AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35444

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35444.t1 AT5G22250 58.803 284 105 5 1 279 1 277 9.28e-113 327
MS.gene35444.t1 AT3G44260 58.007 281 102 6 4 279 10 279 1.39e-108 316
MS.gene35444.t1 AT2G32070 48.399 281 123 9 4 279 5 268 1.54e-81 247
MS.gene35444.t1 AT1G80780 48.043 281 123 10 4 279 5 267 2.10e-79 241
MS.gene35444.t1 AT1G80780 48.043 281 123 10 4 279 5 267 2.10e-79 241
MS.gene35444.t1 AT1G80780 48.043 281 123 10 4 279 5 267 3.50e-79 241
MS.gene35444.t1 AT5G10960 48.746 279 124 9 4 279 5 267 2.50e-78 239
MS.gene35444.t1 AT1G15920 49.446 271 124 9 13 278 14 276 1.22e-77 237
MS.gene35444.t1 AT1G15920 49.446 271 124 9 13 278 14 276 1.22e-77 237
MS.gene35444.t1 AT1G06450 35.743 249 140 5 16 261 10 241 5.24e-44 153
MS.gene35444.t1 AT1G61470 35.887 248 129 8 17 257 4 228 1.96e-35 129
MS.gene35444.t1 AT1G27820 35.827 254 135 9 11 257 2 234 2.63e-34 126
MS.gene35444.t1 AT3G44240 35.470 234 125 9 29 257 3 215 1.37e-33 122
MS.gene35444.t1 AT1G27890 35.887 248 131 9 17 257 3 229 8.19e-32 119

Find 62 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCACAGCTCATATGATTT+TGG 0.097034 2.1:-15375708 MS.gene35444:CDS
TGAAATTAAATTCCCAAATA+TGG 0.172871 2.1:+15375904 None:intergenic
ATGATGCATACAGCCATATT+TGG 0.218260 2.1:-15375917 MS.gene35444:CDS
GAAAATCTTGAGCAGGAATT+TGG 0.225924 2.1:-15376158 MS.gene35444:CDS
AAATTATTCATGCTGAGTTC+TGG 0.286954 2.1:-15375765 MS.gene35444:CDS
TCTTCAACAGTGGAGTTTCT+TGG 0.301458 2.1:-15375737 MS.gene35444:CDS
TTTAAACGTAATCTGATTTA+CGG 0.321741 2.1:-15375810 MS.gene35444:CDS
ATCAAATTCTGCAACTTATA+CGG 0.326856 2.1:-15375576 MS.gene35444:CDS
CGGAGGTGATACGGTATCTT+TGG 0.335479 2.1:+15376050 None:intergenic
CACACCTGACGAATCTTAAT+AGG 0.363291 2.1:+15376185 None:intergenic
TAGCTTAGAAGTGACAGTTT+AGG 0.368361 2.1:-15375394 None:intergenic
CCGGCTGACCTTGAGTTTAG+TGG 0.388578 2.1:+15375536 None:intergenic
CTTCAACAGTGGAGTTTCTT+GGG 0.397678 2.1:-15375736 MS.gene35444:CDS
TCAATTGACACTGAGTTTCC+CGG 0.399581 2.1:-15376098 MS.gene35444:CDS
TAAAGCATCCTCCTTCAGTT+TGG 0.408551 2.1:+15376214 None:intergenic
CGGTATCTTTGGATCAAAGT+TGG 0.440319 2.1:+15376061 None:intergenic
TGATGCATACAGCCATATTT+GGG 0.441326 2.1:-15375916 MS.gene35444:CDS
CTGCAACTTATACGGTGGTC+TGG 0.445810 2.1:-15375568 MS.gene35444:CDS
CGTAGCAAATCGATAGAGTC+TGG 0.460930 2.1:+15375849 None:intergenic
