AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66654

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66654.t1 MTR_4g051538 90.213 235 22 1 1 235 1 234 8.02e-146 406
MS.gene66654.t1 MTR_3g104630 51.969 127 49 3 106 220 16 142 6.34e-31 112
MS.gene66654.t1 MTR_1g012570 29.245 212 122 8 1 192 1 204 1.84e-18 81.6
MS.gene66654.t1 MTR_1g108510 31.902 163 99 4 1 151 1 163 4.69e-18 80.1
MS.gene66654.t1 MTR_1g105910 34.783 138 75 3 1 126 1 135 7.75e-18 79.7
MS.gene66654.t1 MTR_1g105920 34.247 146 85 3 1 140 1 141 8.59e-18 79.7
MS.gene66654.t1 MTR_3g030770 31.902 163 99 4 1 151 1 163 9.43e-18 79.3
MS.gene66654.t1 MTR_8g043650 34.074 135 80 3 1 126 1 135 2.62e-17 78.6
MS.gene66654.t1 MTR_3g052920 34.667 150 82 3 1 137 1 147 4.75e-17 77.8
MS.gene66654.t1 MTR_5g053390 29.515 227 109 8 1 205 1 198 6.17e-17 77.4
MS.gene66654.t1 MTR_3g052870 43.902 82 46 0 1 82 1 82 1.02e-16 76.3
MS.gene66654.t1 MTR_3g080940 45.882 85 45 1 1 85 1 84 1.06e-16 76.3
MS.gene66654.t1 MTR_2g030740 34.815 135 79 3 1 126 1 135 1.32e-16 76.6
MS.gene66654.t1 MTR_1g108580 45.833 72 39 0 1 72 1 72 1.44e-16 76.3
MS.gene66654.t1 MTR_1g077360 42.683 82 47 0 1 82 1 82 1.89e-16 76.3
MS.gene66654.t1 MTR_8g086290 31.410 156 99 2 4 151 7 162 1.93e-16 74.7
MS.gene66654.t1 MTR_1g106070 34.694 147 86 4 1 137 1 147 2.18e-16 74.7
MS.gene66654.t1 MTR_2g085280 31.159 138 86 3 1 129 1 138 3.41e-16 75.5
MS.gene66654.t1 MTR_2g085250 31.852 135 83 3 1 126 1 135 3.41e-16 75.5
MS.gene66654.t1 MTR_2g093190 31.646 158 90 5 1 143 1 155 1.42e-15 73.6
MS.gene66654.t1 MTR_5g055100 27.320 194 115 7 1 181 1 181 2.18e-15 73.2
MS.gene66654.t1 MTR_2g105290 29.747 158 99 4 4 151 7 162 2.32e-15 72.0
MS.gene66654.t1 MTR_0121s0100 33.058 121 72 2 1 115 1 118 4.50e-15 70.1
MS.gene66654.t1 MTR_5g045560 42.857 77 44 0 1 77 1 77 5.14e-15 72.0
MS.gene66654.t1 MTR_1g075600 39.024 82 50 0 1 82 1 82 1.74e-14 70.9
MS.gene66654.t1 MTR_3g030780 41.667 72 42 0 1 72 1 72 3.06e-14 67.8
MS.gene66654.t1 MTR_4g094638 40.580 69 41 0 9 77 2 70 1.16e-13 67.4
MS.gene66654.t1 MTR_4g094632 37.349 83 52 0 9 91 2 84 1.37e-13 66.6
MS.gene66654.t1 MTR_0121s0080 25.000 208 136 6 1 192 1 204 1.85e-13 67.8
MS.gene66654.t1 MTR_8g046350 28.947 114 68 2 9 116 2 108 2.87e-11 60.5
MS.gene66654.t1 MTR_8g079502 33.750 80 52 1 9 87 2 81 7.73e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66654.t1 AT2G34440 36.434 129 74 4 9 130 2 129 4.93e-17 76.3
MS.gene66654.t1 AT4G36590 48.529 68 35 0 5 72 3 70 6.25e-17 77.8
MS.gene66654.t1 AT1G29962 43.421 76 43 0 5 80 4 79 1.76e-15 72.4
MS.gene66654.t1 AT2G24840 42.500 80 46 0 7 86 61 140 5.51e-15 72.4
