.gene013987:intron 40.0%
! TAGCTTTTGCAAAATCGTGG+TGG + chr7.2:18993292-18993311 None:intergenic 40.0%
! TCGTAGCTTTTGCAAAATCG+TGG + chr7.2:18993295-18993314 None:intergenic 40.0%
! TGTCTGAAGTGGTGTATATC+CGG - chr7.2:18992994-18993013 MS.gene013987:intron 40.0%
! TGTTGCATCATAGTGCTACT+AGG + chr7.2:18992335-18992354 None:intergenic 40.0%
!! AGCTGCTTTGAAGAATCACA+AGG - chr7.2:18992451-18992470 MS.gene013987:CDS 40.0%
!! GACTGTTATTTCGTCGGTTT+CGG + chr7.2:18993634-18993653 None:intergenic 40.0%
AAAGCTGAAATGGCCACACT+TGG - chr7.2:18993783-18993802 MS.gene013987:CDS 45.0%
AGAGCTCTATCTTGCTGAGA+GGG + chr7.2:18992431-18992450 None:intergenic 45.0%
AGGAAGCTGAGAAGAGAAGA+AGG - chr7.2:18992471-18992490 MS.gene013987:CDS 45.0%
CACTCAGGTCTTTGTTGGAT+AGG - chr7.2:18993886-18993905 MS.gene013987:CDS 45.0%
GAATATGAGTCTGCCTTCGT+CGG + chr7.2:18993679-18993698 None:intergenic 45.0%
GATTAGGTCGGGAATTAGGT+CGG + chr7.2:18993730-18993749 None:intergenic 45.0%
GGAAGCTGAGAAGAGAAGAA+GGG - chr7.2:18992472-18992491 MS.gene013987:CDS 45.0%
TAGAGCTCTATCTTGCTGAG+AGG + chr7.2:18992432-18992451 None:intergenic 45.0%
TGCGTAATGTGTGTCTGAAG+TGG - chr7.2:18992983-18993002 MS.gene013987:intron 45.0%
!! ATAGATCGAAAAGGCGTCGA+GGG - chr7.2:18993925-18993944 MS.gene013987:CDS 45.0%
!! GTTATTTCGTCGGTTTCGGA+TGG + chr7.2:18993630-18993649 None:intergenic 45.0%
!!! TTTTATTTTTTTACTATTTA+AGG + chr7.2:18993087-18993106 None:intergenic 5.0%
ACGTGTTCTTCCACCAAGTG+TGG + chr7.2:18993799-18993818 None:intergenic 50.0%
CTTGGAGTTGCAAGGGAGAA+GGG + chr7.2:18992531-18992550 None:intergenic 50.0%
TTCGTCGGAGATGTCATTGC+CGG + chr7.2:18993664-18993683 None:intergenic 50.0%
! AAGGGAGAAGGGTACGAAGA+TGG + chr7.2:18992520-18992539 None:intergenic 50.0%
! GAAGGGTACGAAGATGGTCA+AGG + chr7.2:18992514-18992533 None:intergenic 50.0%
!! GATAGATCGAAAAGGCGTCG+AGG - chr7.2:18993924-18993943 MS.gene013987:CDS 50.0%
CCTTCTCCCTTGCAACTCCA+AGG - chr7.2:18992529-18992548 MS.gene013987:CDS 55.0%
CCTTGGAGTTGCAAGGGAGA+AGG + chr7.2:18992532-18992551 None:intergenic 55.0%
GCTGAAATGGCCACACTTGG+TGG - chr7.2:18993786-18993805 MS.gene013987:CDS 55.0%
GGCAATGACATCTCCGACGA+AGG - chr7.2:18993663-18993682 MS.gene013987:CDS 55.0%
!! ATCGAAAAGGCGTCGAGGGT+TGG - chr7.2:18993929-18993948 MS.gene013987:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 18992230 18993971 18992230 ID=MS.gene013987
chr7.2 mRNA 18992230 18993971 18992230 ID=MS.gene013987.t1;Parent=MS.gene013987
chr7.2 exon 18993651 18993971 18993651 ID=MS.gene013987.t1.exon1;Parent=MS.gene013987.t1
chr7.2 CDS 18993651 18993971 18993651 ID=cds.MS.gene013987.t1;Parent=MS.gene013987.t1
chr7.2 exon 18992230 18992664 18992230 ID=MS.gene013987.t1.exon2;Parent=MS.gene013987.t1
chr7.2 CDS 18992230 18992664 18992230 ID=cds.MS.gene013987.t1;Parent=MS.gene013987.t1
Gene Sequence

