AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32349

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32349.t1 MTR_1g028480 83.696 92 15 0 81 172 19 110 1.37e-53 166
MS.gene32349.t1 MTR_1g029070 53.165 158 73 1 1 157 1 158 2.72e-48 154
MS.gene32349.t1 MTR_1g039040 63.333 90 33 0 50 139 5 94 1.50e-39 133
MS.gene32349.t1 MTR_4g133952 48.333 120 58 2 21 139 30 146 2.68e-35 123
MS.gene32349.t1 MTR_7g061270 41.667 132 64 2 44 173 17 137 1.03e-34 120
MS.gene32349.t1 MTR_7g100650 41.667 132 64 2 44 173 17 137 1.61e-34 119
MS.gene32349.t1 MTR_8g091720 53.846 91 42 0 49 139 26 116 5.62e-34 119
MS.gene32349.t1 MTR_3g058980 44.286 140 69 4 29 164 2 136 1.22e-33 118
MS.gene32349.t1 MTR_2g026710 44.444 117 58 1 32 148 5 114 1.75e-33 117
MS.gene32349.t1 MTR_1g072790 52.747 91 43 0 49 139 27 117 4.66e-33 116
MS.gene32349.t1 MTR_5g095740 46.789 109 54 1 50 158 22 126 1.03e-32 115
MS.gene32349.t1 MTR_4g133938 42.308 130 70 1 32 161 5 129 5.13e-32 112
MS.gene32349.t1 MTR_8g093920 45.000 100 55 0 50 149 39 138 1.01e-29 108
MS.gene32349.t1 MTR_4g119500 48.889 90 46 0 50 139 21 110 3.07e-29 104
MS.gene32349.t1 MTR_0392s0020 48.889 90 46 0 50 139 17 106 3.15e-29 105
MS.gene32349.t1 MTR_1g088860 46.316 95 51 0 50 144 35 129 2.05e-27 102
MS.gene32349.t1 MTR_1g029100 48.750 80 41 0 52 131 3 82 3.46e-24 90.9
MS.gene32349.t1 MTR_1g083070 40.230 87 52 0 53 139 6 92 4.10e-21 84.0
MS.gene32349.t1 MTR_5g095900 41.176 85 50 0 56 140 21 105 3.46e-19 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32349.t1 AT5G47670 54.945 91 41 0 49 139 27 117 4.59e-35 122
MS.gene32349.t1 AT1G21970 53.846 91 42 0 49 139 57 147 6.89e-35 122
MS.gene32349.t1 AT5G47670 54.945 91 41 0 49 139 56 146 7.90e-35 122
MS.gene32349.t1 AT5G47670 54.945 91 41 0 49 139 56 146 7.90e-35 122
MS.gene32349.t1 AT4G14540 53.846 91 42 0 49 139 19 109 1.25e-34 119
MS.gene32349.t1 AT2G38880 44.628 121 56 1 49 169 19 128 1.38e-33 116
MS.gene32349.t1 AT2G38880 44.628 121 56 1 49 169 19 128 1.79e-33 116
MS.gene32349.t1 AT2G38880 44.628 121 56 1 49 169 19 128 1.79e-33 116
MS.gene32349.t1 AT2G38880 44.628 121 56 1 49 169 19 128 1.79e-33 116
MS.gene32349.t1 AT2G38880 51.648 91 44 0 49 139 19 109 2.66e-33 115
MS.gene32349.t1 AT2G38880 51.648 91 44 0 49 139 19 109 1.38e-32 112
MS.gene32349.t1 AT5G47640 51.648 91 44 0 50 140 26 116 2.01e-32 115
MS.gene32349.t1 AT2G38880 51.648 91 44 0 49 139 19 109 2.57e-32 114
MS.gene32349.t1 AT2G38880 51.648 91 44 0 49 139 19 109 2.57e-32 114
MS.gene32349.t1 AT2G37060 44.444 117 61 2 26 139 3 118 4.45e-32 113
