AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054128

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054128.t1 MTR_1g028480 82.609 92 16 0 81 172 19 110 7.97e-53 164
MS.gene054128.t1 MTR_1g029070 53.165 158 73 1 1 157 1 158 3.04e-48 154
MS.gene054128.t1 MTR_1g039040 63.333 90 33 0 50 139 5 94 1.60e-39 133
MS.gene054128.t1 MTR_4g133952 47.934 121 59 2 20 139 29 146 2.31e-35 124
MS.gene054128.t1 MTR_7g061270 41.667 132 64 2 44 173 17 137 1.75e-34 119
MS.gene054128.t1 MTR_7g100650 41.667 132 64 2 44 173 17 137 3.09e-34 119
MS.gene054128.t1 MTR_8g091720 53.846 91 42 0 49 139 26 116 6.46e-34 119
MS.gene054128.t1 MTR_3g058980 44.286 140 69 4 29 164 2 136 1.39e-33 117
MS.gene054128.t1 MTR_2g026710 44.444 117 58 1 32 148 5 114 2.04e-33 116
MS.gene054128.t1 MTR_1g072790 52.747 91 43 0 49 139 27 117 5.25e-33 115
MS.gene054128.t1 MTR_5g095740 46.789 109 54 1 50 158 22 126 1.01e-32 115
MS.gene054128.t1 MTR_4g133938 42.308 130 70 1 32 161 5 129 6.04e-32 112
MS.gene054128.t1 MTR_8g093920 45.000 100 55 0 50 149 39 138 1.22e-29 108
MS.gene054128.t1 MTR_4g119500 48.889 90 46 0 50 139 21 110 3.31e-29 104
MS.gene054128.t1 MTR_0392s0020 48.889 90 46 0 50 139 17 106 3.51e-29 105
MS.gene054128.t1 MTR_1g088860 46.316 95 51 0 50 144 35 129 2.48e-27 102
MS.gene054128.t1 MTR_1g029100 48.750 80 41 0 52 131 3 82 3.28e-24 90.9
MS.gene054128.t1 MTR_1g083070 40.230 87 52 0 53 139 6 92 4.71e-21 84.0
MS.gene054128.t1 MTR_5g095900 41.176 85 50 0 56 140 21 105 3.28e-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.gene054128.t1 AT5G47670 54.945 91 41 0 49 139 27 117 5.12e-35 122
MS.gene054128.t1 AT1G21970 42.143 140 76 2 1 139 12 147 5.99e-35 122
MS.gene054128.t1 AT5G47670 41.135 141 78 2 3 139 7 146 7.73e-35 122
MS.gene054128.t1 AT5G47670 41.135 141 78 2 3 139 7 146 7.73e-35 122
MS.gene054128.t1 AT4G14540 53.846 91 42 0 49 139 19 109 1.35e-34 119
MS.gene054128.t1 AT2G38880 46.087 115 51 1 49 163 19 122 2.77e-33 115
MS.gene054128.t1 AT2G38880 46.087 115 51 1 49 163 19 122 3.28e-33 115
MS.gene054128.t1 AT2G38880 46.087 115 51 1 49 163 19 122 3.28e-33 115
MS.gene054128.t1 AT2G38880 46.087 115 51 1 49 163 19 122 3.28e-33 115
MS.gene054128.t1 AT2G38880 51.648 91 44 0 49 139 19 109 3.34e-33 115
MS.gene054128.t1 AT2G38880 51.648 91 44 0 49 139 19 109 1.53e-32 112
MS.gene054128.t1 AT5G47640 51.648 91 44 0 50 140 26 116 2.21e-32 114
MS.gene054128.t1 AT2G38880 51.648 91 44 0 49 139 19 109 2.99e-32 113
MS.gene054128.t1 AT2G38880 51.648 91 44 0 49 139 19 109 2.99e-32 113
MS.gene054128.t1 AT2G37060 44.444 117 61 2 26 139 3 118 5.47e-32 113
MS.gene054128.t1 AT2G37060 44.444 117 61 2 26 139 3 118 5.47e-32 113
