AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43233

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43233.t1 MTR_4g107170 78.498 293 25 2 1 293 1 255 4.15e-164 456
MS.gene43233.t1 MTR_4g045977 47.507 341 115 6 1 293 1 325 8.73e-94 283
MS.gene43233.t1 MTR_2g049610 58.333 156 62 1 1 156 1 153 3.55e-59 189
MS.gene43233.t1 MTR_2g049630 47.449 196 96 5 1 191 1 194 1.43e-51 173
MS.gene43233.t1 MTR_2g049530 50.000 162 78 3 3 162 5 165 6.06e-47 156
MS.gene43233.t1 MTR_1g115290 61.538 117 43 1 38 152 2 118 5.86e-44 147
MS.gene43233.t1 MTR_1g114730 42.581 155 86 1 1 152 1 155 6.86e-36 132
MS.gene43233.t1 MTR_6g018920 38.710 155 92 1 1 152 1 155 7.01e-36 132
MS.gene43233.t1 MTR_6g005440 39.744 156 91 1 1 153 1 156 1.06e-34 128
MS.gene43233.t1 MTR_6g005450 37.419 155 94 1 1 152 1 155 7.93e-30 115
MS.gene43233.t1 MTR_3g466980 32.353 136 86 4 1 135 1 131 5.45e-15 72.8
MS.gene43233.t1 MTR_2g016210 26.452 155 103 3 2 148 3 154 3.32e-13 68.2
MS.gene43233.t1 MTR_3g031240 31.776 107 71 1 1 107 1 105 2.63e-12 64.7
MS.gene43233.t1 MTR_5g075380 32.075 106 68 3 1 105 1 103 2.25e-11 61.6
MS.gene43233.t1 MTR_4g063790 26.115 157 104 4 1 148 1 154 6.88e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43233.t1 AT5G55690 28.402 169 110 2 1 165 1 162 6.94e-16 76.3
MS.gene43233.t1 AT5G55690 28.402 169 110 2 1 165 1 162 6.94e-16 76.3
MS.gene43233.t1 AT1G22590 35.849 106 64 3 1 105 1 103 7.67e-11 60.1

Find 51 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACACTTGTAAGGTCTTC+TGG 0.270047 8.4:+19704088 None:intergenic
TCCTGAGATATTTGATGTTA+AGG 0.348371 8.4:-19704023 MS.gene43233:CDS
GCACTTTGGATGTATTTCAT+AGG 0.357011 8.4:+19704250 None:intergenic
GTCAACCTGATGAGTTTGTT+TGG 0.385592 8.4:-19703427 MS.gene43233:CDS
AGCCCACTAAGTTGGTTTGA+TGG 0.416723 8.4:+19703728 None:intergenic
ACCATCTCACTTGTATAATC+AGG 0.418843 8.4:+19703677 None:intergenic
GATCAACAAGTTGACTAAGT+TGG 0.431119 8.4:+19703498 None:intergenic
ACAATCTCACTCATATAATC+AGG 0.433010 8.4:+19703566 None:intergenic
GCAAGGAGTTTACACTTGTA+AGG 0.440354 8.4:+19704080 None:intergenic
AGTTGGTTTGATGGTGAACT+AGG 0.459766 8.4:+19703737 None:intergenic
AGTTGGTTTGTTGATGAACT+TGG 0.473151 8.4:+19703515 None:intergenic
CTAAAATGTGGATGCCAAGT+TGG 0.479466 8.4:+19703923 None:intergenic
TATTTCCAAACAAACTCATC+AGG 0.484604 8.4:+19703422 None:intergenic
TAAAATGTGGATGCCAAGTT+GGG 0.491000 8.4:+19703924 None:intergenic
GCTTGCTTTATTGTGTATGA+TGG 0.491871 8.4:-19704142 MS.gene43233:CDS
TATAATCAGGATTAGCAACT+TGG 0.493452 8.4:+19703579 None:intergenic
TCATCATCAAACCAACTTAG+TGG 0.501564 8.4:-19703620 MS.gene43233:CDS
TCCTTAACATCAAATATCTC+AGG 0.501707 8.4:+19704022 None:intergenic
