AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39965

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39965.t1 MTR_1g072110 93.750 240 12 2 1 240 1 237 1.06e-135 381
MS.gene39965.t1 MTR_7g095150 51.489 235 67 9 6 238 12 201 8.30e-59 185
MS.gene39965.t1 MTR_1g103640 47.826 138 49 3 102 237 63 179 5.88e-36 127
MS.gene39965.t1 MTR_2g102140 38.636 132 69 3 118 237 142 273 1.82e-17 80.1
MS.gene39965.t1 MTR_7g105780 40.157 127 52 5 111 237 97 199 2.08e-17 79.7
MS.gene39965.t1 MTR_4g012060 50.649 77 35 2 159 234 175 249 9.77e-16 75.1
MS.gene39965.t1 MTR_1g111640 51.429 70 29 2 166 235 135 199 8.67e-15 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39965.t1 AT1G05420 37.220 223 87 7 49 239 19 220 1.17e-27 105
MS.gene39965.t1 AT1G05420 37.220 223 87 7 49 239 35 236 1.33e-27 106
MS.gene39965.t1 AT2G32100 38.608 158 71 5 100 239 89 238 6.56e-24 96.3
MS.gene39965.t1 AT4G14860 57.143 77 31 1 165 239 96 172 3.96e-22 90.1
MS.gene39965.t1 AT1G79960 45.946 74 40 0 164 237 187 260 3.78e-17 79.0
MS.gene39965.t1 AT5G04820 35.156 128 70 4 110 237 98 212 4.10e-15 72.8
MS.gene39965.t1 AT2G36050 33.600 125 55 2 113 237 77 173 9.16e-13 66.2
MS.gene39965.t1 AT3G52540 30.216 139 67 4 101 237 90 200 8.91e-12 63.9

Find 57 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACTGATAGTTGTAGAAAT+TGG 0.240910 1.4:+58878017 None:intergenic
AACACTCACAAGTTCATTCT+TGG 0.302219 1.4:-58877438 MS.gene39965:CDS
CTACTCACCTGATCCTTATA+TGG 0.303517 1.4:-58877577 MS.gene39965:CDS
CTTCTCACGCTCAATACTAT+TGG 0.339069 1.4:+58877656 None:intergenic
TTCCTCAGATTTCTTGTGCT+TGG 0.343096 1.4:+58878095 None:intergenic
AAATCTGCTGGCTCAAGTTC+GGG 0.349712 1.4:+58877798 None:intergenic
TAAAGTGTGGTCTGAGGTTA+AGG 0.350644 1.4:+58877881 None:intergenic
ATGAACTTGTGAGTGTTCTT+TGG 0.354503 1.4:+58877444 None:intergenic
GATCTTCTAAAATCCATATA+AGG 0.364006 1.4:+58877564 None:intergenic
TGATGGATGTGAAATCAAAT+TGG 0.370791 1.4:-58877509 MS.gene39965:CDS
GAAATCTGCTGGCTCAAGTT+CGG 0.374871 1.4:+58877797 None:intergenic
AAGGCTGCTGCGAAATCTGC+TGG 0.394882 1.4:+58877786 None:intergenic
TGAACTTGTGAGTGTTCTTT+GGG 0.402029 1.4:+58877445 None:intergenic
TGTATATTCAATTAATGAGT+TGG 0.404911 1.4:+58877725 None:intergenic
GTTGTAGAAATTGGACTTGT+GGG 0.416852 1.4:+58878026 None:intergenic
CGCTTCTTCTTCTCCTCCCC+CGG 0.419956 1.4:-58877753 MS.gene39965:CDS
GAAACAGGAGAAAGAGAAAG+AGG 0.423520 1.4:-58877634 MS.gene39965:CDS
TATTGAGCGTGAGAAGAAAC+AGG 0.440175 1.4:-58877649 MS.gene39965:CDS
AATTCTTGATCATAATTGAC+GGG 0.444957 1.4:+58877925 None:intergenic
AGAGATGGTGGAGGCGCGAC+CGG 0.455026 1.4:-58877535 MS.gene39965:CDS
CTAAAATCCATATAAGGATC+AGG 0.462583 1.4:+58877570 None:intergenic
AATTAATGAGTTGGAGCTAC+CGG 0.467305 1.4:+58877734 None:intergenic
