AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene75829

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75829.t1 MTR_2g049610 84.170 259 20 2 4 262 2 239 7.74e-162 448
MS.gene75829.t1 MTR_2g049630 58.468 248 79 4 1 245 1 227 2.41e-89 269
MS.gene75829.t1 MTR_2g049530 65.517 174 58 1 1 172 1 174 2.77e-76 230
MS.gene75829.t1 MTR_4g107170 45.701 221 105 5 1 214 1 213 1.63e-59 189
MS.gene75829.t1 MTR_4g045977 44.255 235 102 6 4 222 2 223 1.28e-54 181
MS.gene75829.t1 MTR_1g115290 46.584 161 62 4 40 195 2 143 1.49e-36 127
MS.gene75829.t1 MTR_6g018920 38.065 155 89 2 4 152 2 155 4.25e-31 118
MS.gene75829.t1 MTR_1g114730 39.744 156 87 3 4 153 2 156 6.34e-31 117
MS.gene75829.t1 MTR_6g005440 32.673 202 122 6 4 192 2 202 4.41e-29 112
MS.gene75829.t1 MTR_6g005450 38.710 155 88 3 4 152 2 155 1.12e-26 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75829.t1 AT5G55690 29.870 154 91 5 1 147 1 144 9.10e-12 64.3
MS.gene75829.t1 AT5G55690 29.870 154 91 5 1 147 1 144 9.10e-12 64.3

Find 44 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTGATAATGTTGCATATT+TGG 0.139121 2.1:-42597549 MS.gene75829:CDS
GGAATGGGAAACTCAATTTA+TGG 0.183833 2.1:-42597501 MS.gene75829:CDS
TAAAATCCATCTCTTGTTTC+CGG 0.229766 2.1:+42597464 None:intergenic
GTTGGTCTCCTTCCATGTTC+TGG 0.247380 2.1:+42597864 None:intergenic
CTGTACAATCCATTCTTAAA+AGG 0.279177 2.1:-42598036 MS.gene75829:CDS
ATGCAACAAAGTACTGAAAA+TGG 0.300561 2.1:-42597770 MS.gene75829:CDS
CACAATCTCTTTGTGCACTT+TGG 0.338528 2.1:+42597919 None:intergenic
CCTTCCATGTTCTGGAAACA+TGG 0.385090 2.1:+42597872 None:intergenic
TCCTGACCAGGTTTAGCAAC+TGG 0.388453 2.1:+42597521 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 2.1:+42597814 None:intergenic
TCATGGATATGTTGCATTTG+AGG 0.410645 2.1:+42597656 None:intergenic
ACTTGGTGAAGTTGAAGAAT+TGG 0.421405 2.1:-42597600 MS.gene75829:CDS
CTATTAAACACATTCAAGAT+TGG 0.421571 2.1:-42598204 MS.gene75829:CDS
TGCTAAACCTGGTCAGGAAT+GGG 0.447809 2.1:-42597516 MS.gene75829:CDS
TGTGAGGAGACAACATTATT+CGG 0.449930 2.1:+42597710 None:intergenic
ATGTTGTCTCCTCACATTCA+AGG 0.456551 2.1:-42597703 MS.gene75829:CDS
TCCAGTTGCTAAACCTGGTC+AGG 0.458685 2.1:-42597522 MS.gene75829:CDS
TGAGTTTCCCATTCCTGACC+AGG 0.483105 2.1:+42597509 None:intergenic
TGGAAACATGGGTGCCAAGT+TGG 0.485421 2.1:+42597884 None:intergenic
