AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63947

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63947.t1 MTR_0004s0210 98.160 163 3 0 1 163 1 163 9.05e-114 319
MS.gene63947.t1 MTR_7g011090 32.704 159 98 3 1 150 21 179 1.12e-20 84.0
MS.gene63947.t1 MTR_5g041900 36.601 153 88 2 7 150 27 179 4.23e-20 82.8
MS.gene63947.t1 MTR_4g081880 37.736 159 90 3 1 150 22 180 2.74e-19 80.5
MS.gene63947.t1 MTR_0097s0070 33.858 127 77 2 38 157 66 192 1.56e-17 76.3
MS.gene63947.t1 MTR_8g089300 33.333 162 92 3 10 155 28 189 8.44e-17 74.3
MS.gene63947.t1 MTR_7g108130 28.931 159 103 3 3 151 24 182 3.55e-16 72.4
MS.gene63947.t1 MTR_7g083120 32.000 125 77 1 11 127 33 157 6.14e-16 71.6
MS.gene63947.t1 MTR_1g058540 36.364 143 78 4 7 138 37 177 1.12e-14 68.6
MS.gene63947.t1 MTR_3g064310 29.730 148 94 4 6 148 43 185 1.21e-14 68.9
MS.gene63947.t1 MTR_2g026530 30.464 151 89 3 1 138 4 151 5.60e-13 63.9
MS.gene63947.t1 MTR_1g058560 37.762 143 76 4 7 138 36 176 9.40e-13 63.5
MS.gene63947.t1 MTR_2g026530 30.464 151 89 3 1 138 24 171 1.05e-12 63.5
MS.gene63947.t1 MTR_2g020060 31.410 156 92 2 8 148 23 178 1.30e-11 60.5
MS.gene63947.t1 MTR_4g118800 32.258 155 93 4 10 153 30 183 1.44e-11 60.1
MS.gene63947.t1 MTR_4g118810 27.586 145 89 3 8 136 33 177 1.44e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63947.t1 AT1G03700 59.375 160 65 0 4 163 5 164 7.44e-69 206
MS.gene63947.t1 AT4G03540 61.250 160 62 0 4 163 5 164 4.03e-60 184
MS.gene63947.t1 AT5G44550 36.782 174 92 4 2 157 10 183 4.24e-25 95.9
MS.gene63947.t1 AT5G15290 35.616 146 85 2 1 137 21 166 3.07e-24 93.6
MS.gene63947.t1 AT1G14160 32.450 151 89 4 11 150 54 202 9.46e-18 77.0
MS.gene63947.t1 AT4G15610 33.108 148 84 3 3 136 24 170 1.81e-17 75.9
MS.gene63947.t1 AT2G36100 37.063 143 77 4 7 138 47 187 1.40e-16 73.9
MS.gene63947.t1 AT2G27370 38.168 131 68 4 31 150 85 213 2.49e-16 73.6
MS.gene63947.t1 AT4G25040 37.410 139 83 2 12 146 21 159 9.23e-16 70.9
MS.gene63947.t1 AT5G06200 37.778 135 71 4 27 150 63 195 1.04e-12 63.5
MS.gene63947.t1 AT3G06390 31.884 138 80 4 6 129 35 172 2.65e-11 59.7
MS.gene63947.t1 AT1G17200 27.160 162 103 5 6 157 31 187 4.13e-11 59.3
MS.gene63947.t1 AT4G20390 33.125 160 91 3 12 155 22 181 4.76e-11 58.9

Find 31 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACCTATTGTTAAGGTTCT+TGG 0.122572 4.1:-56225085 MS.gene63947:CDS
