AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55413

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55413.t1 MTR_6g061070 73.600 250 50 4 1 243 62 302 6.61e-118 345
MS.gene55413.t1 MTR_1g035520 54.231 260 91 7 1 243 116 364 1.42e-73 229
MS.gene55413.t1 MTR_1g033740 58.015 131 35 2 1 131 66 176 2.55e-44 148
MS.gene55413.t1 MTR_1g035480 58.015 131 33 2 1 131 61 169 1.22e-43 145
MS.gene55413.t1 MTR_1g035500 57.252 131 37 2 1 131 69 180 3.94e-43 144
MS.gene55413.t1 MTR_1g035510 53.285 137 43 2 1 137 30 145 3.97e-38 132
MS.gene55413.t1 MTR_1g035470 54.198 131 31 4 1 129 30 133 1.37e-34 121
MS.gene55413.t1 MTR_1g035640 36.214 243 120 11 3 243 51 260 8.89e-26 105
MS.gene55413.t1 MTR_1g035620 34.400 250 110 10 3 243 55 259 2.62e-25 103
MS.gene55413.t1 MTR_1g108780 28.631 241 150 11 8 243 47 270 1.80e-18 84.3
MS.gene55413.t1 MTR_5g044670 27.200 250 149 10 1 243 60 283 2.99e-18 82.8
MS.gene55413.t1 MTR_3g098790 29.880 251 140 10 1 243 57 279 2.99e-18 82.4
MS.gene55413.t1 MTR_1g035570 30.739 257 122 11 3 243 51 267 2.17e-17 80.9
MS.gene55413.t1 MTR_1g035650 34.426 183 79 7 3 179 55 202 1.35e-16 75.9
MS.gene55413.t1 MTR_7g050710 28.000 250 154 6 1 243 57 287 3.06e-15 73.9
MS.gene55413.t1 MTR_1g050845 26.230 244 126 7 3 243 55 247 3.00e-14 72.0
MS.gene55413.t1 MTR_6g043890 29.084 251 146 12 1 243 59 285 3.35e-14 71.2
MS.gene55413.t1 MTR_7g050580 26.908 249 141 8 1 243 57 270 7.43e-13 67.4
MS.gene55413.t1 MTR_4g119990 24.800 250 160 10 3 243 61 291 9.18e-13 67.4
MS.gene55413.t1 MTR_7g050590 24.498 249 164 6 1 243 30 260 6.61e-12 64.3
MS.gene55413.t1 MTR_3g061310 28.926 242 134 13 3 240 56 263 1.37e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAACACAGTGATGGTATT+TGG 0.297148 1.2:+20402619 MS.gene55413:CDS
ATGGTATTTGGCTTCAAAAT+TGG 0.298035 1.2:+20402631 MS.gene55413:CDS
TATTCTTTCGAAAAGCAATT+AGG 0.323587 1.2:-20403826 None:intergenic
AATCTGACCCTCCTTTGTAT+TGG 0.356917 1.2:-20402698 None:intergenic
GGTCTGCGTGCAAAATGAAT+TGG 0.448911 1.2:+20402595 None:intergenic
TTAGAAGTGTTGGTGAGGAC+AGG 0.455257 1.2:+20403881 MS.gene55413:CDS
TGTTGAAGGTGATTATAGAT+TGG 0.466803 1.2:+20403409 MS.gene55413:CDS
AAGGAACATGAGTTGAAAGT+TGG 0.478819 1.2:+20403979 MS.gene55413:CDS
TTATCGCCATGTCATGTTGA+AGG 0.488274 1.2:+20403395 MS.gene55413:CDS
GTCTGCGTGCAAAATGAATT+GGG 0.489112 1.2:+20402596 None:intergenic
CATTAAACTTTCGTAAAAGC+AGG 0.501843 1.2:+20403917 MS.gene55413:CDS
