AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83611

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83611.t1 MTR_2g103795 96.154 130 5 0 1 130 146 275 5.42e-90 262
MS.gene83611.t1 MTR_4g010250 69.444 108 33 0 1 108 131 238 9.94e-51 161
MS.gene83611.t1 MTR_2g103795 96.154 78 3 0 1 78 146 223 2.21e-49 157
MS.gene83611.t1 MTR_4g114690 74.444 90 23 0 1 90 169 258 5.66e-43 143
MS.gene83611.t1 MTR_7g098450 52.577 97 46 0 1 97 233 329 5.57e-32 115
MS.gene83611.t1 MTR_7g098450 52.577 97 46 0 1 97 256 352 6.74e-32 116
MS.gene83611.t1 MTR_5g029910 53.261 92 43 0 1 92 129 220 8.80e-31 110
MS.gene83611.t1 MTR_7g099260 49.038 104 50 1 1 101 244 347 1.45e-29 109
MS.gene83611.t1 MTR_1g073230 45.192 104 56 1 1 104 136 238 4.70e-24 95.1
MS.gene83611.t1 MTR_1g073230 46.875 96 51 0 1 96 280 375 3.41e-22 90.1
MS.gene83611.t1 MTR_3g463450 43.023 86 49 0 6 91 411 496 4.95e-18 79.0
MS.gene83611.t1 MTR_5g082130 37.113 97 61 0 2 98 306 402 2.80e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83611.t1 AT5G20190 64.130 92 33 0 1 92 163 254 3.92e-39 133
MS.gene83611.t1 AT1G80130 63.333 90 33 0 1 90 172 261 4.30e-36 125
MS.gene83611.t1 AT4G32340 60.215 93 36 1 1 92 117 209 2.12e-34 119
MS.gene83611.t1 AT4G17940 57.609 92 39 0 1 92 157 248 3.78e-34 120
MS.gene83611.t1 AT2G29670 42.056 107 60 1 2 108 428 532 8.84e-21 87.0
MS.gene83611.t1 AT2G29670 42.056 107 60 1 2 108 428 532 8.84e-21 87.0
MS.gene83611.t1 AT1G04530 47.253 91 47 1 1 91 128 217 1.06e-20 85.5
MS.gene83611.t1 AT1G07280 42.105 95 55 0 2 96 443 537 7.45e-19 81.6
MS.gene83611.t1 AT1G07280 42.105 95 55 0 2 96 443 537 7.45e-19 81.6
MS.gene83611.t1 AT1G07280 42.105 95 55 0 2 96 443 537 7.45e-19 81.6
MS.gene83611.t1 AT3G47080 38.462 91 56 0 6 96 412 502 1.01e-13 67.0

Find 18 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAGTAAAAGAGAATTATT+TGG 0.185235 2.2:+1539326 None:intergenic
CTCTCTATGCTGATTTAATA+TGG 0.230159 2.2:-1538763 MS.gene83611:CDS
TTTAACAGCCCTATCAAAAT+AGG 0.241375 2.2:+1538709 None:intergenic
GTATGTTGAAAGAGCCATTT+TGG 0.262466 2.2:-1538813 MS.gene83611:CDS
AAGTAGGTTCGTGGAGATTA+TGG 0.302005 2.2:-1538848 MS.gene83611:intron
ATCACTAGGGCTAGCCAAAA+TGG 0.330932 2.2:+1538799 None:intergenic
GATTTCTCTTACCAATCATC+TGG 0.360855 2.2:+1538680 None:intergenic
CAAGTAAAAGAGAATTATTT+GGG 0.377661 2.2:+1539327 None:intergenic
CTTCATATGCAAAATTCCTA+TGG 0.391469 2.2:-1537677 MS.gene83611:CDS
AAAGATCAGGTGAAAGTGTA+TGG 0.469919 2.2:+1537604 None:intergenic
TTAAAAGTGATCCAGATGAT+TGG 0.517931 2.2:-1538691 MS.gene83611:intron
TTATCACATCAGCTATGTCC+TGG 0.518059 2.2:-1537700 MS.gene83611:intron