MS.gene32349.t1 AT2G37060 44.444 117 61 2 26 139 3 118 4.45e-32 113
MS.gene32349.t1 AT2G37060 44.444 117 61 2 26 139 3 118 4.45e-32 113
MS.gene32349.t1 AT3G53340 50.549 91 45 0 49 139 27 117 5.33e-32 113
MS.gene32349.t1 AT3G53340 50.549 91 45 0 49 139 27 117 5.33e-32 113
MS.gene32349.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.15e-31 110
MS.gene32349.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.39e-31 111
MS.gene32349.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.39e-31 111
MS.gene32349.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.39e-31 111
MS.gene32349.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.62e-30 108
MS.gene32349.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.62e-30 108
MS.gene32349.t1 AT2G13570 49.451 91 46 0 50 140 35 125 6.87e-30 108
MS.gene32349.t1 AT2G47810 47.253 91 48 0 49 139 49 139 2.67e-27 100
MS.gene32349.t1 AT1G09030 41.573 89 52 0 51 139 3 91 2.55e-23 90.1

Find 33 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACAGCGAACGATTTAATA+TGG 0.243997 1.4:-13876461 MS.gene32349:CDS
TTGTCGAATCCAATTGTAAT+TGG 0.273848 1.4:+13876345 None:intergenic
AGGTAAATGCTGCTTAGTTC+CGG 0.363825 1.4:+13876671 None:intergenic
AATGACATGCCAATTACAAT+TGG 0.392076 1.4:-13876354 MS.gene32349:CDS
GTGTTGAACGACTAAGGTTA+AGG 0.408775 1.4:+13877389 None:intergenic
CCACATAGTTACGATACCTT+TGG 0.434158 1.4:+13876385 None:intergenic
TTGATTGTGTTGAACGACTA+AGG 0.437171 1.4:+13877383 None:intergenic
ATATGGGCAATGGATAGGTT+AGG 0.445811 1.4:-13876444 MS.gene32349:CDS
TGTTGAACGACTAAGGTTAA+GGG 0.465410 1.4:+13877390 None:intergenic
CATAGTTACGATACCTTTGG+AGG 0.481766 1.4:+13876388 None:intergenic
CTTAAAAGTAGTATGGAGAA+TGG 0.482031 1.4:-13877421 None:intergenic
TACAGCGAACGATTTAATAT+GGG 0.483846 1.4:-13876460 MS.gene32349:CDS
ATTCTTGTCAATTGCACGAT+GGG 0.485603 1.4:+13876621 None:intergenic
ATTTAATATGGGCAATGGAT+AGG 0.498662 1.4:-13876449 MS.gene32349:CDS
CGTTCAACACAATCAAGCTC+TGG 0.512773 1.4:-13877376 MS.gene32349:intron
TGGATTCGACAAGGATGGAT+CGG 0.517609 1.4:-13876334 MS.gene32349:CDS
AACGACTAAGGTTAAGGGAC+GGG 0.520234 1.4:+13877395 None:intergenic
ACAATTGGATTCGACAAGGA+TGG 0.533736 1.4:-13876339 MS.gene32349:CDS
GGATTCGACAAGGATGGATC+GGG 0.534384 1.4:-13876333 MS.gene32349:CDS
GGTGCTAGTGGCTCGAACAA+TGG 0.541308 1.4:-13876312 MS.gene32349:CDS
GAACGATTTAATATGGGCAA+TGG 0.552208 1.4:-13876454 MS.gene32349:CDS
TTTACCTAAAACAAAGAATG+AGG 0.564286 1.4:-13876655 MS.gene32349:CDS
AAGGATGGATCGGGTGCTAG+TGG 0.571277 1.4:-13876324 MS.gene32349:CDS
AACAACAATAACTTTCACAC+CGG 0.626294 1.4:-13876690 MS.gene32349:CDS