TGTCATGTGATTGCAAAATT+TGG 0.163683 4.1:+56223614 None:intergenic
AACTCTATTGTAACTGTCTA+TGG 0.255815 4.1:-56224624 MS.gene63947:CDS
ACTTGTGGTCGCCATGGATA+TGG 0.315968 4.1:-56224559 MS.gene63947:intron
GCTTTAGTCGCTAGTTTCAT+TGG 0.393377 4.1:-56223588 MS.gene63947:CDS
CTCAAGCATCTCTGCAGCTT+TGG 0.400682 4.1:-56223703 MS.gene63947:CDS
GTTAAGGTTCTTGGCCTTCT+CGG 0.405136 4.1:-56225076 MS.gene63947:CDS
CTTGTCAGCAGTTGTTGTCA+TGG 0.429083 4.1:-56225049 MS.gene63947:CDS
GTCATGTGATTGCAAAATTT+GGG 0.430792 4.1:+56223615 None:intergenic
GAATCTGCCACCTATTGTTA+AGG 0.432387 4.1:-56225092 MS.gene63947:CDS
CGCCAGAGCAAGCTTTCTGC+AGG 0.458432 4.1:+56224582 None:intergenic
AGGCCAAGAACCTTAACAAT+AGG 0.459316 4.1:+56225082 None:intergenic
GCTGCTTGGCTACCGATTTG+TGG 0.463642 4.1:-56223645 MS.gene63947:CDS
TTCCTGCAGAAAGCTTGCTC+TGG 0.469885 4.1:-56224584 MS.gene63947:CDS
TGCTGACAAGGTGGCCGAGA+AGG 0.484142 4.1:+56225062 None:intergenic
ATGGAAACAATTATGCTGCT+TGG 0.504739 4.1:-56223659 MS.gene63947:CDS
ATAGCTCAAGTGGCAAAGAA+TGG 0.508607 4.1:-56223678 MS.gene63947:CDS
TTGGGAACTGAACCACAAAT+CGG 0.511633 4.1:+56223633 None:intergenic
CATGACAACAACTGCTGACA+AGG 0.513838 4.1:+56225050 None:intergenic
AGGGTCAAGGACAGTATGAA+TGG 0.516263 4.1:+56223533 None:intergenic
AAGCTTGCTCTGGCGACTTG+TGG 0.523109 4.1:-56224574 MS.gene63947:CDS
GAGTTCACTTACTTCAAGGC+AGG 0.535265 4.1:+56224964 None:intergenic
TTCTCAAAAGGAGAGGGTCA+AGG 0.544463 4.1:+56223520 None:intergenic
CTGGCGACTTGTGGTCGCCA+TGG 0.548545 4.1:-56224565 MS.gene63947:CDS
GTGGCAGATTCTACTAGTCT+TGG 0.560428 4.1:+56225104 None:intergenic
GATTCTACTAGTCTTGGCCA+TGG 0.580820 4.1:+56225110 None:intergenic
AGCTTTGGCTATAGCTCAAG+TGG 0.581117 4.1:-56223688 MS.gene63947:CDS
TTAGGACATTACCATATCCA+TGG 0.585943 4.1:+56224548 None:intergenic
AGCTTTCTGCAGGAAGAAAG+AGG 0.586262 4.1:+56224592 None:intergenic
CCAAGAACCTTAACAATAGG+TGG 0.592009 4.1:+56225085 None:intergenic
GACAACAACTGCTGACAAGG+TGG 0.675764 4.1:+56225053 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAATGCTAAATTATTA+TGG - chr4.1:56224822-56224841 MS.gene63947:intron 10.0%
!!! ATTTTATATGATCAAACTTA+GGG + chr4.1:56224584-56224603 None:intergenic 15.0%
!!! GTTTTATTTTTATGGATTTA+AGG + chr4.1:56224514-56224533 None:intergenic 15.0%
!!! TATTTTATATGATCAAACTT+AGG + chr4.1:56224585-56224604 None:intergenic 15.0%