AGTGAAACTAGGACTCTCAT+TGG 0.512039 1.2:-20403366 None:intergenic
TTTGGCTTCAAAATTGGAAG+AGG 0.520115 1.2:+20402637 MS.gene55413:CDS
TAATGGAAACACAGGAGGCA+TGG 0.520474 1.2:+20403286 MS.gene55413:CDS
AAGGCAACAATTAGAAGTGT+TGG 0.542696 1.2:+20403871 MS.gene55413:CDS
AATGGAAACACAGGAGGCAT+GGG 0.543418 1.2:+20403287 MS.gene55413:CDS
TACATGAATGAGTTATTGCA+AGG 0.543984 1.2:+20403847 MS.gene55413:CDS
GTGAAACTAGGACTCTCATT+GGG 0.547777 1.2:-20403365 None:intergenic
ACTACTGCTGCTACACCTCA+AGG 0.560864 1.2:+20402924 MS.gene55413:CDS
TAGAAGTGTTGGTGAGGACA+GGG 0.562489 1.2:+20403882 MS.gene55413:CDS
GATAATTTGACAGTGAAACT+AGG 0.566923 1.2:-20403377 None:intergenic
AAAATTGGAAGAGGTTTGCA+TGG 0.571811 1.2:+20402646 MS.gene55413:CDS
TTGTGAATGTTACTCCCTTG+AGG 0.576438 1.2:-20402939 None:intergenic
TATTCAAGTTTGAGATGCAA+CGG 0.590567 1.2:+20402762 MS.gene55413:CDS
GCAGAGGCTAATGGAAACAC+AGG 0.596384 1.2:+20403278 MS.gene55413:intron
AACAATTAGAAGTGTTGGTG+AGG 0.601806 1.2:+20403876 MS.gene55413:CDS
TTTGCATGGTCGCTCCGATG+TGG 0.602338 1.2:+20402660 MS.gene55413:CDS
GTGTTGGTGAGGACAGGGCA+TGG 0.626789 1.2:+20403887 MS.gene55413:CDS
TAATCACCTTCAACATGACA+TGG 0.641985 1.2:-20403401 None:intergenic
GAATGAGTTATTGCAAGGGA+AGG 0.643476 1.2:+20403852 MS.gene55413:CDS
CTACTGCTGCTACACCTCAA+GGG 0.653810 1.2:+20402925 MS.gene55413:CDS
ACATGAATGAGTTATTGCAA+GGG 0.661417 1.2:+20403848 MS.gene55413:CDS
AATTGGGTGCAACACAGTGA+TGG 0.677488 1.2:+20402612 MS.gene55413:CDS
AAACTAAAAGATCTCCACAT+CGG 0.700040 1.2:-20402674 None:intergenic
GAGGCTAATGGAAACACAGG+AGG 0.702704 1.2:+20403281 MS.gene55413:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATACTTTTGTAATTTGTA+TGG - chr1.2:20403120-20403139 None:intergenic 15.0%
!! ACTAATTGAAAACATATTCA+TGG + chr1.2:20403582-20403601 MS.gene55413:intron 20.0%
!! TAAACAGATGAATGAATAAA+AGG - chr1.2:20403022-20403041 None:intergenic 20.0%
!! TATTACAGAAAAAGTAGTAT+AGG - chr1.2:20403442-20403461 None:intergenic 20.0%
!! TTATTCATTCATCTGTTTAT+GGG + chr1.2:20403023-20403042 MS.gene55413:intron 20.0%
!! TTTATTCATTCATCTGTTTA+TGG + chr1.2:20403022-20403041 MS.gene55413:intron 20.0%
!!! AATTTGTATGGATTAAAAAG+TGG - chr1.2:20403108-20403127 None:intergenic 20.0%
! TATCAACAAGAGAAACATTT+GGG - chr1.2:20403544-20403563 None:intergenic 25.0%
! TATTCTTTCGAAAAGCAATT+AGG - chr1.2:20403829-20403848 None:intergenic 25.0%
!! AACTATTTTCAGCATTTGAA+AGG - chr1.2:20403247-20403266 None:intergenic 25.0%