TTTGGAGGTAAAAGACTAGA+GGG 0.630419 1.4:+13876403 None:intergenic
CATGAGCATCATCACGAGTG+AGG 0.643678 1.4:-13876520 MS.gene32349:CDS
CCAAAGGTATCGTAACTATG+TGG 0.644573 1.4:-13876385 MS.gene32349:CDS
GAACGACTAAGGTTAAGGGA+CGG 0.644933 1.4:+13877394 None:intergenic
GATTCTTGTCAATTGCACGA+TGG 0.645811 1.4:+13876620 None:intergenic
CTTTGGAGGTAAAAGACTAG+AGG 0.649236 1.4:+13876402 None:intergenic
AATTACAATTGGATTCGACA+AGG 0.668467 1.4:-13876343 MS.gene32349:CDS
TCACGAGTGAGGCAAGCGAG+CGG 0.677839 1.4:-13876509 MS.gene32349:CDS
TGCAATTGACAAGAATCATG+CGG 0.689401 1.4:-13876614 MS.gene32349:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAGAATTATTATTTTTAAA+AGG - chr1.4:13876427-13876446 MS.gene32349:CDS 10.0%
!! AAACAAAGATCTAAAAAATA+AGG - chr1.4:13876800-13876819 MS.gene32349:intron 15.0%
!!! TGCTTATATTTTTTTTTTGA+GGG - chr1.4:13876637-13876656 MS.gene32349:CDS 15.0%
!!! TTGCTTATATTTTTTTTTTG+AGG - chr1.4:13876636-13876655 MS.gene32349:CDS 15.0%
!!! TGATTATTTTTGAGAATAAG+AGG + chr1.4:13876409-13876428 None:intergenic 20.0%
! AATCGTATCTTCGTTATTAT+GGG - chr1.4:13876376-13876395 MS.gene32349:CDS 25.0%
! ATGAATTACCTACTTCAAAA+TGG + chr1.4:13876954-13876973 None:intergenic 25.0%
! TTTACCTAAAACAAAGAATG+AGG - chr1.4:13877044-13877063 MS.gene32349:intron 25.0%
!! TCAAACAAAATTGAGGTATT+TGG - chr1.4:13876569-13876588 MS.gene32349:CDS 25.0%
!!! TGTACAATTTTGGTTGTTTA+GGG + chr1.4:13876355-13876374 None:intergenic 25.0%
!!! TTTTACTTTGAAGAAGATTG+AGG - chr1.4:13876486-13876505 MS.gene32349:CDS 25.0%
AACAACAATAACTTTCACAC+CGG - chr1.4:13877009-13877028 MS.gene32349:intron 30.0%
AAGTGAGTCAAACAAAATTG+AGG - chr1.4:13876562-13876581 MS.gene32349:CDS 30.0%
AATGACATGCCAATTACAAT+TGG - chr1.4:13877345-13877364 MS.gene32349:intron 30.0%
AATTACAATTGGATTCGACA+AGG - chr1.4:13877356-13877375 MS.gene32349:intron 30.0%
AGCAAAAAGTAAGTCAAAGA+AGG + chr1.4:13876621-13876640 None:intergenic 30.0%
ATTTAATATGGGCAATGGAT+AGG - chr1.4:13877250-13877269 MS.gene32349:intron 30.0%
CAATCGTATCTTCGTTATTA+TGG - chr1.4:13876375-13876394 MS.gene32349:CDS 30.0%
CTTGTTAAACATCTTGTACA+GGG - chr1.4:13876838-13876857 MS.gene32349:intron 30.0%
TAATGCCTTAAGAATCCAAT+GGG + chr1.4:13876760-13876779 None:intergenic 30.0%
TACAGCGAACGATTTAATAT+GGG - chr1.4:13877239-13877258 MS.gene32349:intron 30.0%
TTACAGCGAACGATTTAATA+TGG - chr1.4:13877238-13877257 MS.gene32349:intron 30.0%
TTGTCGAATCCAATTGTAAT+TGG + chr1.4:13877357-13877376 None:intergenic 30.0%
! ACAGACAGAGTATTCAATTA+TGG + chr1.4:13876526-13876545 None:intergenic 30.0%
! ACTTGTTAAACATCTTGTAC+AGG - chr1.4:13876837-13876856 MS.gene32349:intron 30.0%