GCACCCATGTTTCCAGAACA+TGG 0.507852 2.1:-42597876 MS.gene75829:CDS
CAATCAAAGAAGCAATGGAT+TGG 0.512118 2.1:-42598161 MS.gene75829:CDS
TTGCTAAACCTGGTCAGGAA+TGG 0.512431 2.1:-42597517 MS.gene75829:CDS
TATGAGCTTCAAAAGATTGA+GGG 0.525701 2.1:-42598013 MS.gene75829:CDS
GTATGAGCTTCAAAAGATTG+AGG 0.526267 2.1:-42598014 MS.gene75829:CDS
GTGGCTTCAAATGATCATCA+TGG 0.534306 2.1:+42597639 None:intergenic
GCTTGCTTAATTGTGTATGA+TGG 0.534651 2.1:-42598097 MS.gene75829:CDS
GTTTAATAGTTAATTTCCCA+CGG 0.538383 2.1:+42598218 None:intergenic
CTTCCATGTTCTGGAAACAT+GGG 0.549893 2.1:+42597873 None:intergenic
ACATTCAAGATTGGAGAGCT+CGG 0.553672 2.1:-42598195 MS.gene75829:CDS
ACTTTCAATCAAAGAAGCAA+TGG 0.559273 2.1:-42598166 MS.gene75829:CDS
AAGAATGGATTGTACAGCGA+TGG 0.560045 2.1:+42598042 None:intergenic
GTAGAAATGGGTCGTGCCCG+TGG 0.563669 2.1:-42598235 None:intergenic
TTTAATAGTTAATTTCCCAC+GGG 0.586000 2.1:+42598219 None:intergenic
CCATGTTTCCAGAACATGGA+AGG 0.588690 2.1:-42597872 MS.gene75829:CDS
GATGATCCAGTTGCTAAACC+TGG 0.589750 2.1:-42597527 MS.gene75829:CDS
ATCAAGCTTCCTTGAATGTG+AGG 0.590592 2.1:+42597694 None:intergenic
CTTAGTGATACTAATCGACT+TGG 0.592888 2.1:-42597617 MS.gene75829:CDS
GCTTTGCCGGAAACAAGAGA+TGG 0.607866 2.1:-42597470 MS.gene75829:CDS
TTAATTGTGTATGATGGTGA+TGG 0.608708 2.1:-42598091 MS.gene75829:CDS
TAGAAATGGGTCGTGCCCGT+GGG 0.613629 2.1:-42598234 None:intergenic
CACTACTCAGACGCAAAATG+TGG 0.617631 2.1:-42597735 MS.gene75829:CDS
TGATGAAAATGTATCCAACT+TGG 0.619935 2.1:-42597898 MS.gene75829:CDS
AGTCGATTAGTATCACTAAG+TGG 0.621773 2.1:+42597620 None:intergenic
GTGATGGTAGACTATTGACT+TGG 0.689603 2.1:-42598075 MS.gene75829:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTATTAAACACATTCAAGAT+TGG - chr2.1:42597488-42597507 MS.gene75829:CDS 25.0%
! GTTTAATAGTTAATTTCCCA+CGG + chr2.1:42597477-42597496 None:intergenic 25.0%
! TTTAATAGTTAATTTCCCAC+GGG + chr2.1:42597476-42597495 None:intergenic 25.0%
!! AATTGGATGATTTTATGGAT+TGG - chr2.1:42598109-42598128 MS.gene75829:CDS 25.0%
!! ATTGGATGATTTTATGGATT+GGG - chr2.1:42598110-42598129 MS.gene75829:CDS 25.0%
!! TGAAGAATTGGATGATTTTA+TGG - chr2.1:42598104-42598123 MS.gene75829:CDS 25.0%
!!! ACTTGATAATGTTGCATATT+TGG - chr2.1:42598143-42598162 MS.gene75829:CDS 25.0%
ACTTTCAATCAAAGAAGCAA+TGG - chr2.1:42597526-42597545 MS.gene75829:CDS 30.0%