ATACTATTGGACTTATCCAT+TGG 0.483511 1.4:+58877669 None:intergenic
GGAGGCGCGACCGGAGTTGA+TGG 0.488669 1.4:-58877526 MS.gene39965:CDS
AGATTGCATTCAGCATTCTT+CGG 0.492875 1.4:-58877697 MS.gene39965:CDS
TGTTCTTTGGGTTGAGAGCA+AGG 0.508816 1.4:+58877457 None:intergenic
GAAGAAGCGTTGAGAGGCGA+AGG 0.509416 1.4:+58877767 None:intergenic
ATTAATGAGTTGGAGCTACC+GGG 0.511814 1.4:+58877735 None:intergenic
CTATTGGACTTATCCATTGG+TGG 0.513854 1.4:+58877672 None:intergenic
TTCAACTTCGAGTTCAAAAG+AGG 0.515870 1.4:+58877821 None:intergenic
GCATTCTTCGGTACCACCAA+TGG 0.516823 1.4:-58877685 MS.gene39965:CDS
AAAAGAGGTTGATGTAGTAA+AGG 0.520478 1.4:+58877836 None:intergenic
AAATTCTTGATCATAATTGA+CGG 0.524121 1.4:+58877924 None:intergenic
GATGCAGATGTAGATGAAGA+AGG 0.533865 1.4:+58877951 None:intergenic
AGAGGTTGATGTAGTAAAGG+TGG 0.557401 1.4:+58877839 None:intergenic
ACCATGACTAAAATGACATG+AGG 0.563547 1.4:+58877391 None:intergenic
CATATAAGGATCAGGTGAGT+AGG 0.566346 1.4:+58877578 None:intergenic
GTGTGGTCTGAGGTTAAGGA+AGG 0.576057 1.4:+58877885 None:intergenic
TAGAAGATCGATGCAAGAGA+TGG 0.580424 1.4:-58877550 MS.gene39965:CDS
GATTTCACATCCATCAACTC+CGG 0.581756 1.4:+58877516 None:intergenic
AAGATCGATGCAAGAGATGG+TGG 0.583074 1.4:-58877547 MS.gene39965:CDS
ACAGGAGAAAGAGAAAGAGG+AGG 0.589206 1.4:-58877631 MS.gene39965:CDS
AGTTGTAGAAATTGGACTTG+TGG 0.600672 1.4:+58878025 None:intergenic
ATCGATGCAAGAGATGGTGG+AGG 0.602628 1.4:-58877544 MS.gene39965:CDS
GGAGAAGAAGAAGCGTTGAG+AGG 0.620274 1.4:+58877761 None:intergenic
CATGAGGGTTACGAGAAGAT+CGG 0.623248 1.4:+58877407 None:intergenic
TTAATGAGTTGGAGCTACCG+GGG 0.639288 1.4:+58877736 None:intergenic
GTAGAAATTGGACTTGTGGG+TGG 0.648560 1.4:+58878029 None:intergenic
AGAGCATAAAGTGTGGTCTG+AGG 0.656840 1.4:+58877875 None:intergenic
TAAGGATCAGGTGAGTAGGT+CGG 0.659190 1.4:+58877582 None:intergenic
ATTCTTGATCATAATTGACG+GGG 0.668719 1.4:+58877926 None:intergenic
GTGAAGAAGAGCATAAAGTG+TGG 0.669604 1.4:+58877868 None:intergenic
CCATGACTAAAATGACATGA+GGG 0.681032 1.4:+58877392 None:intergenic
TGTGGTCTGAGGTTAAGGAA+GGG 0.682154 1.4:+58877886 None:intergenic
TTGATGATGATGTTGATGTG+AGG 0.685082 1.4:+58877986 None:intergenic
TAATGAGTTGGAGCTACCGG+GGG 0.686460 1.4:+58877737 None:intergenic
TGCCAAGCACAAGAAATCTG+AGG 0.689018 1.4:-58878097 MS.gene39965:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCTTGATCATAATTGA+CGG + chr1.4:58877575-58877594 None:intergenic 20.0%
!! TGTATATTCAATTAATGAGT+TGG + chr1.4:58877774-58877793 None:intergenic 20.0%
! AATTCTTGATCATAATTGAC+GGG + chr1.4:58877574-58877593 None:intergenic 25.0%
! AATTTGAAAAACATAGGTTG+AGG + chr1.4:58877427-58877446 None:intergenic 25.0%
! GAGTTGAATTTGAAAAACAT+AGG + chr1.4:58877433-58877452 None:intergenic 25.0%
!!! GATCTTCTAAAATCCATATA+AGG + chr1.4:58877935-58877954 None:intergenic 25.0%