MS.gene66654.t1 AT5G60440 31.724 145 86 4 5 148 3 135 1.21e-14 72.0
MS.gene66654.t1 AT1G28460 42.466 73 42 0 5 77 4 76 3.70e-13 66.2
MS.gene66654.t1 AT1G01530 33.645 107 67 1 5 107 3 109 8.56e-13 66.2
MS.gene66654.t1 AT3G04100 36.782 87 52 1 2 88 7 90 3.09e-12 63.9
MS.gene66654.t1 AT1G65360 39.062 64 39 0 5 68 3 66 3.79e-11 61.2
MS.gene66654.t1 AT3G66656 40.000 65 39 0 9 73 2 66 5.54e-11 60.1
MS.gene66654.t1 AT1G28450 38.158 76 47 0 5 80 4 79 6.58e-11 60.1

Find 40 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGAGTTAACAACACTTTC+AGG 0.202264 4.3:-48839199 MS.gene66654:CDS
TTGAAGAAGTTGGAAAGTTC+TGG 0.270990 4.3:-48838968 MS.gene66654:CDS
TGCACCAACTTCATGATCTT+TGG 0.281401 4.3:+48838637 None:intergenic
ACACAAGGAGTCAACCTTAT+TGG 0.301989 4.3:-48838262 MS.gene66654:CDS
ATAACCAATGTCTTGAAAAC+TGG 0.328346 4.3:-48838866 MS.gene66654:CDS
ATCATTTCCTCTTCCATTGA+AGG 0.330256 4.3:+48839073 None:intergenic
CTTATTGGTGTAAGCGGAAT+AGG 0.333563 4.3:-48838247 MS.gene66654:CDS
CTTCTACCATGTCATATATC+TGG 0.335672 4.3:+48838196 None:intergenic
CTATTCCGCTTACACCAATA+AGG 0.352863 4.3:+48838248 None:intergenic
TTTCTTTCACTTGATCATAT+TGG 0.353442 4.3:+48838924 None:intergenic
AAATTATCCTTATGTCTTTG+AGG 0.373229 4.3:-48838666 MS.gene66654:CDS
AGTTGGAAAGTTCTGGATAT+TGG 0.382288 4.3:-48838961 MS.gene66654:CDS
ATTCTCATGCTTTCTCCAAC+GGG 0.403336 4.3:-48839163 MS.gene66654:CDS
TTTGTTATAGATTCAGAAGA+TGG 0.410640 4.3:+48839118 None:intergenic
TTTATTTGCGACAGCAACTA+AGG 0.428054 4.3:+48838892 None:intergenic
GGAAGAGGAAATGATGAAAC+CGG 0.442189 4.3:-48839065 MS.gene66654:CDS
GCATTTACAACGAGAAAGTC+TGG 0.455029 4.3:-48839238 MS.gene66654:CDS
GTGTTGTCCTCAAAGACATA+AGG 0.455692 4.3:+48838659 None:intergenic
CGTAGCAATTTCTACCATTG+AGG 0.467584 4.3:-48838708 MS.gene66654:intron
GAAGGATGAAAATCCTTCAA+TGG 0.468568 4.3:-48839086 MS.gene66654:CDS
GACTCCATTCAGTTCCTCAA+TGG 0.472764 4.3:+48838694 None:intergenic
GGTGTAAGCGGAATAGGATA+TGG 0.475102 4.3:-48838241 MS.gene66654:CDS
CTGAGTTAACAACACTTTCA+GGG 0.482866 4.3:-48839198 MS.gene66654:CDS
TATTCTCATGCTTTCTCCAA+CGG 0.502164 4.3:-48839164 MS.gene66654:CDS
TGAAAATCCTTCAATGGAAG+AGG 0.510231 4.3:-48839080 MS.gene66654:CDS
TGATCCAAAAGGTAAAGGTA+TGG 0.511773 4.3:-48838320 MS.gene66654:intron
TCTACCATTGAGGAACTGAA+TGG 0.512244 4.3:-48838698 MS.gene66654:CDS
AACACCAAAGATCATGAAGT+TGG 0.566706 4.3:-48838641 MS.gene66654:CDS
TGGATATTGGTCGATAAAAG+AGG 0.572226 4.3:-48838948 MS.gene66654:CDS
GTCAACCTTATTGGTGTAAG+CGG 0.584588 4.3:-48838253 MS.gene66654:CDS
ACCAATGTCTTGAAAACTGG+AGG 0.591573 4.3:-48838863 MS.gene66654:CDS
AGCGGAATAGGATATGGAAG+TGG 0.601533 4.3:-48838235 MS.gene66654:CDS
TGAGTTAACAACACTTTCAG+GGG 0.607847 4.3:-48839197 MS.gene66654:CDS