!! AAATGCTAAAATTGTAAAGT+CGG + chr4.1:56224257-56224276 None:intergenic 20.0%
!! AAGAACAAATGTTTCAAATT+TGG + chr4.1:56224186-56224205 None:intergenic 20.0%
!! ATGCTAAATTATTATGGTTA+TGG - chr4.1:56224828-56224847 MS.gene63947:intron 20.0%
!! CAAACATTATATGACTTAAA+TGG + chr4.1:56224316-56224335 None:intergenic 20.0%
!!! CTAACCAATGTATTATTTTT+TGG - chr4.1:56224697-56224716 MS.gene63947:intron 20.0%
!!! TATTTTTATGGATTTAAGGT+TGG + chr4.1:56224510-56224529 None:intergenic 20.0%
!!! TGTTCTTCATGTTTTTAAAA+TGG - chr4.1:56224199-56224218 MS.gene63947:intron 20.0%
!!! TTTAATTGATTTTTATGAGC+AGG - chr4.1:56224875-56224894 MS.gene63947:intron 20.0%
!!! TTTTCGTTTTTTCATTTCAT+TGG + chr4.1:56224776-56224795 None:intergenic 20.0%
! ATCAGTTTAGAGATGAATTA+AGG + chr4.1:56223939-56223958 None:intergenic 25.0%
! ATGATAAAGAGGTTAACTTT+AGG + chr4.1:56224093-56224112 None:intergenic 25.0%
! GACATAACTAGTATTCTAAT+AGG + chr4.1:56224629-56224648 None:intergenic 25.0%
! TATGAACTCTTTAACATAGT+TGG + chr4.1:56224358-56224377 None:intergenic 25.0%
! TATGTTAAAGAGTTCATACA+TGG - chr4.1:56224360-56224379 MS.gene63947:intron 25.0%
! TCAGCCAAAAAATAATACAT+TGG + chr4.1:56224704-56224723 None:intergenic 25.0%
!! GTTAGTATATTTTGCTTCAA+AGG + chr4.1:56223633-56223652 None:intergenic 25.0%
!!! ATGAGGTGGTTTTATTTTTA+TGG + chr4.1:56224522-56224541 None:intergenic 25.0%
!!! TCTTCATGTTTTTAAAATGG+AGG - chr4.1:56224202-56224221 MS.gene63947:intron 25.0%
AAAGTTCTTGCATGATAAAG+AGG + chr4.1:56224104-56224123 None:intergenic 30.0%
AACACGTCAAACAATAAACT+TGG + chr4.1:56224736-56224755 None:intergenic 30.0%
AACTCTATTGTAACTGTCTA+TGG - chr4.1:56223996-56224015 MS.gene63947:intron 30.0%
AACTCTTTAACATAGTTGGA+TGG + chr4.1:56224354-56224373 None:intergenic 30.0%
GTCATGTGATTGCAAAATTT+GGG + chr4.1:56225008-56225027 None:intergenic 30.0%
TACATAAATGCTATGAAGCA+TGG - chr4.1:56223700-56223719 MS.gene63947:CDS 30.0%
TCAAACAATTCCTACTTTCT+AGG - chr4.1:56223958-56223977 MS.gene63947:intron 30.0%
TGTCATGTGATTGCAAAATT+TGG + chr4.1:56225009-56225028 None:intergenic 30.0%
TTCAGTGTAATTACAAGTGT+CGG + chr4.1:56223789-56223808 None:intergenic 30.0%
! AAATTTTGCAATCACATGAC+AGG - chr4.1:56225008-56225027 MS.gene63947:CDS 30.0%
! AAGTTTTTCTCAAAAGGAGA+GGG + chr4.1:56225109-56225128 None:intergenic 30.0%
! GCATTTTTGTTAGTTGAGTT+AGG - chr4.1:56224271-56224290 MS.gene63947:intron 30.0%