CAATTTGAAAAGTAGGTTCG+TGG 0.525753 2.2:-1538857 MS.gene83611:intron
CATCTTCTTCAGCGTCCCAT+AGG 0.538742 2.2:+1537661 None:intergenic
GATAAAGCATCAGCATCACT+AGG 0.552225 2.2:+1538785 None:intergenic
TTCATATGCAAAATTCCTAT+GGG 0.567504 2.2:-1537676 MS.gene83611:CDS
ATAAAGCATCAGCATCACTA+GGG 0.631318 2.2:+1538786 None:intergenic
TGGAGATTATGGTAAAGCAG+AGG 0.689369 2.2:-1538837 MS.gene83611:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACACAAATAAAATTATTT+AGG + chr2.2:1538683-1538702 None:intergenic 10.0%
!! AATTTCATCATAATATTAAT+TGG + chr2.2:1538774-1538793 None:intergenic 10.0%
!! AAAAAAAATCCTACAAAAAA+CGG - chr2.2:1538818-1538837 MS.gene83611:CDS 15.0%
!! AAAATATCAAACTTGAAATT+TGG - chr2.2:1537771-1537790 MS.gene83611:intron 15.0%
!! AATTAGATTATCTATCATTT+GGG - chr2.2:1538940-1538959 MS.gene83611:intron 15.0%
!! ACAATATATAAATGAAGATT+AGG - chr2.2:1537904-1537923 MS.gene83611:intron 15.0%
!! ATGATGAAATTAATTAACAA+GGG - chr2.2:1538783-1538802 MS.gene83611:CDS 15.0%
!! TAATTAGATTATCTATCATT+TGG - chr2.2:1538939-1538958 MS.gene83611:intron 15.0%
!! TATAACATCAAATAAAAATC+AGG + chr2.2:1539146-1539165 None:intergenic 15.0%
!! TATGATGAAATTAATTAACA+AGG - chr2.2:1538782-1538801 MS.gene83611:CDS 15.0%
!! TGTATTGTGATTAAAATATA+TGG - chr2.2:1537991-1538010 MS.gene83611:intron 15.0%
!!! TAGGTAAAATATTTTGTAAT+TGG - chr2.2:1537928-1537947 MS.gene83611:intron 15.0%
!! AAAAAAATCCTACAAAAAAC+GGG - chr2.2:1538819-1538838 MS.gene83611:CDS 20.0%
!! AGAACAAAATATGTTACAAA+GGG + chr2.2:1538497-1538516 None:intergenic 20.0%
!! ATAAACATGAGAAATACTTA+GGG - chr2.2:1538521-1538540 MS.gene83611:intron 20.0%
!! ATAAAGTTCATAGATGAATT+AGG + chr2.2:1538285-1538304 None:intergenic 20.0%
!! CAAGTAAAAGAGAATTATTT+GGG + chr2.2:1537571-1537590 None:intergenic 20.0%
!! TAAACAAACACAAATGTAAA+AGG - chr2.2:1538545-1538564 MS.gene83611:intron 20.0%
!! TAATGTTCAATTTGAAAAGT+AGG - chr2.2:1538031-1538050 MS.gene83611:intron 20.0%
!! TTAAGTTATGTGTTGAAATA+TGG + chr2.2:1537739-1537758 None:intergenic 20.0%
!! TTAGTAATTAGTTGTTAGAT+TGG + chr2.2:1539034-1539053 None:intergenic 20.0%
!! TTCTTTCCAAAAAAATACAA+GGG - chr2.2:1539109-1539128 MS.gene83611:intron 20.0%
!! TTTCTTTCCAAAAAAATACA+AGG - chr2.2:1539108-1539127 MS.gene83611:intron 20.0%
!!! TTTATTTGTGTTTCTAGTTA+AGG - chr2.2:1538690-1538709 MS.gene83611:intron 20.0%
! AAACACAAATGTAAAAGGTT+TGG - chr2.2:1538550-1538569 MS.gene83611:intron 25.0%
! AAGTATTTCTCATGTTTATG+CGG + chr2.2:1538520-1538539 None:intergenic 25.0%
! AGAGAAATCTTAAATCTATG+TGG - chr2.2:1538229-1538248 MS.gene83611:intron 25.0%
! ATATAAACCAAATGATACAG+TGG - chr2.2:1538412-1538431 MS.gene83611:intron 25.0%