! GATACGATTGTGTACAATTT+TGG + chr1.4:13876365-13876384 None:intergenic 30.0%
!! TCAAAGAAGGTTGATGTATT+TGG + chr1.4:13876608-13876627 None:intergenic 30.0%
!!! GTGTACAATTTTGGTTGTTT+AGG + chr1.4:13876356-13876375 None:intergenic 30.0%
!!! TTAGGTTTTGAAGACTATGT+TGG - chr1.4:13877273-13877292 MS.gene32349:intron 30.0%
ATTCTTGTCAATTGCACGAT+GGG + chr1.4:13877081-13877100 None:intergenic 35.0%
GAACGATTTAATATGGGCAA+TGG - chr1.4:13877245-13877264 MS.gene32349:intron 35.0%
GTAATGCCTTAAGAATCCAA+TGG + chr1.4:13876761-13876780 None:intergenic 35.0%
TACTTCCCATTGGATTCTTA+AGG - chr1.4:13876752-13876771 MS.gene32349:intron 35.0%
TCGCATGTAAAAATCTCTGA+TGG - chr1.4:13877120-13877139 MS.gene32349:intron 35.0%
TGCAATTGACAAGAATCATG+CGG - chr1.4:13877085-13877104 MS.gene32349:intron 35.0%
TGTTGAACGACTAAGGTTAA+GGG + chr1.4:13876312-13876331 None:intergenic 35.0%
TTGATTGTGTTGAACGACTA+AGG + chr1.4:13876319-13876338 None:intergenic 35.0%
TTTGGAGGTAAAAGACTAGA+GGG + chr1.4:13877299-13877318 None:intergenic 35.0%
TTTGTTTCACATGTCCAAAG+AGG + chr1.4:13876787-13876806 None:intergenic 35.0%
! ATCAGAGATTTTTACATGCG+AGG + chr1.4:13877121-13877140 None:intergenic 35.0%
! TAAGGCATTACTTTCCTCTT+TGG - chr1.4:13876770-13876789 MS.gene32349:intron 35.0%
! TCAGAGATTTTTACATGCGA+GGG + chr1.4:13877120-13877139 None:intergenic 35.0%
!! AATCCAATGGGAAGTATTCA+AGG + chr1.4:13876748-13876767 None:intergenic 35.0%
!! ATCCAATGGGAAGTATTCAA+GGG + chr1.4:13876747-13876766 None:intergenic 35.0%
!! TTACTTAGCTCTGATCTGTT+TGG - chr1.4:13876922-13876941 MS.gene32349:intron 35.0%
!!! GGATTAGTCCATTTTGAAGT+AGG - chr1.4:13876943-13876962 MS.gene32349:intron 35.0%
!!! TGCTCCTCATTCTTTGTTTT+AGG + chr1.4:13877051-13877070 None:intergenic 35.0%
ACAATTGGATTCGACAAGGA+TGG - chr1.4:13877360-13877379 MS.gene32349:intron 40.0%
ATATGGGCAATGGATAGGTT+AGG - chr1.4:13877255-13877274 MS.gene32349:intron 40.0%
CATAGTTACGATACCTTTGG+AGG + chr1.4:13877314-13877333 None:intergenic 40.0%
CCACATAGTTACGATACCTT+TGG + chr1.4:13877317-13877336 None:intergenic 40.0%
GATTCTTGTCAATTGCACGA+TGG + chr1.4:13877082-13877101 None:intergenic 40.0%
GTGTTGAACGACTAAGGTTA+AGG + chr1.4:13876313-13876332 None:intergenic 40.0%
TTCCCTTGAATACTTCCCAT+TGG - chr1.4:13876742-13876761 MS.gene32349:intron 40.0%
! AGGTAAATGCTGCTTAGTTC+CGG + chr1.4:13877031-13877050 None:intergenic 40.0%
! CTTTGGAGGTAAAAGACTAG+AGG + chr1.4:13877300-13877319 None:intergenic 40.0%
!! CCAAAGGTATCGTAACTATG+TGG - chr1.4:13877314-13877333 MS.gene32349:intron 40.0%
!! CTCTAGTCTTTTACCTCCAA+AGG - chr1.4:13877298-13877317 MS.gene32349:intron 40.0%