MS.gene054128.t1 AT2G37060 44.444 117 61 2 26 139 3 118 5.47e-32 113
MS.gene054128.t1 AT3G53340 50.549 91 45 0 49 139 27 117 5.81e-32 113
MS.gene054128.t1 AT3G53340 50.549 91 45 0 49 139 27 117 5.81e-32 113
MS.gene054128.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.27e-31 110
MS.gene054128.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.55e-31 111
MS.gene054128.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.55e-31 111
MS.gene054128.t1 AT2G38880 49.474 95 48 0 49 143 19 113 1.55e-31 111
MS.gene054128.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.78e-30 108
MS.gene054128.t1 AT3G53340 50.549 91 45 0 49 139 27 117 1.78e-30 108
MS.gene054128.t1 AT2G13570 49.451 91 46 0 50 140 35 125 7.81e-30 108
MS.gene054128.t1 AT2G47810 47.253 91 48 0 49 139 49 139 3.03e-27 100
MS.gene054128.t1 AT1G09030 41.573 89 52 0 51 139 3 91 2.66e-23 90.1

Find 35 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACAGCGAACGATTTAATA+TGG 0.243997 1.3:-14658246 MS.gene054128:CDS
TTGTCGAATCCAATTGTAAT+TGG 0.273848 1.3:+14658130 None:intergenic
AGGTAAATGCTGCTTAGTTC+CGG 0.363825 1.3:+14658456 None:intergenic
AATGACATGCCAATTACAAT+TGG 0.392076 1.3:-14658139 MS.gene054128:CDS
GTGTTGAACGACTAAGGTTA+AGG 0.408775 1.3:+14659176 None:intergenic
CCACATAGTTACGATACCTT+TGG 0.434158 1.3:+14658170 None:intergenic
TTGATTGTGTTGAACGACTA+AGG 0.437171 1.3:+14659170 None:intergenic
ATATGGGCAATGGATAGGTT+AGG 0.445811 1.3:-14658229 MS.gene054128:CDS
TGTTGAACGACTAAGGTTAA+GGG 0.465410 1.3:+14659177 None:intergenic
CATAGTTACGATACCTTTGG+AGG 0.481766 1.3:+14658173 None:intergenic
CTTAAAAGTAGTATGGAGAA+TGG 0.482031 1.3:-14659208 None:intergenic
TACAGCGAACGATTTAATAT+GGG 0.483846 1.3:-14658245 MS.gene054128:CDS
ATTCTTGTCAATTGCACGAT+GGG 0.485603 1.3:+14658406 None:intergenic
ATTTAATATGGGCAATGGAT+AGG 0.498662 1.3:-14658234 MS.gene054128:CDS
CGTTCAACACAATCAAGCTC+TGG 0.512773 1.3:-14659163 MS.gene054128:intron
TGGATTCGACAAGGATGGAT+CGG 0.517609 1.3:-14658119 MS.gene054128:CDS
GGTGCTAGTGGCTCGAACAA+TGG 0.519839 1.3:-14658097 MS.gene054128:CDS
AACGACTAAGGTTAAGGGAC+GGG 0.520234 1.3:+14659182 None:intergenic
AATTGACTCTTTAGCACCAT+CGG 0.524561 1.3:+14658348 None:intergenic
ACAATTGGATTCGACAAGGA+TGG 0.533736 1.3:-14658124 MS.gene054128:CDS
GGATTCGACAAGGATGGATC+GGG 0.534384 1.3:-14658118 MS.gene054128:CDS
GAACGATTTAATATGGGCAA+TGG 0.552208 1.3:-14658239 MS.gene054128:CDS
TTTACCTAAAACAAAGAATG+AGG 0.564286 1.3:-14658440 MS.gene054128:CDS
AAGGATGGATCGGGTGCTAG+TGG 0.571277 1.3:-14658109 MS.gene054128:CDS
AACAACAATAACTTTCACAC+CGG 0.626294 1.3:-14658475 MS.gene054128:CDS
TTTGGAGGTAAAAGACTAGA+GGG 0.630419 1.3:+14658188 None:intergenic