! TGTAACTGTCTATGGATTTT+TGG - chr4.1:56224004-56224023 MS.gene63947:intron 30.0%
!!! TGTTTTTAAAATGGAGGTGT+TGG - chr4.1:56224208-56224227 MS.gene63947:intron 30.0%
AATGGAGTTCACTTACTTCA+AGG + chr4.1:56223663-56223682 None:intergenic 35.0%
ATGGAAACAATTATGCTGCT+TGG - chr4.1:56224961-56224980 MS.gene63947:intron 35.0%
GAATACTAGTTATGTCTCGA+TGG - chr4.1:56224633-56224652 MS.gene63947:CDS 35.0%
TTAGGACATTACCATATCCA+TGG + chr4.1:56224075-56224094 None:intergenic 35.0%
! ACATTGGTTAGTCACACATT+GGG + chr4.1:56224688-56224707 None:intergenic 35.0%
! CAAGTTTTTCTCAAAAGGAG+AGG + chr4.1:56225110-56225129 None:intergenic 35.0%
! TACATTGGTTAGTCACACAT+TGG + chr4.1:56224689-56224708 None:intergenic 35.0%
! TCACAAAGTACCTAGAAAGT+AGG + chr4.1:56223971-56223990 None:intergenic 35.0%
!! TATGGATTTAAGGTTGGTGA+TGG + chr4.1:56224504-56224523 None:intergenic 35.0%
!!! TGAAGAAGCTAGCTTTTTCA+TGG + chr4.1:56223604-56223623 None:intergenic 35.0%
AGGCCAAGAACCTTAACAAT+AGG + chr4.1:56223541-56223560 None:intergenic 40.0%
ATAGCTCAAGTGGCAAAGAA+TGG - chr4.1:56224942-56224961 MS.gene63947:intron 40.0%
CACATATATGCTATGAAGCG+AGG + chr4.1:56223880-56223899 None:intergenic 40.0%
CCAAGAACCTTAACAATAGG+TGG + chr4.1:56223538-56223557 None:intergenic 40.0%
CCACCTATTGTTAAGGTTCT+TGG - chr4.1:56223535-56223554 MS.gene63947:CDS 40.0%
GAATCTGCCACCTATTGTTA+AGG - chr4.1:56223528-56223547 MS.gene63947:CDS 40.0%
GTAAAGTCGGACGTTATGAT+CGG + chr4.1:56224244-56224263 None:intergenic 40.0%
TAAAGTCGGACGTTATGATC+GGG + chr4.1:56224243-56224262 None:intergenic 40.0%
TTAAGCGTGTTTGAGAGATG+AGG + chr4.1:56224539-56224558 None:intergenic 40.0%
TTGGGAACTGAACCACAAAT+CGG + chr4.1:56224990-56225009 None:intergenic 40.0%
! GCTTTAGTCGCTAGTTTCAT+TGG - chr4.1:56225032-56225051 MS.gene63947:CDS 40.0%
AAAGTCGGACGTTATGATCG+GGG + chr4.1:56224242-56224261 None:intergenic 45.0%
AGCTTTCTGCAGGAAGAAAG+AGG + chr4.1:56224031-56224050 None:intergenic 45.0%
AGGGTCAAGGACAGTATGAA+TGG + chr4.1:56225090-56225109 None:intergenic 45.0%
ATGAAGCGAGGATACAGACA+CGG + chr4.1:56223868-56223887 None:intergenic 45.0%
CATGACAACAACTGCTGACA+AGG + chr4.1:56223573-56223592 None:intergenic 45.0%
CTTGTCAGCAGTTGTTGTCA+TGG - chr4.1:56223571-56223590 MS.gene63947:CDS 45.0%
GAGTTCACTTACTTCAAGGC+AGG + chr4.1:56223659-56223678 None:intergenic 45.0%