ACCGTATCACCTCCGCCATA+TGG 0.464161 2.1:-15376042 MS.gene35444:CDS
GGTATCTTTGGATCAAAGTT+GGG 0.485052 2.1:+15376062 None:intergenic
TTACTTACCGTCTCGATTGG+AGG 0.501224 2.1:-15375658 MS.gene35444:CDS
GAATTACTTACCGTCTCGAT+TGG 0.501806 2.1:-15375661 MS.gene35444:CDS
GGAACAGTACAGTTTCTTGA+AGG 0.502233 2.1:-15376012 MS.gene35444:CDS
TCCATATGGCGGAGGTGATA+CGG 0.503585 2.1:+15376041 None:intergenic
CCACTAAACTCAAGGTCAGC+CGG 0.505537 2.1:-15375536 MS.gene35444:CDS
TAAACCTATTAAGATTCGTC+AGG 0.509471 2.1:-15376189 MS.gene35444:CDS
CACTAAACTCAAGGTCAGCC+GGG 0.523942 2.1:-15375535 MS.gene35444:CDS
GATGCGAGTTTCCGACCGCC+CGG 0.526672 2.1:+15375517 None:intergenic
GTGGAATCACGACGCACGCA+GGG 0.530027 2.1:-15375425 MS.gene35444:CDS
ATCGATTTGCTACGTCGTCA+AGG 0.532230 2.1:-15375840 MS.gene35444:CDS
CTCAAGGTCAGCCGGGCGGT+CGG 0.542861 2.1:-15375528 MS.gene35444:CDS
CAGTTTCTTGAAGGCTAACG+TGG 0.548252 2.1:-15376003 MS.gene35444:CDS
GTGGGCTGAAAATCTTGAGC+AGG 0.549309 2.1:-15376165 MS.gene35444:CDS
TTGGGAGCAACGACGACACC+GGG 0.553441 2.1:+15376080 None:intergenic
TGGCTGTATGCATCATCTCC+AGG 0.554456 2.1:+15375924 None:intergenic
CGTCTGATAGTTTGTTGACA+TGG 0.556250 2.1:-15375488 MS.gene35444:CDS
AAGAAACTGTACTGTTCCGA+TGG 0.557618 2.1:+15376017 None:intergenic
CCTCCGCCATATGGATCCAT+CGG 0.570889 2.1:-15376033 MS.gene35444:CDS
TTCCATCATGACCAAACTGA+AGG 0.577229 2.1:-15376225 None:intergenic
CTATTAAGATTCGTCAGGTG+TGG 0.577747 2.1:-15376184 MS.gene35444:CDS
GATGCAGATGGTAACCTACC+TGG 0.578547 2.1:-15375942 MS.gene35444:CDS
ACTGTTCCGATGGATCCATA+TGG 0.582137 2.1:+15376027 None:intergenic
GTTGGGAGCAACGACGACAC+CGG 0.582313 2.1:+15376079 None:intergenic
CAGGAATTTGGTCTTATCAG+AGG 0.582964 2.1:-15376146 MS.gene35444:CDS
CTCAGTGTCAATTGAAACGT+AGG 0.588650 2.1:+15376106 None:intergenic
TATTAAGATTCGTCAGGTGT+GGG 0.593844 2.1:-15376183 MS.gene35444:CDS
CATCATGACCAAACTGAAGG+AGG 0.606578 2.1:-15376222 None:intergenic
ACGTGTTGCCACTAAACTCA+AGG 0.613697 2.1:-15375544 MS.gene35444:CDS
CCGATGGATCCATATGGCGG+AGG 0.627796 2.1:+15376033 None:intergenic
AGTGGAATCACGACGCACGC+AGG 0.630622 2.1:-15375426 MS.gene35444:CDS
AAATTCTGCAACTTATACGG+TGG 0.630970 2.1:-15375573 MS.gene35444:CDS
TCTGGACTAGTCTTCAACAG+TGG 0.633561 2.1:-15375747 MS.gene35444:CDS
CTTACTCTGACTGATGCAGA+TGG 0.647611 2.1:-15375954 MS.gene35444:CDS
TCAGTGTCAATTGAAACGTA+GGG 0.648759 2.1:+15376107 None:intergenic