CATGAGCATCATCACGAGTG+AGG 0.643678 1.3:-14658305 MS.gene054128:CDS
CCAAAGGTATCGTAACTATG+TGG 0.644573 1.3:-14658170 MS.gene054128:CDS
GAACGACTAAGGTTAAGGGA+CGG 0.644933 1.3:+14659181 None:intergenic
GATTCTTGTCAATTGCACGA+TGG 0.645811 1.3:+14658405 None:intergenic
CTTTGGAGGTAAAAGACTAG+AGG 0.649236 1.3:+14658187 None:intergenic
GCTAGTGGCTCGAACAATGG+CGG 0.649770 1.3:-14658094 MS.gene054128:CDS
AATTACAATTGGATTCGACA+AGG 0.668467 1.3:-14658128 MS.gene054128:CDS
TCACGAGTGAGGCAAGCGAG+CGG 0.677839 1.3:-14658294 MS.gene054128:CDS
TGCAATTGACAAGAATCATG+CGG 0.689401 1.3:-14658399 MS.gene054128:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAGAATTATTATTTTTAAA+AGG - chr1.3:14658213-14658232 MS.gene054128:CDS 10.0%
!! AAACAAAGATCTAAAAAATA+AGG - chr1.3:14658585-14658604 MS.gene054128:intron 15.0%
!!! TGCTTATATTTTTTTTTTGA+GGG - chr1.3:14658422-14658441 MS.gene054128:CDS 15.0%
!!! TTGCTTATATTTTTTTTTTG+AGG - chr1.3:14658421-14658440 MS.gene054128:CDS 15.0%
!!! GATTATTTTTGAGAAATAAG+AGG + chr1.3:14658194-14658213 None:intergenic 20.0%
! AATCGTATCTTCGTTATTAT+GGG - chr1.3:14658161-14658180 MS.gene054128:CDS 25.0%
! ATGAATTACCTACTTCAAAA+TGG + chr1.3:14658741-14658760 None:intergenic 25.0%
! TTTACCTAAAACAAAGAATG+AGG - chr1.3:14658831-14658850 MS.gene054128:intron 25.0%
!! TCAAACAAAATTGAGGTATT+TGG - chr1.3:14658354-14658373 MS.gene054128:CDS 25.0%
!!! TGTACAATTTTGGTTGTTTA+GGG + chr1.3:14658140-14658159 None:intergenic 25.0%
AACAACAATAACTTTCACAC+CGG - chr1.3:14658796-14658815 MS.gene054128:intron 30.0%
AAGTGAGTCAAACAAAATTG+AGG - chr1.3:14658347-14658366 MS.gene054128:CDS 30.0%
AATGACATGCCAATTACAAT+TGG - chr1.3:14659132-14659151 MS.gene054128:intron 30.0%
AATTACAATTGGATTCGACA+AGG - chr1.3:14659143-14659162 MS.gene054128:intron 30.0%
AGCAAAAAGTAAGTCAAAGA+AGG + chr1.3:14658406-14658425 None:intergenic 30.0%
ATTTAATATGGGCAATGGAT+AGG - chr1.3:14659037-14659056 MS.gene054128:intron 30.0%
CAATCGTATCTTCGTTATTA+TGG - chr1.3:14658160-14658179 MS.gene054128:CDS 30.0%
TAATGCCTTAAGAATCCAAT+GGG + chr1.3:14658545-14658564 None:intergenic 30.0%
TACAGCGAACGATTTAATAT+GGG - chr1.3:14659026-14659045 MS.gene054128:intron 30.0%
TTACAGCGAACGATTTAATA+TGG - chr1.3:14659025-14659044 MS.gene054128:intron 30.0%
TTGTCGAATCCAATTGTAAT+TGG + chr1.3:14659144-14659163 None:intergenic 30.0%
! GATACGATTGTGTACAATTT+TGG + chr1.3:14658150-14658169 None:intergenic 30.0%
!! TCAAAGAAGGTTGATGTATT+TGG + chr1.3:14658393-14658412 None:intergenic 30.0%
!! TGTTACTTTGAAGAAGATTG+AGG - chr1.3:14658271-14658290 MS.gene054128:CDS 30.0%
!! TTACTTAGCTCTGATATGTT+TGG - chr1.3:14658709-14658728 MS.gene054128:intron 30.0%
!!! GTGTACAATTTTGGTTGTTT+AGG + chr1.3:14658141-14658160 None:intergenic 30.0%