CTGTACAATCCATTCTTAAA+AGG - chr2.1:42597656-42597675 MS.gene75829:CDS 30.0%
TATGAGCTTCAAAAGATTGA+GGG - chr2.1:42597679-42597698 MS.gene75829:CDS 30.0%
TGATGAAAATGTATCCAACT+TGG - chr2.1:42597794-42597813 MS.gene75829:CDS 30.0%
! TAAAATCCATCTCTTGTTTC+CGG + chr2.1:42598231-42598250 None:intergenic 30.0%
! TTAATTGTGTATGATGGTGA+TGG - chr2.1:42597601-42597620 MS.gene75829:CDS 30.0%
!! AAGCTCATACCTTTTAAGAA+TGG + chr2.1:42597668-42597687 None:intergenic 30.0%
!! ATGCAACAAAGTACTGAAAA+TGG - chr2.1:42597922-42597941 MS.gene75829:CDS 30.0%
!! TCTGAATTTTCTAGCAAGTT+TGG - chr2.1:42597565-42597584 MS.gene75829:CDS 30.0%
!!! TCGCAATAAAAGTTTTGAGT+TGG + chr2.1:42597849-42597868 None:intergenic 30.0%
AGTCGATTAGTATCACTAAG+TGG + chr2.1:42598075-42598094 None:intergenic 35.0%
CAATCAAAGAAGCAATGGAT+TGG - chr2.1:42597531-42597550 MS.gene75829:CDS 35.0%
CTTAGTGATACTAATCGACT+TGG - chr2.1:42598075-42598094 MS.gene75829:CDS 35.0%
GCTTGCTTAATTGTGTATGA+TGG - chr2.1:42597595-42597614 MS.gene75829:CDS 35.0%
GGAATGGGAAACTCAATTTA+TGG - chr2.1:42598191-42598210 MS.gene75829:CDS 35.0%
GTATGAGCTTCAAAAGATTG+AGG - chr2.1:42597678-42597697 MS.gene75829:CDS 35.0%
GTGATTACAAGCTTGAATCT+TGG + chr2.1:42597881-42597900 None:intergenic 35.0%
TCATGGATATGTTGCATTTG+AGG + chr2.1:42598039-42598058 None:intergenic 35.0%
TGTGAGGAGACAACATTATT+CGG + chr2.1:42597985-42598004 None:intergenic 35.0%
! ACTTGGTGAAGTTGAAGAAT+TGG - chr2.1:42598092-42598111 MS.gene75829:CDS 35.0%
!! TATGGATTTTGATGCTTTGC+CGG - chr2.1:42598209-42598228 MS.gene75829:CDS 35.0%
ACATTCAAGATTGGAGAGCT+CGG - chr2.1:42597497-42597516 MS.gene75829:CDS 40.0%
ATCAAGCTTCCTTGAATGTG+AGG + chr2.1:42598001-42598020 None:intergenic 40.0%
ATGTTGTCTCCTCACATTCA+AGG - chr2.1:42597989-42598008 MS.gene75829:CDS 40.0%
CACAATCTCTTTGTGCACTT+TGG + chr2.1:42597776-42597795 None:intergenic 40.0%
GTGGCTTCAAATGATCATCA+TGG + chr2.1:42598056-42598075 None:intergenic 40.0%
! GTGATGGTAGACTATTGACT+TGG - chr2.1:42597617-42597636 MS.gene75829:CDS 40.0%
!! AAGAATGGATTGTACAGCGA+TGG + chr2.1:42597653-42597672 None:intergenic 40.0%
!! CTTCCATGTTCTGGAAACAT+GGG + chr2.1:42597822-42597841 None:intergenic 40.0%
CACTACTCAGACGCAAAATG+TGG - chr2.1:42597957-42597976 MS.gene75829:CDS 45.0%
CCATGTTTCCAGAACATGGA+AGG - chr2.1:42597820-42597839 MS.gene75829:CDS 45.0%
GATGATCCAGTTGCTAAACC+TGG - chr2.1:42598165-42598184 MS.gene75829:CDS 45.0%