! ATATAAATGAAGATTAGGCT+AGG - chr2.2:1537909-1537928 MS.gene83611:intron 25.0%
! ATGTGCAAATTTGTATATGT+AGG + chr2.2:1538740-1538759 None:intergenic 25.0%
! CATAAACATGAGAAATACTT+AGG - chr2.2:1538520-1538539 MS.gene83611:intron 25.0%
! CCAAGTAAAAGAGAATTATT+TGG + chr2.2:1537572-1537591 None:intergenic 25.0%
! GAGAACAAAATATGTTACAA+AGG + chr2.2:1538498-1538517 None:intergenic 25.0%
! TGTGCAAATTTGTATATGTA+GGG + chr2.2:1538739-1538758 None:intergenic 25.0%
! TTCATATGCAAAATTCCTAT+GGG - chr2.2:1539219-1539238 MS.gene83611:intron 25.0%
!! ACGAATTAGACTTAAACTTT+TGG + chr2.2:1537866-1537885 None:intergenic 25.0%
!! CCAAATAATTCTCTTTTACT+TGG - chr2.2:1537569-1537588 MS.gene83611:CDS 25.0%
!!! AACAAACCCTTGTATTTTTT+TGG + chr2.2:1539118-1539137 None:intergenic 25.0%
!!! TTATGCTAAGTTTTTGAAAG+AGG - chr2.2:1537595-1537614 MS.gene83611:CDS 25.0%
AATTAACAAGGGAACAACAA+GGG - chr2.2:1538794-1538813 MS.gene83611:CDS 30.0%
AGCTCAACTAATTTACGATA+GGG - chr2.2:1538970-1538989 MS.gene83611:intron 30.0%
CTTCATATGCAAAATTCCTA+TGG - chr2.2:1539218-1539237 MS.gene83611:intron 30.0%
TAATTAACAAGGGAACAACA+AGG - chr2.2:1538793-1538812 MS.gene83611:CDS 30.0%
TAGCTCAACTAATTTACGAT+AGG - chr2.2:1538969-1538988 MS.gene83611:intron 30.0%
TTAAAAGTGATCCAGATGAT+TGG - chr2.2:1538204-1538223 MS.gene83611:intron 30.0%
TTAGGAGAATGTATACATAG+AGG + chr2.2:1538267-1538286 None:intergenic 30.0%
TTTAACAGCCCTATCAAAAT+AGG + chr2.2:1538189-1538208 None:intergenic 30.0%
! GATTATCTATCATTTGGGAT+TGG - chr2.2:1538945-1538964 MS.gene83611:intron 30.0%
!! CTCTCTATGCTGATTTAATA+TGG - chr2.2:1538132-1538151 MS.gene83611:intron 30.0%
!!! AGACGTTTTGCTTTATTTTC+TGG - chr2.2:1539078-1539097 MS.gene83611:intron 30.0%
ATAACATGATCAAGCTCAAG+TGG + chr2.2:1537658-1537677 None:intergenic 35.0%
CAATTTGAAAAGTAGGTTCG+TGG - chr2.2:1538038-1538057 MS.gene83611:intron 35.0%
GAATTCATATTGCATGCAGT+CGG + chr2.2:1537831-1537850 None:intergenic 35.0%
GATTTCTCTTACCAATCATC+TGG + chr2.2:1538218-1538237 None:intergenic 35.0%
TACGATAGGGTCAAAAAAGT+TGG - chr2.2:1538983-1539002 MS.gene83611:intron 35.0%
TAGAGACACTATATGTGACA+TGG - chr2.2:1538321-1538340 MS.gene83611:intron 35.0%
TCTTGATCCACTGTATCATT+TGG + chr2.2:1538422-1538441 None:intergenic 35.0%
TTAGCTCCTAGAAAAAGATC+AGG + chr2.2:1539307-1539326 None:intergenic 35.0%
! AAAGATCAGGTGAAAGTGTA+TGG + chr2.2:1539294-1539313 None:intergenic 35.0%
! ATAAAGCATCAGCATCACTA+GGG + chr2.2:1538112-1538131 None:intergenic 35.0%
! CTTTCACCTGATCTTTTTCT+AGG - chr2.2:1539298-1539317 MS.gene83611:intron 35.0%
! GTATGTTGAAAGAGCCATTT+TGG - chr2.2:1538082-1538101 MS.gene83611:intron 35.0%