!!! TTAGGTTTTGAAGACTATGT+TGG - chr1.3:14659060-14659079 MS.gene054128:intron 30.0%
ATTCTTGTCAATTGCACGAT+GGG + chr1.3:14658868-14658887 None:intergenic 35.0%
CTTGTTGAACATCTTGTACA+GGG - chr1.3:14658623-14658642 MS.gene054128:intron 35.0%
GAACGATTTAATATGGGCAA+TGG - chr1.3:14659032-14659051 MS.gene054128:intron 35.0%
GTAATGCCTTAAGAATCCAA+TGG + chr1.3:14658546-14658565 None:intergenic 35.0%
TACTTCCCATTGGATTCTTA+AGG - chr1.3:14658537-14658556 MS.gene054128:intron 35.0%
TGCAATTGACAAGAATCATG+CGG - chr1.3:14658872-14658891 MS.gene054128:intron 35.0%
TGTTGAACGACTAAGGTTAA+GGG + chr1.3:14658097-14658116 None:intergenic 35.0%
TTGATTGTGTTGAACGACTA+AGG + chr1.3:14658104-14658123 None:intergenic 35.0%
TTTGGAGGTAAAAGACTAGA+GGG + chr1.3:14659086-14659105 None:intergenic 35.0%
TTTGTTTCACATGTCCAAAG+AGG + chr1.3:14658572-14658591 None:intergenic 35.0%
! AATTGACTCTTTAGCACCAT+CGG + chr1.3:14658926-14658945 None:intergenic 35.0%
! ACAGACAGAGCATTCAATTA+TGG + chr1.3:14658311-14658330 None:intergenic 35.0%
! ACTTGTTGAACATCTTGTAC+AGG - chr1.3:14658622-14658641 MS.gene054128:intron 35.0%
! TAAGGCATTACTTTCCTCTT+TGG - chr1.3:14658555-14658574 MS.gene054128:intron 35.0%
!! AATCCAATGGGAAGTATTCA+AGG + chr1.3:14658533-14658552 None:intergenic 35.0%
!! ATCCAATGGGAAGTATTCAA+GGG + chr1.3:14658532-14658551 None:intergenic 35.0%
!!! GGATTAGTCCATTTTGAAGT+AGG - chr1.3:14658730-14658749 MS.gene054128:intron 35.0%
!!! TGCTCCTCATTCTTTGTTTT+AGG + chr1.3:14658838-14658857 None:intergenic 35.0%
ACAATTGGATTCGACAAGGA+TGG - chr1.3:14659147-14659166 MS.gene054128:intron 40.0%
ATATGGGCAATGGATAGGTT+AGG - chr1.3:14659042-14659061 MS.gene054128:intron 40.0%
CATAGTTACGATACCTTTGG+AGG + chr1.3:14659101-14659120 None:intergenic 40.0%
CCACATAGTTACGATACCTT+TGG + chr1.3:14659104-14659123 None:intergenic 40.0%
GATTCTTGTCAATTGCACGA+TGG + chr1.3:14658869-14658888 None:intergenic 40.0%
GTGTTGAACGACTAAGGTTA+AGG + chr1.3:14658098-14658117 None:intergenic 40.0%
TCGCATGTAAAAATCTCCGA+TGG - chr1.3:14658907-14658926 MS.gene054128:intron 40.0%
TTCCCTTGAATACTTCCCAT+TGG - chr1.3:14658527-14658546 MS.gene054128:intron 40.0%
! AGGTAAATGCTGCTTAGTTC+CGG + chr1.3:14658818-14658837 None:intergenic 40.0%
! ATCGGAGATTTTTACATGCG+AGG + chr1.3:14658908-14658927 None:intergenic 40.0%
! CTTTGGAGGTAAAAGACTAG+AGG + chr1.3:14659087-14659106 None:intergenic 40.0%
! TCGGAGATTTTTACATGCGA+GGG + chr1.3:14658907-14658926 None:intergenic 40.0%
!! CCAAAGGTATCGTAACTATG+TGG - chr1.3:14659101-14659120 MS.gene054128:intron 40.0%
!! CTCTAGTCTTTTACCTCCAA+AGG - chr1.3:14659085-14659104 MS.gene054128:intron 40.0%
AACGACTAAGGTTAAGGGAC+GGG + chr1.3:14658092-14658111 None:intergenic 45.0%