!! CAAAATTTGAGATGAACTAA+GGG - chr1.2:20403070-20403089 None:intergenic 25.0%
!!! AATTGATTCTCTTTTTCTTG+AGG - chr1.2:20402890-20402909 None:intergenic 25.0%
!!! ATTGATTCTCTTTTTCTTGA+GGG - chr1.2:20402889-20402908 None:intergenic 25.0%
!!! CTTTTAGTTTTCCAATACAA+AGG + chr1.2:20402687-20402706 MS.gene55413:CDS 25.0%
!!! TAGTTTTTAAAGTTTTGCAG+AGG + chr1.2:20403262-20403281 MS.gene55413:intron 25.0%
AAACTAAAAGATCTCCACAT+CGG - chr1.2:20402677-20402696 None:intergenic 30.0%
ACATGAATGAGTTATTGCAA+GGG + chr1.2:20403848-20403867 MS.gene55413:CDS 30.0%
AGAGTGTACGTAAATAAAGT+GGG - chr1.2:20403158-20403177 None:intergenic 30.0%
ATCAACAAGAGAAACATTTG+GGG - chr1.2:20403543-20403562 None:intergenic 30.0%
CATTAAACTTTCGTAAAAGC+AGG + chr1.2:20403917-20403936 MS.gene55413:CDS 30.0%
CTATCAACAAGAGAAACATT+TGG - chr1.2:20403545-20403564 None:intergenic 30.0%
GATAATTTGACAGTGAAACT+AGG - chr1.2:20403380-20403399 None:intergenic 30.0%
TACATGAATGAGTTATTGCA+AGG + chr1.2:20403847-20403866 MS.gene55413:CDS 30.0%
TGTTGAAGGTGATTATAGAT+TGG + chr1.2:20403409-20403428 MS.gene55413:CDS 30.0%
! AAGAGTGTACGTAAATAAAG+TGG - chr1.2:20403159-20403178 None:intergenic 30.0%
! ACTTACCTGAAACTTTTTGT+TGG - chr1.2:20402989-20403008 None:intergenic 30.0%
! ATGGTATTTGGCTTCAAAAT+TGG + chr1.2:20402631-20402650 MS.gene55413:CDS 30.0%
! CCAAAATTTGAGATGAACTA+AGG - chr1.2:20403071-20403090 None:intergenic 30.0%
! CCTTAGTTCATCTCAAATTT+TGG + chr1.2:20403068-20403087 MS.gene55413:intron 30.0%
! CTTACCTGAAACTTTTTGTT+GGG - chr1.2:20402988-20403007 None:intergenic 30.0%
! TAGTTTTCCAATACAAAGGA+GGG + chr1.2:20402691-20402710 MS.gene55413:CDS 30.0%
! TATTCAAGTTTGAGATGCAA+CGG + chr1.2:20402762-20402781 MS.gene55413:CDS 30.0%
! TTGATTCTCTTTTTCTTGAG+GGG - chr1.2:20402888-20402907 None:intergenic 30.0%
!! AGAGGCTTTCATTTTTCTAT+AGG + chr1.2:20403487-20403506 MS.gene55413:intron 30.0%
!! TTAGTATTTTCAGTGTCACT+AGG - chr1.2:20402861-20402880 None:intergenic 30.0%
!! TTAGTTTTCCAATACAAAGG+AGG + chr1.2:20402690-20402709 MS.gene55413:CDS 30.0%
AAAATTGGAAGAGGTTTGCA+TGG + chr1.2:20402646-20402665 MS.gene55413:CDS 35.0%
AACTAGCAGAAGAGACATTT+AGG + chr1.2:20403688-20403707 MS.gene55413:intron 35.0%
TAATCACCTTCAACATGACA+TGG - chr1.2:20403404-20403423 None:intergenic 35.0%
! AAGGAACATGAGTTGAAAGT+TGG + chr1.2:20403979-20403998 MS.gene55413:CDS 35.0%
! AAGGCAACAATTAGAAGTGT+TGG + chr1.2:20403871-20403890 MS.gene55413:CDS 35.0%
! AATTAGGTATCGTCTGTTTC+AGG - chr1.2:20403813-20403832 None:intergenic 35.0%