GGAGGAGAGATTGACCCTCA+TGG 0.634950 4.3:-48838845 MS.gene66654:intron
GAGTAAGAATGGCGTCGAAG+AGG 0.640220 4.3:-48839324 None:intergenic
TGAAAGTGTTGTTAACTCAG+AGG 0.669188 4.3:+48839201 None:intergenic
GCGTCGAAGAGGTCATCAAG+AGG 0.671296 4.3:-48839313 MS.gene66654:CDS
AAGATGTACACATACCATGA+GGG 0.689701 4.3:+48838831 None:intergenic
AAGCATGAGAATATCAACTG+AGG 0.718686 4.3:+48839174 None:intergenic
AAAGTCTGGAATTTACAACA+AGG 0.757794 4.3:-48839224 MS.gene66654:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAATTGAATCAATGAA+AGG + chr4.3:48839184-48839203 None:intergenic 15.0%
!! ATTGAAAAAAATTGAGAAAA+AGG - chr4.3:48838248-48838267 MS.gene66654:CDS 15.0%
!! CTTAAAATAATTAGGTAAAA+AGG + chr4.3:48838775-48838794 None:intergenic 15.0%
!! CAATACATGATATATATGTT+AGG + chr4.3:48839156-48839175 None:intergenic 20.0%
!! CAGATTCACTTAAAATAATT+AGG + chr4.3:48838783-48838802 None:intergenic 20.0%
!! TATTACTTGAAATATTCTAG+CGG - chr4.3:48838943-48838962 MS.gene66654:CDS 20.0%
!! TCTTATTAATTTCCATTACT+AGG - chr4.3:48839093-48839112 MS.gene66654:CDS 20.0%
!!! CTAATTATTTTAAGTGAATC+TGG - chr4.3:48838781-48838800 MS.gene66654:intron 20.0%
!!! TATAACAAAAACTAGTTTGA+AGG - chr4.3:48838419-48838438 MS.gene66654:intron 20.0%
!!! TGAAAAAAATGATGATCTTT+TGG - chr4.3:48838497-48838516 MS.gene66654:intron 20.0%
!!! TTCAATTTTTTTGATCCAAA+AGG - chr4.3:48839192-48839211 MS.gene66654:CDS 20.0%
! AAATTATCCTTATGTCTTTG+AGG - chr4.3:48838857-48838876 MS.gene66654:CDS 25.0%
! ACGTAAAAATTTGAAGAAGT+TGG - chr4.3:48838545-48838564 MS.gene66654:intron 25.0%
! ATAGCTACAAAAAAAACACA+AGG - chr4.3:48839246-48839265 MS.gene66654:CDS 25.0%
! TTTCTTTCACTTGATCATAT+TGG + chr4.3:48838602-48838621 None:intergenic 25.0%
!! ACTTCTTCAAATTTTTACGT+TGG + chr4.3:48838545-48838564 None:intergenic 25.0%
!! CTTCTTCAAATTTTTACGTT+GGG + chr4.3:48838544-48838563 None:intergenic 25.0%
!! TTTGTTATAGATTCAGAAGA+TGG + chr4.3:48838408-48838427 None:intergenic 25.0%
!!! TTTTTTGATCCAAAAGGTAA+AGG - chr4.3:48839198-48839217 MS.gene66654:CDS 25.0%
AAAGGATGACATGAAATCAT+TGG + chr4.3:48838757-48838776 None:intergenic 30.0%
ATAACCAATGTCTTGAAAAC+TGG - chr4.3:48838657-48838676 MS.gene66654:CDS 30.0%
! AAAGTCTGGAATTTACAACA+AGG - chr4.3:48838299-48838318 MS.gene66654:CDS 30.0%
! GATGGTTTTCCATAACAAAA+TGG + chr4.3:48838390-48838409 None:intergenic 30.0%
! TCATTTTGCTCTATAATCTC+CGG + chr4.3:48838480-48838499 None:intergenic 30.0%
! TTTGGATAAAAAGCATGTTG+CGG - chr4.3:48838515-48838534 MS.gene66654:intron 30.0%
! TTTTAGACAAGAGATGTTGT+TGG - chr4.3:48838985-48839004 MS.gene66654:CDS 30.0%
!! ACCATTTAAGTTGCACTTAT+GGG - chr4.3:48839052-48839071 MS.gene66654:CDS 30.0%