TGCTAAACCTGGTCAGGAAT+GGG - chr2.1:42598176-42598195 MS.gene75829:CDS 45.0%
TTGCTAAACCTGGTCAGGAA+TGG - chr2.1:42598175-42598194 MS.gene75829:CDS 45.0%
! TGTACAGCGATGGAGTTTTG+TGG + chr2.1:42597643-42597662 None:intergenic 45.0%
!! CCTTCCATGTTCTGGAAACA+TGG + chr2.1:42597823-42597842 None:intergenic 45.0%
GCACCCATGTTTCCAGAACA+TGG - chr2.1:42597816-42597835 MS.gene75829:CDS 50.0%
GCTTTGCCGGAAACAAGAGA+TGG - chr2.1:42598222-42598241 MS.gene75829:CDS 50.0%
TCCAGTTGCTAAACCTGGTC+AGG - chr2.1:42598170-42598189 MS.gene75829:CDS 50.0%
TCCTGACCAGGTTTAGCAAC+TGG + chr2.1:42598174-42598193 None:intergenic 50.0%
TGAGTTTCCCATTCCTGACC+AGG + chr2.1:42598186-42598205 None:intergenic 50.0%
TGGAAACATGGGTGCCAAGT+TGG + chr2.1:42597811-42597830 None:intergenic 50.0%
! GTTGGTCTCCTTCCATGTTC+TGG + chr2.1:42597831-42597850 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 42597463 42598251 42597463 ID=MS.gene75829
chr2.1 mRNA 42597463 42598251 42597463 ID=MS.gene75829.t1;Parent=MS.gene75829
chr2.1 exon 42597463 42598251 42597463 ID=MS.gene75829.t1.exon1;Parent=MS.gene75829.t1
chr2.1 CDS 42597463 42598251 42597463 ID=cds.MS.gene75829.t1;Parent=MS.gene75829.t1
Gene Sequence

>MS.gene75829

ATGGGTCGTGCCCGTGGGAAATTAACTATTAAACACATTCAAGATTGGAGAGCTCGGAAATCAACTTTCAATCAAAGAAGCAATGGATTGGCAAAAAAAGTTTCTGAATTTTCTAGCAAGTTTGGAGTTGAAGCTTGCTTAATTGTGTATGATGGTGATGGTAGACTATTGACTTGGCCACAAAACTCCATCGCTGTACAATCCATTCTTAAAAGGTATGAGCTTCAAAAGATTGAGGGTACAACTACAAAGATCTTTGATGTGAAAGACTATTTTGCAAATAAGAAGAATAAGATTGAAGCTGATATTTCCAAAGTGCACAAAGAGATTGTGATGAAAATGTATCCAACTTGGCACCCATGTTTCCAGAACATGGAAGGAGACCAACTCAAAACTTTTATTGCGATTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATTAACATGCTAAAGAAAATGCAACAAAGTACTGAAAATGGTTTCATGCTAAACACTACTCAGACGCAAAATGTGGCTCCGAATAATGTTGTCTCCTCACATTCAAGGAAGCTTGATGTCACTGATAGATTTCCTCAAATGCAACATATCCATGATGATCATTTGAAGCCACTTAGTGATACTAATCGACTTGGTGAAGTTGAAGAATTGGATGATTTTATGGATTGGGCTAATCAAGTACTTGATAATGTTGCATATTTGGATGATCCAGTTGCTAAACCTGGTCAGGAATGGGAAACTCAATTTATGGATTTTGATGCTTTGCCGGAAACAAGAGATGGATTTTAA
Protein sequence

>MS.gene75829.t1

MGRARGKLTIKHIQDWRARKSTFNQRSNGLAKKVSEFSSKFGVEACLIVYDGDGRLLTWPQNSIAVQSILKRYELQKIEGTTTKIFDVKDYFANKKNKIEADISKVHKEIVMKMYPTWHPCFQNMEGDQLKTFIAIVDAKIQACNHKINMLKKMQQSTENGFMLNTTQTQNVAPNNVVSSHSRKLDVTDRFPQMQHIHDDHLKPLSDTNRLGEVEELDDFMDWANQVLDNVAYLDDPVAKPGQEWETQFMDFDALPETRDGF