! TAAAGTTTTGCAGAGGCTAA+TGG + chr1.2:20403269-20403288 MS.gene55413:intron 35.0%
! TTTGGCTTCAAAATTGGAAG+AGG + chr1.2:20402637-20402656 MS.gene55413:CDS 35.0%
!! AACAATTAGAAGTGTTGGTG+AGG + chr1.2:20403876-20403895 MS.gene55413:CDS 35.0%
!! TGGTTGGAAGTCATTTTCAA+AGG + chr1.2:20403960-20403979 MS.gene55413:CDS 35.0%
AATCTGACCCTCCTTTGTAT+TGG - chr1.2:20402701-20402720 None:intergenic 40.0%
AGTGAAACTAGGACTCTCAT+TGG - chr1.2:20403369-20403388 None:intergenic 40.0%
GAATGAGTTATTGCAAGGGA+AGG + chr1.2:20403852-20403871 MS.gene55413:CDS 40.0%
GCAACCCAACAAAAAGTTTC+AGG + chr1.2:20402981-20403000 MS.gene55413:CDS 40.0%
GTGAAACTAGGACTCTCATT+GGG - chr1.2:20403368-20403387 None:intergenic 40.0%
TGCAACACAGTGATGGTATT+TGG + chr1.2:20402619-20402638 MS.gene55413:CDS 40.0%
TTATCGCCATGTCATGTTGA+AGG + chr1.2:20403395-20403414 MS.gene55413:CDS 40.0%
TTGTGAATGTTACTCCCTTG+AGG - chr1.2:20402942-20402961 None:intergenic 40.0%
TTTGTACCTAACTGTGTGAG+AGG + chr1.2:20403469-20403488 MS.gene55413:intron 40.0%
!! CAGGAGCAGTTTTGTAATGA+GGG + chr1.2:20403936-20403955 MS.gene55413:CDS 40.0%
AATTGGGTGCAACACAGTGA+TGG + chr1.2:20402612-20402631 MS.gene55413:CDS 45.0%
ATTCGTGCACGAAATGTGCA+AGG - chr1.2:20403759-20403778 None:intergenic 45.0%
TAATGGAAACACAGGAGGCA+TGG + chr1.2:20403286-20403305 MS.gene55413:CDS 45.0%
TGAAAGCCTCTCACACAGTT+AGG - chr1.2:20403478-20403497 None:intergenic 45.0%
! AATGGAAACACAGGAGGCAT+GGG + chr1.2:20403287-20403306 MS.gene55413:CDS 45.0%
! GTATCGTCTGTTTCAGGTCA+TGG - chr1.2:20403807-20403826 None:intergenic 45.0%
!! AGCAGTTTTGTAATGAGGGC+TGG + chr1.2:20403940-20403959 MS.gene55413:CDS 45.0%
!! GCAGGAGCAGTTTTGTAATG+AGG + chr1.2:20403935-20403954 MS.gene55413:CDS 45.0%
!! GTTTTGTAATGAGGGCTGGT+TGG + chr1.2:20403944-20403963 MS.gene55413:CDS 45.0%
!! TAGAAGTGTTGGTGAGGACA+GGG + chr1.2:20403882-20403901 MS.gene55413:CDS 45.0%
!! TTAGAAGTGTTGGTGAGGAC+AGG + chr1.2:20403881-20403900 MS.gene55413:CDS 45.0%
ACTACTGCTGCTACACCTCA+AGG + chr1.2:20402924-20402943 MS.gene55413:CDS 50.0%
CTACTGCTGCTACACCTCAA+GGG + chr1.2:20402925-20402944 MS.gene55413:CDS 50.0%
GAGGCTAATGGAAACACAGG+AGG + chr1.2:20403281-20403300 MS.gene55413:intron 50.0%
GCAGAGGCTAATGGAAACAC+AGG + chr1.2:20403278-20403297 MS.gene55413:intron 50.0%
TTTGCATGGTCGCTCCGATG+TGG + chr1.2:20402660-20402679 MS.gene55413:CDS 55.0%