!! TACCATTTAAGTTGCACTTA+TGG - chr4.3:48839051-48839070 MS.gene66654:CDS 30.0%
AACACCAAAGATCATGAAGT+TGG - chr4.3:48838882-48838901 MS.gene66654:CDS 35.0%
AAGATGTACACATACCATGA+GGG + chr4.3:48838695-48838714 None:intergenic 35.0%
AAGCATGAGAATATCAACTG+AGG + chr4.3:48838352-48838371 None:intergenic 35.0%
AATGTTTGCATGCCTAGTAA+TGG + chr4.3:48839108-48839127 None:intergenic 35.0%
ATCATTTCCTCTTCCATTGA+AGG + chr4.3:48838453-48838472 None:intergenic 35.0%
CTGAGTTAACAACACTTTCA+GGG - chr4.3:48838325-48838344 MS.gene66654:intron 35.0%
GAAGGATGAAAATCCTTCAA+TGG - chr4.3:48838437-48838456 MS.gene66654:intron 35.0%
TATTCTCATGCTTTCTCCAA+CGG - chr4.3:48838359-48838378 MS.gene66654:intron 35.0%
TCCCATAAGTGCAACTTAAA+TGG + chr4.3:48839056-48839075 None:intergenic 35.0%
TCTGAGTTAACAACACTTTC+AGG - chr4.3:48838324-48838343 MS.gene66654:intron 35.0%
TGAAAATCCTTCAATGGAAG+AGG - chr4.3:48838443-48838462 MS.gene66654:intron 35.0%
TGAGTTAACAACACTTTCAG+GGG - chr4.3:48838326-48838345 MS.gene66654:intron 35.0%
TGATCCAAAAGGTAAAGGTA+TGG - chr4.3:48839203-48839222 MS.gene66654:CDS 35.0%
TGGATATTGGTCGATAAAAG+AGG - chr4.3:48838575-48838594 MS.gene66654:intron 35.0%
TTGAAGAAGTTGGAAAGTTC+TGG - chr4.3:48838555-48838574 MS.gene66654:intron 35.0%
TTTATTTGCGACAGCAACTA+AGG + chr4.3:48838634-48838653 None:intergenic 35.0%
! ACGGGAAAACCATTTTGTTA+TGG - chr4.3:48838378-48838397 MS.gene66654:intron 35.0%
! TAACAAAATGGTTTTCCCGT+TGG + chr4.3:48838378-48838397 None:intergenic 35.0%
!! AGTTGGAAAGTTCTGGATAT+TGG - chr4.3:48838562-48838581 MS.gene66654:intron 35.0%
!! TGAAAGTGTTGTTAACTCAG+AGG + chr4.3:48838325-48838344 None:intergenic 35.0%
ACACAAGGAGTCAACCTTAT+TGG - chr4.3:48839261-48839280 MS.gene66654:CDS 40.0%
ACCAATGTCTTGAAAACTGG+AGG - chr4.3:48838660-48838679 MS.gene66654:CDS 40.0%
ATTCTCATGCTTTCTCCAAC+GGG - chr4.3:48838360-48838379 MS.gene66654:intron 40.0%
CGTAGCAATTTCTACCATTG+AGG - chr4.3:48838815-48838834 MS.gene66654:intron 40.0%
CTATTCCGCTTACACCAATA+AGG + chr4.3:48839278-48839297 None:intergenic 40.0%
CTTATTGGTGTAAGCGGAAT+AGG - chr4.3:48839276-48839295 MS.gene66654:CDS 40.0%
GAAGATGTACACATACCATG+AGG + chr4.3:48838696-48838715 None:intergenic 40.0%
GCATTTACAACGAGAAAGTC+TGG - chr4.3:48838285-48838304 MS.gene66654:CDS 40.0%
GGAAGAGGAAATGATGAAAC+CGG - chr4.3:48838458-48838477 MS.gene66654:intron 40.0%
GTCAACCTTATTGGTGTAAG+CGG - chr4.3:48839270-48839289 MS.gene66654:CDS 40.0%
GTGTTGTCCTCAAAGACATA+AGG + chr4.3:48838867-48838886 None:intergenic 40.0%
TCTACCATTGAGGAACTGAA+TGG - chr4.3:48838825-48838844 MS.gene66654:intron 40.0%
TGCACCAACTTCATGATCTT+TGG + chr4.3:48838889-48838908 None:intergenic 40.0%