ATACTATTGGACTTATCCAT+TGG + chr1.4:58877830-58877849 None:intergenic 30.0%
ATTCTTGATCATAATTGACG+GGG + chr1.4:58877573-58877592 None:intergenic 30.0%
CTAAAATCCATATAAGGATC+AGG + chr1.4:58877929-58877948 None:intergenic 30.0%
TCACTGATAGTTGTAGAAAT+TGG + chr1.4:58877482-58877501 None:intergenic 30.0%
! TGATGGATGTGAAATCAAAT+TGG - chr1.4:58877987-58878006 MS.gene39965:CDS 30.0%
!! AAAAGAGGTTGATGTAGTAA+AGG + chr1.4:58877663-58877682 None:intergenic 30.0%
AACACTCACAAGTTCATTCT+TGG - chr1.4:58878058-58878077 MS.gene39965:CDS 35.0%
AGATTGCATTCAGCATTCTT+CGG - chr1.4:58877799-58877818 MS.gene39965:CDS 35.0%
AGTTGTAGAAATTGGACTTG+TGG + chr1.4:58877474-58877493 None:intergenic 35.0%
ATGAACTTGTGAGTGTTCTT+TGG + chr1.4:58878055-58878074 None:intergenic 35.0%
GTTGTAGAAATTGGACTTGT+GGG + chr1.4:58877473-58877492 None:intergenic 35.0%
TGAACTTGTGAGTGTTCTTT+GGG + chr1.4:58878054-58878073 None:intergenic 35.0%
! AATTAATGAGTTGGAGCTAC+CGG + chr1.4:58877765-58877784 None:intergenic 35.0%
! TTCAACTTCGAGTTCAAAAG+AGG + chr1.4:58877678-58877697 None:intergenic 35.0%
!! TTGATGATGATGTTGATGTG+AGG + chr1.4:58877513-58877532 None:intergenic 35.0%
!!! AAAGAGGAGGTTTTGTTCAA+CGG - chr1.4:58877878-58877897 MS.gene39965:CDS 35.0%
CATATAAGGATCAGGTGAGT+AGG + chr1.4:58877921-58877940 None:intergenic 40.0%
CTACTCACCTGATCCTTATA+TGG - chr1.4:58877919-58877938 MS.gene39965:CDS 40.0%
CTATTGGACTTATCCATTGG+TGG + chr1.4:58877827-58877846 None:intergenic 40.0%
CTTCTCACGCTCAATACTAT+TGG + chr1.4:58877843-58877862 None:intergenic 40.0%
GAAACAGGAGAAAGAGAAAG+AGG - chr1.4:58877862-58877881 MS.gene39965:CDS 40.0%
GATGCAGATGTAGATGAAGA+AGG + chr1.4:58877548-58877567 None:intergenic 40.0%
GATTTCACATCCATCAACTC+CGG + chr1.4:58877983-58878002 None:intergenic 40.0%
TAGAAGATCGATGCAAGAGA+TGG - chr1.4:58877946-58877965 MS.gene39965:CDS 40.0%
TATTGAGCGTGAGAAGAAAC+AGG - chr1.4:58877847-58877866 MS.gene39965:CDS 40.0%
TTCCTCAGATTTCTTGTGCT+TGG + chr1.4:58877404-58877423 None:intergenic 40.0%
! ATTAATGAGTTGGAGCTACC+GGG + chr1.4:58877764-58877783 None:intergenic 40.0%
! GTGAAGAAGAGCATAAAGTG+TGG + chr1.4:58877631-58877650 None:intergenic 40.0%
! TAAAGTGTGGTCTGAGGTTA+AGG + chr1.4:58877618-58877637 None:intergenic 40.0%
!! AGAGGTTGATGTAGTAAAGG+TGG + chr1.4:58877660-58877679 None:intergenic 40.0%
AAGATCGATGCAAGAGATGG+TGG - chr1.4:58877949-58877968 MS.gene39965:CDS 45.0%
ACAGGAGAAAGAGAAAGAGG+AGG - chr1.4:58877865-58877884 MS.gene39965:CDS 45.0%
AGAGCATAAAGTGTGGTCTG+AGG + chr1.4:58877624-58877643 None:intergenic 45.0%
CATGAGGGTTACGAGAAGAT+CGG + chr1.4:58878092-58878111 None:intergenic 45.0%
GTAGAAATTGGACTTGTGGG+TGG + chr1.4:58877470-58877489 None:intergenic 45.0%
TAAGGATCAGGTGAGTAGGT+CGG + chr1.4:58877917-58877936 None:intergenic 45.0%