AATCTCAAGTTGATTCAACT+AGG 0.649799 2.1:-15375978 MS.gene35444:CDS
TGTATGCATCATCTCCAGGT+AGG 0.654004 2.1:+15375928 None:intergenic
AAGAAATCCTCCAATCGAGA+CGG 0.657540 2.1:+15375651 None:intergenic
TTGAAACGTAGGGAAACATG+TGG 0.672478 2.1:+15376117 None:intergenic
GTTCCGATGGATCCATATGG+CGG 0.683790 2.1:+15376030 None:intergenic
TGGAATCACGACGCACGCAG+GGG 0.699241 2.1:-15375424 MS.gene35444:CDS
TAAACTCAAGGTCAGCCGGG+CGG 0.755265 2.1:-15375532 MS.gene35444:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAATTAAATTCCCAAATA+TGG + chr2.1:15375712-15375731 None:intergenic 20.0%
!! TTTAAACGTAATCTGATTTA+CGG - chr2.1:15375803-15375822 MS.gene35444:CDS 20.0%
!!! TAATTTCAAAGATTTTGATG+TGG - chr2.1:15375724-15375743 MS.gene35444:CDS 20.0%
! ATCAAATTCTGCAACTTATA+CGG - chr2.1:15376037-15376056 MS.gene35444:CDS 25.0%
!! TTTTAACACGAATATTTGGA+CGG - chr2.1:15375990-15376009 MS.gene35444:CDS 25.0%
!!! AGCATTTTAACACGAATATT+TGG - chr2.1:15375986-15376005 MS.gene35444:CDS 25.0%
AAATTATTCATGCTGAGTTC+TGG - chr2.1:15375848-15375867 MS.gene35444:CDS 30.0%
TAAACCTATTAAGATTCGTC+AGG - chr2.1:15375424-15375443 MS.gene35444:CDS 30.0%
! TTCACAGCTCATATGATTTT+GGG - chr2.1:15375906-15375925 MS.gene35444:CDS 30.0%
! TTTCACAGCTCATATGATTT+TGG - chr2.1:15375905-15375924 MS.gene35444:CDS 30.0%
!! AATCTCAAGTTGATTCAACT+AGG - chr2.1:15375635-15375654 MS.gene35444:CDS 30.0%
!! ATGATTTTGGGTATCTAGTT+AGG - chr2.1:15375918-15375937 MS.gene35444:CDS 30.0%
!!! ATCTAGTTAGGATTTTGACT+CGG - chr2.1:15375930-15375949 MS.gene35444:CDS 30.0%
!!! GACATTTATTTTGTCAACAG+TGG - chr2.1:15376169-15376188 MS.gene35444:CDS 30.0%
AAATTCTGCAACTTATACGG+TGG - chr2.1:15376040-15376059 MS.gene35444:CDS 35.0%
ATGATGCATACAGCCATATT+TGG - chr2.1:15375696-15375715 MS.gene35444:CDS 35.0%
GAAAATCTTGAGCAGGAATT+TGG - chr2.1:15375455-15375474 MS.gene35444:CDS 35.0%
GGTATCTTTGGATCAAAGTT+GGG + chr2.1:15375554-15375573 None:intergenic 35.0%
TATTAAGATTCGTCAGGTGT+GGG - chr2.1:15375430-15375449 MS.gene35444:CDS 35.0%
TCAGTGTCAATTGAAACGTA+GGG + chr2.1:15375509-15375528 None:intergenic 35.0%
TGATGCATACAGCCATATTT+GGG - chr2.1:15375697-15375716 MS.gene35444:CDS 35.0%
!! GCAAGCTTTTAAGAAGATGA+AGG - chr2.1:15376147-15376166 MS.gene35444:CDS 35.0%
AAGAAACTGTACTGTTCCGA+TGG + chr2.1:15375599-15375618 None:intergenic 40.0%
AAGAAATCCTCCAATCGAGA+CGG + chr2.1:15375965-15375984 None:intergenic 40.0%
CACACCTGACGAATCTTAAT+AGG + chr2.1:15375431-15375450 None:intergenic 40.0%