AACGACTAAGGTTAAGGGAC+GGG + chr1.4:13876307-13876326 None:intergenic 45.0%
CGTTCAACACAATCAAGCTC+TGG - chr1.4:13876323-13876342 MS.gene32349:CDS 45.0%
GAACGACTAAGGTTAAGGGA+CGG + chr1.4:13876308-13876327 None:intergenic 45.0%
TGGATTCGACAAGGATGGAT+CGG - chr1.4:13877365-13877384 MS.gene32349:intron 45.0%
CATGAGCATCATCACGAGTG+AGG - chr1.4:13877179-13877198 MS.gene32349:intron 50.0%
GGATTCGACAAGGATGGATC+GGG - chr1.4:13877366-13877385 MS.gene32349:intron 50.0%
AAGGATGGATCGGGTGCTAG+TGG - chr1.4:13877375-13877394 MS.gene32349:intron 55.0%
GGTGCTAGTGGCTCGAACAA+TGG - chr1.4:13877387-13877406 MS.gene32349:CDS 55.0%
TCACGAGTGAGGCAAGCGAG+CGG - chr1.4:13877190-13877209 MS.gene32349:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 13876290 13877431 13876290 ID=MS.gene32349
chr1.4 mRNA 13876290 13877431 13876290 ID=MS.gene32349.t1;Parent=MS.gene32349
chr1.4 exon 13877377 13877431 13877377 ID=MS.gene32349.t1.exon1;Parent=MS.gene32349.t1
chr1.4 CDS 13877377 13877431 13877377 ID=cds.MS.gene32349.t1;Parent=MS.gene32349.t1
chr1.4 exon 13876290 13876756 13876290 ID=MS.gene32349.t1.exon2;Parent=MS.gene32349.t1
chr1.4 CDS 13876290 13876756 13876290 ID=cds.MS.gene32349.t1;Parent=MS.gene32349.t1
Gene Sequence

>MS.gene32349

ATGGAGAATGGAATCCCGTCCCTTAACCTTAGTCGTTCAACACAATCAAGCTCTGGTAAGCACCCTAAACAACCAAAATTGTACACAATCGTATCTTCGTTATTATGGGTTTAGATCCTCTTATTCTCAAAAATAATCAAGAATTATTATTTTTAAAAGGAGTGATGATACATATTTTAAATATTCTTTTTTTTTTTTTTACTTTGAAGAAGATTGAGGAATAAAGATGATCTCCATAATTGAATACTCTGTCTGTTACAAAAAATAAACAAAAGTGAGTCAAACAAAATTGAGGTATTTGGTTTAAAATTTAGTCCAAATACATCAACCTTCTTTGACTTACTTTTTGCTTATATTTTTTTTTTGAGGGATGCTTATATTTTGTTATAGAGTGAATAATATACAATATTATTTCAATTTTTTTACTAGTATTTTTCTTTGTTTATTTGTTATTCCCTTGAATACTTCCCATTGGATTCTTAAGGCATTACTTTCCTCTTTGGACATGTGAAACAAAGATCTAAAAAATAAGGTTTGATTTTGCATCACTTGTTAAACATCTTGTACAGGGATAAATATTTATTTTTGAATGAAATTTTCATCATAAATTACAAAACTATTTTTTGTCTAAATTACTTAGCTCTGATCTGTTTGGATTAGTCCATTTTGAAGTAGGTAATTCATCAACAAACATTGAATCTCAAAGCAACGTCGACAACAACAACAATAACTTTCACACCGGAACTAAGCAGCATTTACCTAAAACAAAGAATGAGGAGCAGCACATTCCCATCGTGCAATTGACAAGAATCATGCGGCGTGCTCTTCCCTCGCATGTAAAAATCTCTGATGGTGCTAAAGAGTCAATTCAATTGTGTTTATCTGAATTCATGAGCATCATCACGAGTGAGGCAAGCGAGCGGTGCAAGATAGAGCATCGAAAGATCGTTACAGCGAACGATTTAATATGGGCAATGGATAGGTTAGGTTTTGAAGACTATGTTGGCCCTCTAGTCTTTTACCTCCAAAGGTATCGTAACTATGTGGCTCAGCTAAATGACATGCCAATTACAATTGGATTCGACAAGGATGGATCGGGTGCTAGTGGCTCGAACAATGGCAGTGACAATGTTCACCATTGA
Protein sequence

>MS.gene32349.t1

MENGIPSLNLSRSTQSSSGNSSTNIESQSNVDNNNNNFHTGTKQHLPKTKNEEQHIPIVQLTRIMRRALPSHVKISDGAKESIQLCLSEFMSIITSEASERCKIEHRKIVTANDLIWAMDRLGFEDYVGPLVFYLQRYRNYVAQLNDMPITIGFDKDGSGASGSNNGSDNVHH