TGCCAAGCACAAGAAATCTG+AGG - chr1.4:58877399-58877418 MS.gene39965:CDS 45.0%
! TGTGGTCTGAGGTTAAGGAA+GGG + chr1.4:58877613-58877632 None:intergenic 45.0%
! TTAATGAGTTGGAGCTACCG+GGG + chr1.4:58877763-58877782 None:intergenic 45.0%
!! AAATCTGCTGGCTCAAGTTC+GGG + chr1.4:58877701-58877720 None:intergenic 45.0%
!! GAAATCTGCTGGCTCAAGTT+CGG + chr1.4:58877702-58877721 None:intergenic 45.0%
!! TGTTCTTTGGGTTGAGAGCA+AGG + chr1.4:58878042-58878061 None:intergenic 45.0%
!!! GGTTTTGTTCAACGGAAGTG+TGG - chr1.4:58877886-58877905 MS.gene39965:CDS 45.0%
GCATTCTTCGGTACCACCAA+TGG - chr1.4:58877811-58877830 MS.gene39965:CDS 50.0%
! ATCGATGCAAGAGATGGTGG+AGG - chr1.4:58877952-58877971 MS.gene39965:CDS 50.0%
! GTGTGGTCTGAGGTTAAGGA+AGG + chr1.4:58877614-58877633 None:intergenic 50.0%
! TAATGAGTTGGAGCTACCGG+GGG + chr1.4:58877762-58877781 None:intergenic 50.0%
!! GGAGAAGAAGAAGCGTTGAG+AGG + chr1.4:58877738-58877757 None:intergenic 50.0%
AAGGCTGCTGCGAAATCTGC+TGG + chr1.4:58877713-58877732 None:intergenic 55.0%
!! GAAGAAGCGTTGAGAGGCGA+AGG + chr1.4:58877732-58877751 None:intergenic 55.0%
CGCTTCTTCTTCTCCTCCCC+CGG - chr1.4:58877743-58877762 MS.gene39965:CDS 60.0%
! TGAGTTGGAGCTACCGGGGG+AGG + chr1.4:58877759-58877778 None:intergenic 65.0%
!! AGAGATGGTGGAGGCGCGAC+CGG - chr1.4:58877961-58877980 MS.gene39965:CDS 65.0%
! GGAGGCGCGACCGGAGTTGA+TGG - chr1.4:58877970-58877989 MS.gene39965:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 58877398 58878120 58877398 ID=MS.gene39965
chr1.4 mRNA 58877398 58878120 58877398 ID=MS.gene39965.t1;Parent=MS.gene39965
chr1.4 exon 58877398 58878120 58877398 ID=MS.gene39965.t1.exon1;Parent=MS.gene39965.t1
chr1.4 CDS 58877398 58878120 58877398 ID=cds.MS.gene39965.t1;Parent=MS.gene39965.t1
Gene Sequence

>MS.gene39965

ATGCCAAGCACAAGAAATCTGAGGAACCTCAACCTATGTTTTTCAAATTCAACTCTTGAATCAAAATCTCCACCCACAAGTCCAATTTCTACAACTATCAGTGAAGCAGCTTCCTCACATCAACATCATCATCAAATTCATCACAAACCTTCTTCATCTACATCTGCATCTTCCCCGTCAATTATGATCAAGAATTTCAACTCTCTCTATGACCCTTCCTTAACCTCAGACCACACTTTATGCTCTTCTTCACTCTCTACCACCTTTACTACATCAACCTCTTTTGAACTCGAAGTTGAACCCGAACTTGAGCCAGCAGATTTCGCAGCAGCCTTCGCCTCTCAACGCTTCTTCTTCTCCTCCCCCGGTAGCTCCAACTCATTAATTGAATATACAAACACAGATTGCATTCAGCATTCTTCGGTACCACCAATGGATAAGTCCAATAGTATTGAGCGTGAGAAGAAACAGGAGAAAGAGAAAGAGGAGGTTTTGTTCAACGGAAGTGTGGCAGTACCGACCTACTCACCTGATCCTTATATGGATTTTAGAAGATCGATGCAAGAGATGGTGGAGGCGCGACCGGAGTTGATGGATGTGAAATCAAATTGGAACATCTTGCATGAGTTGCTTCTTTGTTACCTTGCTCTCAACCCAAAGAACACTCACAAGTTCATTCTTGGTGCTTTTGCCGATCTTCTCGTAACCCTCATGTCATTTTAG
Protein sequence

>MS.gene39965.t1

MPSTRNLRNLNLCFSNSTLESKSPPTSPISTTISEAASSHQHHHQIHHKPSSSTSASSPSIMIKNFNSLYDPSLTSDHTLCSSSLSTTFTTSTSFELEVEPELEPADFAAAFASQRFFFSSPGSSNSLIEYTNTDCIQHSSVPPMDKSNSIEREKKQEKEKEEVLFNGSVAVPTYSPDPYMDFRRSMQEMVEARPELMDVKSNWNILHELLLCYLALNPKNTHKFILGAFADLLVTLMSF