CGGTATCTTTGGATCAAAGT+TGG + chr2.1:15375555-15375574 None:intergenic 40.0%
CTATTAAGATTCGTCAGGTG+TGG - chr2.1:15375429-15375448 MS.gene35444:CDS 40.0%
CTCAGTGTCAATTGAAACGT+AGG + chr2.1:15375510-15375529 None:intergenic 40.0%
CTTCAACAGTGGAGTTTCTT+GGG - chr2.1:15375877-15375896 MS.gene35444:CDS 40.0%
GAATTACTTACCGTCTCGAT+TGG - chr2.1:15375952-15375971 MS.gene35444:CDS 40.0%
GGAACAGTACAGTTTCTTGA+AGG - chr2.1:15375601-15375620 MS.gene35444:CDS 40.0%
TCAATTGACACTGAGTTTCC+CGG - chr2.1:15375515-15375534 MS.gene35444:CDS 40.0%
TCTTCAACAGTGGAGTTTCT+TGG - chr2.1:15375876-15375895 MS.gene35444:CDS 40.0%
TTGAAACGTAGGGAAACATG+TGG + chr2.1:15375499-15375518 None:intergenic 40.0%
! TAAAGCATCCTCCTTCAGTT+TGG + chr2.1:15375402-15375421 None:intergenic 40.0%
!! CAGGAATTTGGTCTTATCAG+AGG - chr2.1:15375467-15375486 MS.gene35444:CDS 40.0%
!! CGTCTGATAGTTTGTTGACA+TGG - chr2.1:15376125-15376144 MS.gene35444:CDS 40.0%
ACGTGTTGCCACTAAACTCA+AGG - chr2.1:15376069-15376088 MS.gene35444:CDS 45.0%
ACTGTTCCGATGGATCCATA+TGG + chr2.1:15375589-15375608 None:intergenic 45.0%
CAGTTTCTTGAAGGCTAACG+TGG - chr2.1:15375610-15375629 MS.gene35444:CDS 45.0%
CGTAGCAAATCGATAGAGTC+TGG + chr2.1:15375767-15375786 None:intergenic 45.0%
CTTACTCTGACTGATGCAGA+TGG - chr2.1:15375659-15375678 MS.gene35444:CDS 45.0%
TGTATGCATCATCTCCAGGT+AGG + chr2.1:15375688-15375707 None:intergenic 45.0%
TTACTTACCGTCTCGATTGG+AGG - chr2.1:15375955-15375974 MS.gene35444:CDS 45.0%
!! ATCGATTTGCTACGTCGTCA+AGG - chr2.1:15375773-15375792 MS.gene35444:CDS 45.0%
!! TCTGGACTAGTCTTCAACAG+TGG - chr2.1:15375866-15375885 MS.gene35444:CDS 45.0%
CACTAAACTCAAGGTCAGCC+GGG - chr2.1:15376078-15376097 MS.gene35444:CDS 50.0%
CCACTAAACTCAAGGTCAGC+CGG - chr2.1:15376077-15376096 MS.gene35444:CDS 50.0%
CGGAGGTGATACGGTATCTT+TGG + chr2.1:15375566-15375585 None:intergenic 50.0%
CTGCAACTTATACGGTGGTC+TGG - chr2.1:15376045-15376064 MS.gene35444:CDS 50.0%
GATGCAGATGGTAACCTACC+TGG - chr2.1:15375671-15375690 MS.gene35444:CDS 50.0%
GTTCCGATGGATCCATATGG+CGG + chr2.1:15375586-15375605 None:intergenic 50.0%
TGGCTGTATGCATCATCTCC+AGG + chr2.1:15375692-15375711 None:intergenic 50.0%
! GTGGGCTGAAAATCTTGAGC+AGG - chr2.1:15375448-15375467 MS.gene35444:CDS 50.0%
! TCCATATGGCGGAGGTGATA+CGG + chr2.1:15375575-15375594 None:intergenic 50.0%
ACCGTATCACCTCCGCCATA+TGG - chr2.1:15375571-15375590 MS.gene35444:CDS 55.0%