! GCAACCATACCTTTACCTTT+TGG + chr4.3:48839210-48839229 None:intergenic 40.0%
!! TCCTCCAGTTTTCAAGACAT+TGG + chr4.3:48838664-48838683 None:intergenic 40.0%
AGCGGAATAGGATATGGAAG+TGG - chr4.3:48839288-48839307 MS.gene66654:CDS 45.0%
GACTCCATTCAGTTCCTCAA+TGG + chr4.3:48838832-48838851 None:intergenic 45.0%
GGTGTAAGCGGAATAGGATA+TGG - chr4.3:48839282-48839301 MS.gene66654:CDS 45.0%
GCGTCGAAGAGGTCATCAAG+AGG - chr4.3:48838210-48838229 MS.gene66654:CDS 55.0%
GGAGGAGAGATTGACCCTCA+TGG - chr4.3:48838678-48838697 MS.gene66654:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 48838207 48839338 48838207 ID=MS.gene66654
chr4.3 mRNA 48838207 48839338 48838207 ID=MS.gene66654.t1;Parent=MS.gene66654
chr4.3 exon 48838846 48839338 48838846 ID=MS.gene66654.t1.exon1;Parent=MS.gene66654.t1
chr4.3 CDS 48838846 48839338 48838846 ID=cds.MS.gene66654.t1;Parent=MS.gene66654.t1
chr4.3 exon 48838636 48838725 48838636 ID=MS.gene66654.t1.exon2;Parent=MS.gene66654.t1
chr4.3 CDS 48838636 48838725 48838636 ID=cds.MS.gene66654.t1;Parent=MS.gene66654.t1
chr4.3 exon 48838207 48838331 48838207 ID=MS.gene66654.t1.exon3;Parent=MS.gene66654.t1
chr4.3 CDS 48838207 48838331 48838207 ID=cds.MS.gene66654.t1;Parent=MS.gene66654.t1
Gene Sequence

>MS.gene66654

ATGGCGTCGAAGAGGTCATCAAGAGGAAAACAAAAAATTGAATTGAAAAAAATTGAGAAAAAGGATGATCTCTTTGTTGCATTTACAACGAGAAAGTCTGGAATTTACAACAAGGCCTCTGAGTTAACAACACTTTCAGGGGCCTCAGTTGATATTCTCATGCTTTCTCCAACGGGAAAACCATTTTGTTATGGAAAACCATCTTCTGAATCTATAACAAAAACTAGTTTGAAGGATGAAAATCCTTCAATGGAAGAGGAAATGATGAAACCGGAGATTATAGAGCAAAATGAAAAAAATGATGATCTTTTGGATAAAAAGCATGTTGCGGAAGCCCAACGTAAAAATTTGAAGAAGTTGGAAAGTTCTGGATATTGGTCGATAAAAGAGGACCAATATGATCAAGTGAAAGAAATTGACAAATCCTTAGTTGCTGTCGCAAATAAATTGATAACCAATGTCTTGAAAACTGGAGGAGAGATTGACCCTCATGGTATGTGTACATCTTCTAACTAACTATGTGTTATATTTGATCTATTAATGACGTCCAATGATTTCATGTCATCCTTTTTACCTAATTATTTTAAGTGAATCTGGTTATAATTTTTCGTAGCAATTTCTACCATTGAGGAACTGAATGGAGTCAAAACAAATTATCCTTATGTCTTTGAGGACAACACCAAAGATCATGAAGTTGGTGCAAGTAAGAATTCTCATTCATGTTTTTAATTTTTTTTATTACTTGAAATATTCTAGCGGCGACACTCACACATTAAACTTTTAGACAAGAGATGTTGTTGGATAATCATGTCTCAACACATCAAATATCTCTATATAAAACTTTTACCATTTAAGTTGCACTTATGGGAAAAATCTCAATTATTTTTCTTATTAATTTCCATTACTAGGCATGCAAACATTTACTTTTAATATTTCATGCGACAAACCTAACATATATATCATGTATTGTCTTTCCTTTCATTGATTCAATTTTTTTGATCCAAAAGGTAAAGGTATGGTTGCTAAAGCTTCTCAAGATATAGCTACAAAAAAAACACAAGGAGTCAACCTTATTGGTGTAAGCGGAATAGGATATGGAAGTGGTGTTGATCATGCTTCTCCAGATATATGA
Protein sequence

>MS.gene66654.t1

MASKRSSRGKQKIELKKIEKKDDLFVAFTTRKSGIYNKASELTTLSGASVDILMLSPTGKPFCYGKPSSESITKTSLKDENPSMEEEMMKPEIIEQNEKNDDLLDKKHVAEAQRKNLKKLESSGYWSIKEDQYDQVKEIDKSLVAVANKLITNVLKTGGEIDPHAISTIEELNGVKTNYPYVFEDNTKDHEVGASKGMVAKASQDIATKKTQGVNLIGVSGIGYGSGVDHASPDI