TCTCCACAAGCCCACTAAGT+TGG 0.502348 8.4:+19703720 None:intergenic
CTTTGAAAATAAGATAGAAA+AGG 0.507369 8.4:-19703996 MS.gene43233:CDS
TCTCCACAAGCCCACTAAGT+TGG 0.508925 8.4:+19703609 None:intergenic
TTGTAAGAAGTCTGGAGCAA+AGG 0.512867 8.4:-19704164 MS.gene43233:CDS
AACTTGTTGATCTCGATGAC+TGG 0.514836 8.4:-19703487 MS.gene43233:CDS
TCACCATCAAACCAACTTAG+TGG 0.519319 8.4:-19703731 MS.gene43233:CDS
ATTGTGGATTTCAATAGTCT+TGG 0.530083 8.4:-19703548 MS.gene43233:CDS
AGTTGGTTTGATGATGAACT+AGG 0.530891 8.4:+19703626 None:intergenic
AAACCAACTTAGTGGGCTTG+TGG 0.552156 8.4:-19703612 MS.gene43233:CDS
AAACCAACTTAGTGGGCTTG+TGG 0.552156 8.4:-19703723 MS.gene43233:CDS
CATCATCAAACCAACTTAGT+GGG 0.554520 8.4:-19703619 MS.gene43233:CDS
AGGTCTTCTGGCCATGTCGT+AGG 0.557005 8.4:+19704100 None:intergenic
TGATTATATGAGTGAGATTG+TGG 0.565961 8.4:-19703564 MS.gene43233:CDS
TCATCCAAGTTACTAAAATG+TGG 0.567439 8.4:+19703911 None:intergenic
ATGGTGGATTTCACAAGTCT+TGG 0.570027 8.4:-19703659 MS.gene43233:CDS
ACTTTCAAACAAAGAAAGCA+TGG 0.571291 8.4:-19704211 MS.gene43233:CDS
TCAGTAAGATCTACCCAACT+TGG 0.575658 8.4:-19703937 MS.gene43233:CDS
TATAATCAGGATCAACAACT+TGG 0.576059 8.4:+19703690 None:intergenic
CACCATCAAACCAACTTAGT+GGG 0.576425 8.4:-19703730 MS.gene43233:CDS
AGTGGGCTTGTGGAGAGGAA+TGG 0.577682 8.4:-19703713 MS.gene43233:CDS
ATTCTGATACTCTTGAAGCA+AGG 0.580425 8.4:+19704063 None:intergenic
AACTTAGTGGGCTTGTGGAG+AGG 0.584533 8.4:-19703718 MS.gene43233:CDS
TGGTTTGTTGATGAACTTGG+AGG 0.590987 8.4:+19703518 None:intergenic
TGATTATACAAGTGAGATGG+TGG 0.591946 8.4:-19703675 MS.gene43233:CDS
ACAAATAGAAACTAGCACCT+TGG 0.593239 8.4:-19703804 MS.gene43233:CDS
TGGTTTGATGGTGAACTAGG+AGG 0.598871 8.4:+19703740 None:intergenic
AATCATCTCACATATATCCA+AGG 0.609547 8.4:+19703787 None:intergenic
TGGATAAATCAACTAGATGA+TGG 0.621105 8.4:-19703467 MS.gene43233:CDS
AAACAAAGATTAAGAAAGTG+CGG 0.626571 8.4:-19703970 MS.gene43233:CDS
TGGTTTGATGATGAACTAGG+AGG 0.662339 8.4:+19703629 None:intergenic
TCCTGATTATACAAGTGAGA+TGG 0.678910 8.4:-19703678 MS.gene43233:CDS
ATAATATTGAACCTACGACA+TGG 0.717032 8.4:-19704111 MS.gene43233:CDS
AAGTTGGGTAGATCTTACTG+AGG 0.750378 8.4:+19703939 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAAATAAGATAGAAA+AGG - chr8.4:19703681-19703700 MS.gene43233:CDS 20.0%
! AAACAAAGATTAAGAAAGTG+CGG - chr8.4:19703707-19703726 MS.gene43233:CDS 25.0%
!!! ATGATTGATTTTTCTGATCT+TGG - chr8.4:19703907-19703926 MS.gene43233:CDS 25.0%
AATCATCTCACATATATCCA+AGG + chr8.4:19703893-19703912 None:intergenic 30.0%
ACAATCTCACTCATATAATC+AGG + chr8.4:19704114-19704133 None:intergenic 30.0%
ACTTTCAAACAAAGAAAGCA+TGG - chr8.4:19703466-19703485 MS.gene43233:CDS 30.0%