CCGGCTGACCTTGAGTTTAG+TGG + chr2.1:15376080-15376099 None:intergenic 55.0%
CCTCCGCCATATGGATCCAT+CGG - chr2.1:15375580-15375599 MS.gene35444:CDS 55.0%
TAAACTCAAGGTCAGCCGGG+CGG - chr2.1:15376081-15376100 MS.gene35444:CDS 55.0%
AGTGGAATCACGACGCACGC+AGG - chr2.1:15376187-15376206 MS.gene35444:CDS 60.0%
CCGATGGATCCATATGGCGG+AGG + chr2.1:15375583-15375602 None:intergenic 60.0%
GTGGAATCACGACGCACGCA+GGG - chr2.1:15376188-15376207 MS.gene35444:CDS 60.0%
GTTGGGAGCAACGACGACAC+CGG + chr2.1:15375537-15375556 None:intergenic 60.0%
TGGAATCACGACGCACGCAG+GGG - chr2.1:15376189-15376208 MS.gene35444:CDS 60.0%
TTGGGAGCAACGACGACACC+GGG + chr2.1:15375536-15375555 None:intergenic 60.0%
GATGCGAGTTTCCGACCGCC+CGG + chr2.1:15376099-15376118 None:intergenic 65.0%
CTCAAGGTCAGCCGGGCGGT+CGG - chr2.1:15376085-15376104 MS.gene35444:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 15375395 15376240 15375395 ID=MS.gene35444
chr2.1 mRNA 15375395 15376240 15375395 ID=MS.gene35444.t1;Parent=MS.gene35444
chr2.1 exon 15375395 15376240 15375395 ID=MS.gene35444.t1.exon1;Parent=MS.gene35444.t1
chr2.1 CDS 15375395 15376240 15375395 ID=cds.MS.gene35444.t1;Parent=MS.gene35444.t1
Gene Sequence

>MS.gene35444

ATGACCAAACTGAAGGAGGATGCTTTAACTAAACCTATTAAGATTCGTCAGGTGTGGGCTGAAAATCTTGAGCAGGAATTTGGTCTTATCAGAGGCATCATCCACATGTTTCCCTACGTTTCAATTGACACTGAGTTTCCCGGTGTCGTCGTTGCTCCCAACTTTGATCCAAAGATACCGTATCACCTCCGCCATATGGATCCATCGGAACAGTACAGTTTCTTGAAGGCTAACGTGGATAATCTCAAGTTGATTCAACTAGGTCTTACTCTGACTGATGCAGATGGTAACCTACCTGGAGATGATGCATACAGCCATATTTGGGAATTTAATTTCAAAGATTTTGATGTGGAGCGTGATCTTCAAAATCCAGACTCTATCGATTTGCTACGTCGTCAAGGCGTCGATTTTAAACGTAATCTGATTTACGGTGTCGACTCTCTAGAATTTGCTAAATTATTCATGCTGAGTTCTGGACTAGTCTTCAACAGTGGAGTTTCTTGGGTTACATTTCACAGCTCATATGATTTTGGGTATCTAGTTAGGATTTTGACTCGGAATTACTTACCGTCTCGATTGGAGGATTTCTTAAGCATTTTAACACGAATATTTGGACGGAATGTCTATGATATGAAGTATATGATCAAATTCTGCAACTTATACGGTGGTCTGGAACGTGTTGCCACTAAACTCAAGGTCAGCCGGGCGGTCGGAAACTCGCATCAAGCTGCGTCTGATAGTTTGTTGACATGGCAAGCTTTTAAGAAGATGAAGGACATTTATTTTGTCAACAGTGGAATCACGACGCACGCAGGGGTGTTATTTAGCTTAGAAGTGACAGTTTAG
Protein sequence

>MS.gene35444.t1

MTKLKEDALTKPIKIRQVWAENLEQEFGLIRGIIHMFPYVSIDTEFPGVVVAPNFDPKIPYHLRHMDPSEQYSFLKANVDNLKLIQLGLTLTDADGNLPGDDAYSHIWEFNFKDFDVERDLQNPDSIDLLRRQGVDFKRNLIYGVDSLEFAKLFMLSSGLVFNSGVSWVTFHSSYDFGYLVRILTRNYLPSRLEDFLSILTRIFGRNVYDMKYMIKFCNLYGGLERVATKLKVSRAVGNSHQAASDSLLTWQAFKKMKDIYFVNSGITTHAGVLFSLEVTV