!! GATCTTTTTCTAGGAGCTAA+TGG - chr2.2:1539307-1539326 MS.gene83611:CDS 35.0%
!! GGCTCTTATCAGTTTTATGT+TGG + chr2.2:1539273-1539292 None:intergenic 35.0%
!!! AGCTGAAGCCTATTTTGATA+GGG - chr2.2:1538178-1538197 MS.gene83611:intron 35.0%
!!! CCTGATAGTTGGTCTTTTAA+GGG + chr2.2:1538880-1538899 None:intergenic 35.0%
!!! TATACAGACCCGTTTTTTGT+AGG + chr2.2:1538830-1538849 None:intergenic 35.0%
!!! TCCTGATAGTTGGTCTTTTA+AGG + chr2.2:1538881-1538900 None:intergenic 35.0%
AAGTAGGTTCGTGGAGATTA+TGG - chr2.2:1538047-1538066 MS.gene83611:intron 40.0%
AGACCAACTATCAGGAACAA+AGG - chr2.2:1538885-1538904 MS.gene83611:intron 40.0%
ATAAATTTCCCGCATTCACG+CGG - chr2.2:1537676-1537695 MS.gene83611:CDS 40.0%
CCCTTAAAAGACCAACTATC+AGG - chr2.2:1538877-1538896 MS.gene83611:intron 40.0%
CTTCCTTTGTTCCTGATAGT+TGG + chr2.2:1538891-1538910 None:intergenic 40.0%
GATAGGGTCAAAAAAGTTGG+AGG - chr2.2:1538986-1539005 MS.gene83611:intron 40.0%
TGGAGATTATGGTAAAGCAG+AGG - chr2.2:1538058-1538077 MS.gene83611:intron 40.0%
TTATCACATCAGCTATGTCC+TGG - chr2.2:1539195-1539214 MS.gene83611:intron 40.0%
! GATAAAGCATCAGCATCACT+AGG + chr2.2:1538113-1538132 None:intergenic 40.0%
! GGAATTTTGCATATGAAGCC+AGG + chr2.2:1539216-1539235 None:intergenic 40.0%
! GTCGGTACATTGATGATTGT+TGG + chr2.2:1537813-1537832 None:intergenic 40.0%
!!! GAGCTGAAGCCTATTTTGAT+AGG - chr2.2:1538177-1538196 MS.gene83611:intron 40.0%
!!! GATAGTTGGTCTTTTAAGGG+TGG + chr2.2:1538877-1538896 None:intergenic 40.0%
AGGTGGTTGTTGATCGAGAT+AGG - chr2.2:1537708-1537727 MS.gene83611:intron 45.0%
! AGTTGTTAGATTGGTCCGCA+GGG + chr2.2:1539025-1539044 None:intergenic 45.0%
! TAGTTGTTAGATTGGTCCGC+AGG + chr2.2:1539026-1539045 None:intergenic 45.0%
!! ATCACTAGGGCTAGCCAAAA+TGG + chr2.2:1538099-1538118 None:intergenic 45.0%
!!! TTATTTAATTTTTTTTATTG+TGG - chr2.2:1538649-1538668 MS.gene83611:intron 5.0%
!!! TTTTTATTTTTAAGATAAAT+TGG - chr2.2:1538591-1538610 MS.gene83611:intron 5.0%
ATGTGCTAACCGCGTGAATG+CGG + chr2.2:1537688-1537707 None:intergenic 50.0%
CATCTTCTTCAGCGTCCCAT+AGG + chr2.2:1539237-1539256 None:intergenic 50.0%
CATTCACGCGGTTAGCACAT+AGG - chr2.2:1537688-1537707 MS.gene83611:CDS 50.0%
TGGTCCGCAGGGTTTGAATT+CGG + chr2.2:1539014-1539033 None:intergenic 50.0%
GGACCCGAATTCAAACCCTG+CGG - chr2.2:1539007-1539026 MS.gene83611:intron 55.0%
GGTCCGCAGGGTTTGAATTC+GGG + chr2.2:1539013-1539032 None:intergenic 55.0%
TCACGCGGTTAGCACATAGG+TGG - chr2.2:1537691-1537710 MS.gene83611:CDS 55.0%
TGTGCTAACCGCGTGAATGC+GGG + chr2.2:1537687-1537706 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 1537554 1539363 1537554 ID=MS.gene83611