>MS.gene013987

ATGCTTCAGCAACAGATTCAGAATAATATTGGGATGGAAAACAACTCTGAACTCTTTCAATTCCTTGTTGCTAACAACCCTTCATTCTTTGAATACTCAACACCTAGTAGCACTATGATGCAACAAAGTTTCTGCAGTTCTTCCGATAACAACAATAACTATTACCACCCCTTTGAAGTTTCTGAAATTACTGATACACCCTCTCAGCAAGATAGAGCTCTAGCTGCTTTGAAGAATCACAAGGAAGCTGAGAAGAGAAGAAGGGAAAGAATTAACTCTCACCTTGACCATCTTCGTACCCTTCTCCCTTGCAACTCCAAGGTTATTATTTTCATCATTCTTAATTATTTGTCTTGGACAAATTATCTTAAAGCATATTTCTTTAGATTTTCTTTTTTGTTCTTTTGTTCTCAAAGGTTAACTACTTTTTGACCAGCAAAGATAATTGTGTGTGTTTTAGTTGACTAAATAATTATGATTTACTTCATTCCATCCAAAAAAAGAGTGAAAACATGTAGTACTTTTCTACCAGAATGAGTGAAAATATGCCTTTCTCACTTTAGTAATTAAGTTGCCATGGAACATGTAGTACTTTACAATAGTAGAATGAGTGAAAATGAAAAAGAAAATAGTAAATAAAAATTAAAGAAACTCTAGATCCTTAATTATTTTTTGGAACATCAACAAAATTGAAAGAAATATTAACTGATGTATTTATAAAAAAAATCTTATGAGTTTAGCACAAGTGGTCGGTGCGTAATGTGTGTCTGAAGTGGTGTATATCCGGATGTTTTGAGTTCGATACTTACCTACAAAAAATATGTAATCCAATGAACTTAATCACTCATCAAAATCCTTAAATAGTAAAAAAATAAAACCAAAATTATTTGCAAATTAAGCTAGGGAAGTCACTTAGGTTTTAGGAGACTACTTTCTTCACTCAAACATCACTTTTGCATAAAAAATAACCATCAAGTTTTATACATGACTATACATATTTTCTAGATAATTTGAGTTGTTAAGATGAGATTCATGACGAGTCTCTCAGAATTACATTCACCACCACGATTTTGCAAAAGCTACGACACCTCAATTTTACAAAACCTACAAGGAGCCTCTTCTAAATCACAATGGTTTACTTTGAACTCACCACATATGCAAACATGTACTAGAATGATGAAGAAAGCAAAGCCTAGGTTTTGAGACAAAAATGATGAAGAAAGCAAAACCTAGGTTTTGTGACAAGATTGATTCAACATGTTAATAGTTAATTCTTTATTTTAATATTTGCGTTTGATTGATTTCAGACAGACAAGGCTTCACTTCTAGCAAAAGTAGTAGAACGTGTGAAAGAATTAAAGCAACAAACATCTCAAATCACACAACTCGAAACTGTTCCATCCGAAACCGACGAAATAACAGTCATATCTGCCGGCAATGACATCTCCGACGAAGGCAGACTCATATTCAAAGCTTCATTATGCTGCGAAGATCGCTCCGACCTAATTCCCGACCTAATCGAAATCCTCAAGTCTCTTCACCTAAAAACTCTCAAAGCTGAAATGGCCACACTTGGTGGAAGAACACGTAACGTTCTTGTTGTTGCTGCTGAGAAAGAACATAATAGCATTGAATCTATTCATTTTCTTCAGAATTCACTCAGGTCTTTGTTGGATAGGTCTAGTGGTTGTAACGATAGATCGAAAAGGCGTCGAGGGTTGGATAGAAGAATGATGCCTTAA
Protein sequence

>MS.gene013987.t1

MLQQQIQNNIGMENNSELFQFLVANNPSFFEYSTPSSTMMQQSFCSSSDNNNNYYHPFEVSEITDTPSQQDRALAALKNHKEAEKRRRERINSHLDHLRTLLPCNSKTDKASLLAKVVERVKELKQQTSQITQLETVPSETDEITVISAGNDISDEGRLIFKASLCCEDRSDLIPDLIEILKSLHLKTLKAEMATLGGRTRNVLVVAAEKEHNSIESIHFLQNSLRSLLDRSSGCNDRSKRRRGLDRRMMP