ATAATATTGAACCTACGACA+TGG - chr8.4:19703566-19703585 MS.gene43233:CDS 30.0%
ATTGTGGATTTCAATAGTCT+TGG - chr8.4:19704129-19704148 MS.gene43233:CDS 30.0%
TATAATCAGGATCAACAACT+TGG + chr8.4:19703990-19704009 None:intergenic 30.0%
TATTTCCAAACAAACTCATC+AGG + chr8.4:19704258-19704277 None:intergenic 30.0%
TCATCCAAGTTACTAAAATG+TGG + chr8.4:19703769-19703788 None:intergenic 30.0%
TCCTGAGATATTTGATGTTA+AGG - chr8.4:19703654-19703673 MS.gene43233:CDS 30.0%
TCCTTAACATCAAATATCTC+AGG + chr8.4:19703658-19703677 None:intergenic 30.0%
TGATTATATGAGTGAGATTG+TGG - chr8.4:19704113-19704132 MS.gene43233:CDS 30.0%
TGGATAAATCAACTAGATGA+TGG - chr8.4:19704210-19704229 MS.gene43233:CDS 30.0%
! TATAATCAGGATTAGCAACT+TGG + chr8.4:19704101-19704120 None:intergenic 30.0%
! TCTGAATTTTGTAAGAAGTC+TGG - chr8.4:19703505-19703524 MS.gene43233:CDS 30.0%
!! AGATGATGGTGTTTTGTATT+GGG - chr8.4:19704224-19704243 MS.gene43233:CDS 30.0%
!! TAGATGATGGTGTTTTGTAT+TGG - chr8.4:19704223-19704242 MS.gene43233:CDS 30.0%
ACAAATAGAAACTAGCACCT+TGG - chr8.4:19703873-19703892 MS.gene43233:CDS 35.0%
ACCATCTCACTTGTATAATC+AGG + chr8.4:19704003-19704022 None:intergenic 35.0%
ATTCTGATACTCTTGAAGCA+AGG + chr8.4:19703617-19703636 None:intergenic 35.0%
CATCATCAAACCAACTTAGT+GGG - chr8.4:19704058-19704077 MS.gene43233:CDS 35.0%
GCACTTTGGATGTATTTCAT+AGG + chr8.4:19703430-19703449 None:intergenic 35.0%
TAAAATGTGGATGCCAAGTT+GGG + chr8.4:19703756-19703775 None:intergenic 35.0%
TCATCATCAAACCAACTTAG+TGG - chr8.4:19704057-19704076 MS.gene43233:CDS 35.0%
TCCTGATTATACAAGTGAGA+TGG - chr8.4:19703999-19704018 MS.gene43233:CDS 35.0%
TGATTATACAAGTGAGATGG+TGG - chr8.4:19704002-19704021 MS.gene43233:CDS 35.0%
TTTACACTTGTAAGGTCTTC+TGG + chr8.4:19703592-19703611 None:intergenic 35.0%
! GATCAACAAGTTGACTAAGT+TGG + chr8.4:19704182-19704201 None:intergenic 35.0%
! GCTTGCTTTATTGTGTATGA+TGG - chr8.4:19703535-19703554 MS.gene43233:CDS 35.0%
!! AGTTGGTTTGATGATGAACT+AGG + chr8.4:19704054-19704073 None:intergenic 35.0%
!! AGTTGGTTTGTTGATGAACT+TGG + chr8.4:19704165-19704184 None:intergenic 35.0%
!! GCATCCACATTTTAGTAACT+TGG - chr8.4:19703762-19703781 MS.gene43233:CDS 35.0%
AAGTTGGGTAGATCTTACTG+AGG + chr8.4:19703741-19703760 None:intergenic 40.0%
CACCATCAAACCAACTTAGT+GGG - chr8.4:19703947-19703966 MS.gene43233:CDS 40.0%
CTAAAATGTGGATGCCAAGT+TGG + chr8.4:19703757-19703776 None:intergenic 40.0%
GCAAGGAGTTTACACTTGTA+AGG + chr8.4:19703600-19703619 None:intergenic 40.0%
TCACCATCAAACCAACTTAG+TGG - chr8.4:19703946-19703965 MS.gene43233:CDS 40.0%
TCAGTAAGATCTACCCAACT+TGG - chr8.4:19703740-19703759 MS.gene43233:CDS 40.0%
! GTCAACCTGATGAGTTTGTT+TGG - chr8.4:19704250-19704269 MS.gene43233:CDS 40.0%