chr2.2 mRNA 1537554 1539363 1537554 ID=MS.gene83611.t1;Parent=MS.gene83611
chr2.2 exon 1539301 1539363 1539301 ID=MS.gene83611.t1.exon1;Parent=MS.gene83611.t1
chr2.2 CDS 1539301 1539363 1539301 ID=cds.MS.gene83611.t1;Parent=MS.gene83611.t1
chr2.2 exon 1538692 1538864 1538692 ID=MS.gene83611.t1.exon2;Parent=MS.gene83611.t1
chr2.2 CDS 1538692 1538864 1538692 ID=cds.MS.gene83611.t1;Parent=MS.gene83611.t1
chr2.2 exon 1537554 1537710 1537554 ID=MS.gene83611.t1.exon3;Parent=MS.gene83611.t1
chr2.2 CDS 1537554 1537710 1537554 ID=cds.MS.gene83611.t1;Parent=MS.gene83611.t1
Gene Sequence

>MS.gene83611

ATGATTGAAGCAAACCCAAATAATTCTCTTTTACTTGGAAATTATGCTAAGTTTTTGAAAGAGGTAATTAATTTGATTTATATTTGAGTAAGAGTGATTGACCACTTGAGCTTGATCATGTTATAAATTTCCCGCATTCACGCGGTTAGCACATAGGTGGTTGTTGATCGAGATAGGACGTTCCATATTTCAACACATAACTTAATTTTTTTAAACTAAAATATCAAACTTGAAATTTGGATCGTTTAATCTAGATCCAACAATCATCAATGTACCGACTGCATGCAATATGAATTCGAAAACTATGAACCAAAAGTTTAAGTCTAATTCGTCAGATCAAATACTTACTTACAATATATAAATGAAGATTAGGCTAGGTAAAATATTTTGTAATTGGATCATCATTTTGAGAAATTAAAATGTAAAGAGAAATATAGTGTATTGTGATTAAAATATATGGTTTGTCACATAATAAATTAATGTTCAATTTGAAAAGTAGGTTCGTGGAGATTATGGTAAAGCAGAGGAGTATGTTGAAAGAGCCATTTTGGCTAGCCCTAGTGATGCTGATGCTTTATCTCTCTATGCTGATTTAATATGGCAAACAGAGAAGAATGCTGATCGAGCTGAAGCCTATTTTGATAGGGCTGTTAAAAGTGATCCAGATGATTGGTAAGAGAAATCTTAAATCTATGTGGATTATGTCTTTTCCTCTATGTATACATTCTCCTAATTCATCTATGAACTTTATTGTTTGAACATCAAACTAGAGACACTATATGTGACATGGTAGATGTTTATATCTCTCTTTTTCTTTTGCTTTTTATCTTCTATAATTTACATATTTAAAAAATGCAAATATAAACCAAATGATACAGTGGATCAAGATTTTGATGTTTAAAAGTCATTTATCTATATAGAACTAGATGCATCTTTCATTCCCTTTGTAACATATTTTGTTCTCCGCATAAACATGAGAAATACTTAGGGATAAACAAACACAAATGTAAAAGGTTTGGACACACTCACACAAATGCTTTTTATTTTTAAGATAAATTGGTTTAATGATGTTGAAAGATGTGACTAATTTATTTATTATTTAATTTTTTTTATTGTGGAGTGTGTGCCTAAATAATTTTATTTGTGTTTCTAGTTAAGGCTTGTTAATGTGTTAAACTGCATCCCTACATATACAAATTTGCACATGATAGAATAATCCAATTAATATTATGATGAAATTAATTAACAAGGGAACAACAAGGGTAAAAAAAATCCTACAAAAAACGGGTCTGTATATATAAATTGATTGTTTCTAAGTGTCCACCCTTAAAAGACCAACTATCAGGAACAAAGGAAGTTCTAGTGATTAGCAAAATGTGATGTGATAATTAGATTATCTATCATTTGGGATTGGATAGCTCAACTAATTTACGATAGGGTCAAAAAAGTTGGAGGACCCGAATTCAAACCCTGCGGACCAATCTAACAACTAATTACTAACATTGACTGCTGCAAAAATTCTTTAGACGTTTTGCTTTATTTTCTGGCTTTTTTTTTCTTTCCAAAAAAATACAAGGGTTTGTTTGTGTCCTGATTTTTATTTGATGTTATATATAAAAACTTATGTGTAAGTTCATATTATTATCACATCAGCTATGTCCTGGCTTCATATGCAAAATTCCTATGGGACGCTGAAGAAGATGAAGATAATGACTGCCAACATAAAACTGATAAGAGCCATACACTTTCACCTGATCTTTTTCTAGGAGCTAATGGTCGTTCTCATGTCACTGCAACCTCTAAAATCTAA
Protein sequence

>MS.gene83611.t1

MIEANPNNSLLLGNYAKFLKEVRGDYGKAEEYVERAILASPSDADALSLYADLIWQTEKNADRAEAYFDRAVKSDPDDCYVLASYAKFLWDAEEDEDNDCQHKTDKSHTLSPDLFLGANGRSHVTATSKI