TCGATGGAGATTGAGTCTAC+AGG - chr4.1:56224649-56224668 MS.gene63947:intron 45.0%
TTCTCAAAAGGAGAGGGTCA+AGG + chr4.1:56225103-56225122 None:intergenic 45.0%
! AGCTTTGGCTATAGCTCAAG+TGG - chr4.1:56224932-56224951 MS.gene63947:intron 45.0%
! GTGGCAGATTCTACTAGTCT+TGG + chr4.1:56223519-56223538 None:intergenic 45.0%
! GTTAAGGTTCTTGGCCTTCT+CGG - chr4.1:56223544-56223563 MS.gene63947:CDS 45.0%
!! TACAAGTGTCGGTGTCGTAT+CGG + chr4.1:56223778-56223797 None:intergenic 45.0%
!! AATAATTTAAATAAAACAAA+TGG + chr4.1:56223681-56223700 None:intergenic 5.0%
ACTTGTGGTCGCCATGGATA+TGG - chr4.1:56224061-56224080 MS.gene63947:intron 50.0%
AGCGTGTTTGAGAGATGAGG+TGG + chr4.1:56224536-56224555 None:intergenic 50.0%
CTCAAGCATCTCTGCAGCTT+TGG - chr4.1:56224917-56224936 MS.gene63947:intron 50.0%
GACAACAACTGCTGACAAGG+TGG + chr4.1:56223570-56223589 None:intergenic 50.0%
TATGAAGCATGGACACGCCT+CGG - chr4.1:56223711-56223730 MS.gene63947:CDS 50.0%
! TTCCTGCAGAAAGCTTGCTC+TGG - chr4.1:56224036-56224055 MS.gene63947:intron 50.0%
GTCAGTGTCCATGTCGTGTC+TGG - chr4.1:56223839-56223858 MS.gene63947:intron 55.0%
! AAGCTTGCTCTGGCGACTTG+TGG - chr4.1:56224046-56224065 MS.gene63947:intron 55.0%
!! GCTGCTTGGCTACCGATTTG+TGG - chr4.1:56224975-56224994 MS.gene63947:intron 55.0%
!! TGTCGGTGTCGTATCGGTGT+CGG + chr4.1:56223772-56223791 None:intergenic 55.0%
ACACGACACGTGTCCGACAC+CGG + chr4.1:56223749-56223768 None:intergenic 60.0%
CACGGACACCAGACACGACA+TGG + chr4.1:56223850-56223869 None:intergenic 60.0%
CGCCAGAGCAAGCTTTCTGC+AGG + chr4.1:56224041-56224060 None:intergenic 60.0%
GATTAGGCGTGTCCCGGTGT+CGG - chr4.1:56223733-56223752 MS.gene63947:intron 60.0%
GCATGGACACGCCTCGGATT+AGG - chr4.1:56223717-56223736 MS.gene63947:CDS 60.0%
TGCTGACAAGGTGGCCGAGA+AGG + chr4.1:56223561-56223580 None:intergenic 60.0%
ACCGGGACACGCCTAATCCG+AGG + chr4.1:56223731-56223750 None:intergenic 65.0%
CACGACACGTGTCCGACACC+GGG + chr4.1:56223748-56223767 None:intergenic 65.0%
CTGGCGACTTGTGGTCGCCA+TGG - chr4.1:56224055-56224074 MS.gene63947:intron 65.0%
! GCCTCGGATTAGGCGTGTCC+CGG - chr4.1:56223727-56223746 MS.gene63947:intron 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 56223512 56225130 56223512 ID=MS.gene63947
chr4.1 mRNA 56223512 56225130 56223512 ID=MS.gene63947.t1;Parent=MS.gene63947
chr4.1 exon 56224976 56225130 56224976 ID=MS.gene63947.t1.exon1;Parent=MS.gene63947.t1