! GTGTTGGTGAGGACAGGGCA+TGG + chr1.2:20403887-20403906 MS.gene55413:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 20402609 20404005 20402609 ID=MS.gene55413
chr1.2 mRNA 20402609 20404005 20402609 ID=MS.gene55413.t1;Parent=MS.gene55413
chr1.2 exon 20402609 20403002 20402609 ID=MS.gene55413.t1.exon1;Parent=MS.gene55413.t1
chr1.2 CDS 20402609 20403002 20402609 ID=cds.MS.gene55413.t1;Parent=MS.gene55413.t1
chr1.2 exon 20403282 20403430 20403282 ID=MS.gene55413.t1.exon2;Parent=MS.gene55413.t1
chr1.2 CDS 20403282 20403430 20403282 ID=cds.MS.gene55413.t1;Parent=MS.gene55413.t1
chr1.2 exon 20403820 20404005 20403820 ID=MS.gene55413.t1.exon3;Parent=MS.gene55413.t1
chr1.2 CDS 20403820 20404005 20403820 ID=cds.MS.gene55413.t1;Parent=MS.gene55413.t1
Gene Sequence

>MS.gene55413

ATGAATTGGGTGCAACACAGTGATGGTATTTGGCTTCAAAATTGGAAGAGGTTTGCATGGTCGCTCCGATGTGGAGATCTTTTAGTTTTCCAATACAAAGGAGGGTCAGATTTTAATGTCATTATATTAGATGATAGTAAATTAGAAATTGACTATTCAAGTTTGAGATGCAACGGCGATCAAGAAAATACTAAAGAGAGTCATGATGATGCTGACGACGACAACAATGATTATGAGTGTGTTGAGATTCCTAGTGACACTGAAAATACTAAAATTCCCCTCAAGAAAAAGAGAATCAATTCAAATGACATTGCTACTACTGCTGCTACACCTCAAGGGAGTAACATTCACAAGAGAAAAACTAATATCAATGCAACCCAACAAAAAGTTTCAGGTAAGTTATTCTACTTCCTTTTATTCATTCATCTGTTTATGGGCAAAATATGTTTTTAATTAGTCCCTTAGTTCATCTCAAATTTTGGTTTTAGTCTTCTTTCCACTTTTTAATCCATACAAATTACAAAAGTATATGTTTTTAGTTCTATACCCACTTTATTTACGTACACTCTTTTAAGATTAAATCAATTTTCAAGACTGTCATACAAAAAAATCAAGACGCAAACTTTTATTTTGTACCTTTCAAATGCTGAAAATAGTTTTTAAAGTTTTGCAGAGGCTAATGGAAACACAGGAGGCATGGGTAAGAAAGCTAAAAATGCACAAAAACTAAATGAGAGAAGTTGCACAAATTCTCATCCCAATGAGAGTCCTAGTTTCACTGTCAAATTATCGCCATGTCATGTTGAAGGTGATTATAGATTGGTATGTTTCCTATACTACTTTTTCTGTAATAGTGACATTTTGTACCTAACTGTGTGAGAGGCTTTCATTTTTCTATAGGAACTGAATGTATTGAAATTACAAACGAAATCCCCAAATGTTTCTCTTGTTGATAGTTTTATTGAATAAATTTACTAATTGAAAACATATTCATGGATTAATGTAAATTTATTCATTAAATTATTAACAAAAGAAAAAAGTATAGCAAACATACTAAAGACAGATTTGAAGATCAAAATAACTAGCAGAAGAGACATTTAGGCATATTTTTATAATTTTTGATACATTTAAGTACTGTTTGAATGAGCCTTGCACATTTCGTGCACGAATATATTTTAATCAATATTTGTTTAAACCATGACCTGAAACAGACGATACCTAATTGCTTTTCGAAAGAATACATGAATGAGTTATTGCAAGGGAAGGCAACAATTAGAAGTGTTGGTGAGGACAGGGCATGGCACGTGACATTAAACTTTCGTAAAAGCAGGAGCAGTTTTGTAATGAGGGCTGGTTGGAAGTCATTTTCAAAGGAACATGAGTTGAAAGTTGGTGAT
Protein sequence

>MS.gene55413.t1

MNWVQHSDGIWLQNWKRFAWSLRCGDLLVFQYKGGSDFNVIILDDSKLEIDYSSLRCNGDQENTKESHDDADDDNNDYECVEIPSDTENTKIPLKKKRINSNDIATTAATPQGSNIHKRKTNINATQQKVSEANGNTGGMGKKAKNAQKLNERSCTNSHPNESPSFTVKLSPCHVEGDYRLTIPNCFSKEYMNELLQGKATIRSVGEDRAWHVTLNFRKSRSSFVMRAGWKSFSKEHELKVGD