CGTTCAACACAATCAAGCTC+TGG - chr1.3:14658108-14658127 MS.gene054128:CDS 45.0%
GAACGACTAAGGTTAAGGGA+CGG + chr1.3:14658093-14658112 None:intergenic 45.0%
TGGATTCGACAAGGATGGAT+CGG - chr1.3:14659152-14659171 MS.gene054128:intron 45.0%
CATGAGCATCATCACGAGTG+AGG - chr1.3:14658966-14658985 MS.gene054128:intron 50.0%
GGATTCGACAAGGATGGATC+GGG - chr1.3:14659153-14659172 MS.gene054128:intron 50.0%
AAGGATGGATCGGGTGCTAG+TGG - chr1.3:14659162-14659181 MS.gene054128:intron 55.0%
GCTAGTGGCTCGAACAATGG+CGG - chr1.3:14659177-14659196 MS.gene054128:CDS 55.0%
GGTGCTAGTGGCTCGAACAA+TGG - chr1.3:14659174-14659193 MS.gene054128:CDS 55.0%
TCACGAGTGAGGCAAGCGAG+CGG - chr1.3:14658977-14658996 MS.gene054128:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 14658075 14659218 14658075 ID=MS.gene054128
chr1.3 mRNA 14658075 14659218 14658075 ID=MS.gene054128.t1;Parent=MS.gene054128
chr1.3 exon 14659164 14659218 14659164 ID=MS.gene054128.t1.exon1;Parent=MS.gene054128.t1
chr1.3 CDS 14659164 14659218 14659164 ID=cds.MS.gene054128.t1;Parent=MS.gene054128.t1
chr1.3 exon 14658075 14658541 14658075 ID=MS.gene054128.t1.exon2;Parent=MS.gene054128.t1
chr1.3 CDS 14658075 14658541 14658075 ID=cds.MS.gene054128.t1;Parent=MS.gene054128.t1
Gene Sequence

>MS.gene054128

ATGGAGAATGGAATCCCGTCCCTTAACCTTAGTCGTTCAACACAATCAAGCTCTGGTAAGCACCCTAAACAACCAAAATTGTACACAATCGTATCTTCGTTATTATGGGTTTAGATCCTCTTATTTCTCAAAAATAATCAAGAATTATTATTTTTAAAAGGAGTGATGATACATATTTTAAATATTCTTTTTTTTTTGTTACTTTGAAGAAGATTGAGGAATAAAGATGATCTCCATAATTGAATGCTCTGTCTGTTACAAAAAATAAACAAAAGTGAGTCAAACAAAATTGAGGTATTTGGTTTAAAATTTAGTCCAAATACATCAACCTTCTTTGACTTACTTTTTGCTTATATTTTTTTTTTGAGGGATGCTTATATTTTGTTATAGAGTGAATAATATACAATATTATTTCAATTTTTTTACTAGTATTTTTCTTTGTTTATTTGTTATTCCCTTGAATACTTCCCATTGGATTCTTAAGGCATTACTTTCCTCTTTGGACATGTGAAACAAAGATCTAAAAAATAAGGTTTGATTTTGCATCACTTGTTGAACATCTTGTACAGGGATAAATATTTGATTTTTGAATGAAATTTTCAATCATAAATTACAAAACTATTTTTTGTCTAAATTACTTAGCTCTGATATGTTTGGATTAGTCCATTTTGAAGTAGGTAATTCATCAACAAACATTGAATCTCAAAGCAACGTCGACAACAACAACAATAACTTTCACACCGGAACTAAGCAGCATTTACCTAAAACAAAGAATGAGGAGCAGCACATTCCCATCGTGCAATTGACAAGAATCATGCGGCGTGCTCTTCCCTCGCATGTAAAAATCTCCGATGGTGCTAAAGAGTCAATTCAATTGTGTTTATCTGAATTCATGAGCATCATCACGAGTGAGGCAAGCGAGCGGTGCAAGATAGAGCATCGAAAGATCGTTACAGCGAACGATTTAATATGGGCAATGGATAGGTTAGGTTTTGAAGACTATGTTGGCCCTCTAGTCTTTTACCTCCAAAGGTATCGTAACTATGTGGCTCAGCTAAATGACATGCCAATTACAATTGGATTCGACAAGGATGGATCGGGTGCTAGTGGCTCGAACAATGGCGGTGACAATGTTCACCATTGA
Protein sequence

>MS.gene054128.t1

MENGIPSLNLSRSTQSSSGNSSTNIESQSNVDNNNNNFHTGTKQHLPKTKNEEQHIPIVQLTRIMRRALPSHVKISDGAKESIQLCLSEFMSIITSEASERCKIEHRKIVTANDLIWAMDRLGFEDYVGPLVFYLQRYRNYVAQLNDMPITIGFDKDGSGASGSNNGGDNVHH