chr4.1 CDS 56224976 56225130 56224976 ID=cds.MS.gene63947.t1;Parent=MS.gene63947.t1
chr4.1 exon 56224560 56224662 56224560 ID=MS.gene63947.t1.exon2;Parent=MS.gene63947.t1
chr4.1 CDS 56224560 56224662 56224560 ID=cds.MS.gene63947.t1;Parent=MS.gene63947.t1
chr4.1 exon 56223512 56223745 56223512 ID=MS.gene63947.t1.exon3;Parent=MS.gene63947.t1
chr4.1 CDS 56223512 56223745 56223512 ID=cds.MS.gene63947.t1;Parent=MS.gene63947.t1
Gene Sequence

>MS.gene63947

ATGGCCAAGACTAGTAGAATCTGCCACCTATTGTTAAGGTTCTTGGCCTTCTCGGCCACCTTGTCAGCAGTTGTTGTCATGGTTTCTAGCCATGAAAAAGCTAGCTTCTTCACTGTTTCCTTTGAAGCAAAATATACTAACTCTCCTGCCTTGAAGTAAGTGAACTCCATTTGTTTTATTTAAATTATTACATAAATGCTATGAAGCATGGACACGCCTCGGATTAGGCGTGTCCCGGTGTCGGACACGTGTCGTGTCCGACACCGATACGACACCGACACTTGTAATTACACTGAATTATGTCATTTTTTCAAATTGTGTCGACGTGTCAGTGTCCATGTCGTGTCTGGTGTCCGTGTCTGTATCCTCGCTTCATAGCATATATGTGTAACTAACTAATTTCTTTTGTTCAACAAAATTGTTTCCTTAATTCATCTCTAAACTGATCAAACAATTCCTACTTTCTAGGTACTTTGTGATTGCAAACTCTATTGTAACTGTCTATGGATTTTTGGTCCTCTTTCTTCCTGCAGAAAGCTTGCTCTGGCGACTTGTGGTCGCCATGGATATGGTAATGTCCTAAAGTTAACCTCTTTATCATGCAAGAACTTTTGTAAAAGTTTTGTTTCACAAATCGTTAAAATTTGTAACTTGTTTTAATTTATGTTAAGCCAAATTTGAAACATTTGTTCTTCATGTTTTTAAAATGGAGGTGTTGGAGTTTGAACCCCGATCATAACGTCCGACTTTACAATTTTAGCATTTTTGTTAGTTGAGTTAGGATTTATGAGACTAAATTGACCATTTAAGTCATATAATGTTTGCATAGTTAGTATTTTCCATCCAACTATGTTAAAGAGTTCATACATGGTTGTTAAATGTAGACGTCGTATGTTGTATGTTCAGTTGAGAAAAAAATAATTTAATTAGATTTTTTATCAAAAAACTCAAAATAATTAAAACAAAAAAAAAAAATCATCATCTTCACTCCATCACCAACCTTAAATCCATAAAAATAAAACCACCTCATCTCTCAAACACGCTTAAATATGATGTTTTCAATAAATAACCCTAAGTTTGATCATATAAAATAAAATAATGATTCTAATAAAAACCTATTAGAATACTAGTTATGTCTCGATGGAGATTGAGTCTACAGGAAAAGATTATACTCCCAATGTGTGACTAACCAATGTATTATTTTTTGGCTGAGAGATGTATCCAAGTTTATTGTTTGACGTGTTAAAAAAAAATCTCATCTCCAATGAAATGAAAAAACGAAAAAGAAATGCTAAATTATTTTTTTTGACAAAAAAATGCTAAATTATTATGGTTATGGAACTATAATAGTATTACTTATTGCTTTAATTGATTTTTATGAGCAGGTGTTGACAATGTTACTCATCTCAAGCATCTCTGCAGCTTTGGCTATAGCTCAAGTGGCAAAGAATGGAAACAATTATGCTGCTTGGCTACCGATTTGTGGTTCAGTTCCCAAATTTTGCAATCACATGACAGGAGCTTTAGTCGCTAGTTTCATTGGAGTCATAATATATTTGATTCTTCTGTTGCATTCCATTCATACTGTCCTTGACCCTCTCCTTTTGAGAAAAACTTGA
Protein sequence

>MS.gene63947.t1

MAKTSRICHLLLRFLAFSATLSAVVVMVSSHEKASFFTVSFEAKYTNSPALKYFVIANSIVTVYGFLVLFLPAESLLWRLVVAMDMVLTMLLISSISAALAIAQVAKNGNNYAAWLPICGSVPKFCNHMTGALVASFIGVIIYLILLLHSIHTVLDPLLLRKT