! TTGTAAGAAGTCTGGAGCAA+AGG - chr8.4:19703513-19703532 MS.gene43233:CDS 40.0%
! TTTTGCGAGATTTCGCACTT+TGG + chr8.4:19703444-19703463 None:intergenic 40.0%
!! AACTTGTTGATCTCGATGAC+TGG - chr8.4:19704190-19704209 MS.gene43233:CDS 40.0%
!! AGTTGGTTTGATGGTGAACT+AGG + chr8.4:19703943-19703962 None:intergenic 40.0%
!! ATGGTGGATTTCACAAGTCT+TGG - chr8.4:19704018-19704037 MS.gene43233:CDS 40.0%
!! TGGTTTGATGATGAACTAGG+AGG + chr8.4:19704051-19704070 None:intergenic 40.0%
!! TGGTTTGTTGATGAACTTGG+AGG + chr8.4:19704162-19704181 None:intergenic 40.0%
!! AAACCAACTTAGTGGGCTTG+TGG - chr8.4:19703954-19703973 MS.gene43233:CDS 45.0%
!! AGCCCACTAAGTTGGTTTGA+TGG + chr8.4:19703952-19703971 None:intergenic 45.0%
!! TGGTTTGATGGTGAACTAGG+AGG + chr8.4:19703940-19703959 None:intergenic 45.0%
TCTCCACAAGCCCACTAAGT+TGG + chr8.4:19703960-19703979 None:intergenic 50.0%
!! AACTTAGTGGGCTTGTGGAG+AGG - chr8.4:19703959-19703978 MS.gene43233:CDS 50.0%
AGGTCTTCTGGCCATGTCGT+AGG + chr8.4:19703580-19703599 None:intergenic 55.0%
! AGTGGGCTTGTGGAGAGGAA+TGG - chr8.4:19703964-19703983 MS.gene43233:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 19703409 19704290 19703409 ID=MS.gene43233
chr8.4 mRNA 19703409 19704290 19703409 ID=MS.gene43233.t1;Parent=MS.gene43233
chr8.4 exon 19703409 19704290 19703409 ID=MS.gene43233.t1.exon1;Parent=MS.gene43233.t1
chr8.4 CDS 19703409 19704290 19703409 ID=cds.MS.gene43233.t1;Parent=MS.gene43233.t1
Gene Sequence

>MS.gene43233

ATGGGTCGCGCAAAAATACCTATGAAATACATCCAAAGTGCGAAATCTCGCAAAATAACTTTCAAACAAAGAAAGCATGGATTAGAAAAGAAAATTTCTGAATTTTGTAAGAAGTCTGGAGCAAAGGCTTGCTTTATTGTGTATGATGGTGATCATAATAATATTGAACCTACGACATGGCCAGAAGACCTTACAAGTGTAAACTCCTTGCTTCAAGAGTATCAGAATCAAAAGATTGAGAAAACTCCTGAGATATTTGATGTTAAGGACTACTTTGAAAATAAGATAGAAAAGGTTGAAACAAAGATTAAGAAAGTGCGGAGAGATATCCTCAGTAAGATCTACCCAACTTGGCATCCACATTTTAGTAACTTGGATGAGAATCAACTCAGAGACTTCATTGCTACAATAAATGCTAAGATTCAAGCTTGCAATCACAAAATTAGCATGTTGAAAAATATGCAACAAATAGAAACTAGCACCTTGGATATATGTGAGATGATTGATTTTTCTGATCTTGGTGATTTTCCTCCTAGTTCACCATCAAACCAACTTAGTGGGCTTGTGGAGAGGAATGGCCAAGTTGTTGATCCTGATTATACAAGTGAGATGGTGGATTTCACAAGTCTTGGTGATTTGCCTCCTAGTTCATCATCAAACCAACTTAGTGGGCTTGTGGAGATGAGTGACCAAGTTGCTAATCCTGATTATATGAGTGAGATTGTGGATTTCAATAGTCTTGGTGATTTGCCTCCAAGTTCATCAACAAACCAACTTAGTCAACTTGTTGATCTCGATGACTGGATAAATCAACTAGATGATGGTGTTTTGTATTGGGATTGTCAACCTGATGAGTTTGTTTGGAAATATCTTGCTTTTTAA
Protein sequence

>MS.gene43233.t1

MGRAKIPMKYIQSAKSRKITFKQRKHGLEKKISEFCKKSGAKACFIVYDGDHNNIEPTTWPEDLTSVNSLLQEYQNQKIEKTPEIFDVKDYFENKIEKVETKIKKVRRDILSKIYPTWHPHFSNLDENQLRDFIATINAKIQACNHKISMLKNMQQIETSTLDICEMIDFSDLGDFPPSSPSNQLSGLVERNGQVVDPDYTSEMVDFTSLGDLPPSSSSNQLSGLVEMSDQVANPDYMSEIVDFNSLGDLPPSSSTNQLSQLVDLDDWINQLDDGVLYWDCQPDEFVWKYLAF