AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025030.t1 MTR_0004s0210 96.319 163 6 0 1 163 1 163 5.74e-111 312
MS.gene025030.t1 MTR_7g011090 31.447 159 100 3 1 150 21 179 3.28e-18 77.8
MS.gene025030.t1 MTR_5g041900 35.948 153 89 2 7 150 27 179 4.36e-18 77.4
MS.gene025030.t1 MTR_4g081880 36.478 159 92 3 1 150 22 180 4.98e-17 74.7
MS.gene025030.t1 MTR_7g083120 32.800 125 76 1 11 127 33 157 8.75e-17 73.9
MS.gene025030.t1 MTR_0097s0070 32.414 145 87 3 20 157 52 192 2.05e-16 73.2
MS.gene025030.t1 MTR_7g108130 28.302 159 104 3 3 151 24 182 1.18e-15 71.2
MS.gene025030.t1 MTR_8g089300 30.769 143 83 3 10 136 28 170 1.23e-14 68.6
MS.gene025030.t1 MTR_1g058540 34.965 143 80 4 7 138 37 177 1.76e-12 62.8
MS.gene025030.t1 MTR_3g064310 27.703 148 97 4 6 148 43 185 1.02e-11 60.8
MS.gene025030.t1 MTR_4g118800 31.613 155 94 4 10 153 30 183 1.33e-11 60.1
MS.gene025030.t1 MTR_2g026530 31.250 144 83 3 6 136 9 149 1.46e-11 60.1
MS.gene025030.t1 MTR_4g118810 28.082 146 87 4 8 136 33 177 2.26e-11 59.7
MS.gene025030.t1 MTR_2g026530 31.250 144 83 3 6 136 29 169 2.32e-11 59.7
MS.gene025030.t1 MTR_2g020060 31.410 156 92 2 8 148 23 178 5.15e-11 58.5
MS.gene025030.t1 MTR_1g058560 37.190 121 63 4 29 138 58 176 5.77e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025030.t1 AT1G03700 58.125 160 67 0 4 163 5 164 4.98e-67 201
MS.gene025030.t1 AT4G03540 59.375 160 65 0 4 163 5 164 5.66e-57 176
MS.gene025030.t1 AT5G44550 35.632 174 94 4 2 157 10 183 8.23e-23 90.1
MS.gene025030.t1 AT5G15290 34.483 145 86 2 1 136 21 165 5.80e-22 87.4
MS.gene025030.t1 AT4G15610 32.432 148 85 3 3 136 24 170 2.26e-16 73.2
MS.gene025030.t1 AT2G36100 36.364 143 78 4 7 138 47 187 1.95e-15 70.9
MS.gene025030.t1 AT1G14160 31.126 151 91 4 11 150 54 202 3.35e-15 70.5
MS.gene025030.t1 AT2G27370 37.405 131 69 4 31 150 85 213 4.81e-15 70.1
MS.gene025030.t1 AT4G25040 35.252 139 86 2 12 146 21 159 1.07e-12 62.8
MS.gene025030.t1 AT5G06200 36.842 133 71 4 29 150 65 195 5.24e-11 58.9

Find 31 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCATGTGATTGCAAAATT+TGG 0.071795 4.3:+57528098 None:intergenic
CCACCTATTGCTAAGGTTCT+TGG 0.187843 4.3:-57529535 MS.gene025030:CDS
AACTCTATTGTAACTGTCTA+TGG 0.255815 4.3:-57529073 MS.gene025030:CDS
ACTTGTGGTCGCCATGGATA+TGG 0.315968 4.3:-57529008 MS.gene025030:intron
CTCATGTGATTGCAAAATTT+GGG 0.342731 4.3:+57528099 None:intergenic
CTCAAGCATCTCTGCAGCTT+TGG 0.400682 4.3:-57528187 MS.gene025030:CDS
GCTTTAGTCGCTAGTGTCAT+TGG 0.404288 4.3:-57528072 MS.gene025030:CDS
GCTAAGGTTCTTGGCCTTCT+CGG 0.405136 4.3:-57529526 MS.gene025030:CDS
CGCCAGAGCAAGCTTTCTGC+AGG 0.458432 4.3:+57529031 None:intergenic
AGGCCAAGAACCTTAGCAAT+AGG 0.460604 4.3:+57529532 None:intergenic
GCTGCTTGGCTACCGATTTG+TGG 0.463642 4.3:-57528129 MS.gene025030:CDS
TTCCTGCAGAAAGCTTGCTC+TGG 0.469885 4.3:-57529033 MS.gene025030:CDS
ATGGAAACAATTATGCTGCT+TGG 0.504739 4.3:-57528143 MS.gene025030:CDS
ATAGCTCAAGTGGCAAAGAA+TGG 0.508607 4.3:-57528162 MS.gene025030:CDS
TGCTGACAAGGTGGCCGAGA+AGG 0.510239 4.3:+57529512 None:intergenic
TTGGGAACTGAACCACAAAT+CGG 0.511633 4.3:+57528117 None:intergenic
AGGGTCAAGGACAGTATGAA+TGG 0.516263 4.3:+57528017 None:intergenic
AAGCTTGCTCTGGCGACTTG+TGG 0.523109 4.3:-57529023 MS.gene025030:CDS
GAGTTCACTTACTTCAAGGC+AGG 0.535265 4.3:+57529414 None:intergenic
TTCTCAAAAGGAGAGGGTCA+AGG 0.544463 4.3:+57528004 None:intergenic
CTGGCGACTTGTGGTCGCCA+TGG 0.548545 4.3:-57529014 MS.gene025030:CDS
TTATGACATTACCATATCCA+TGG 0.553523 4.3:+57528997 None:intergenic
CGTGACAACTACTGCTGACA+AGG 0.554198 4.3:+57529500 None:intergenic
GTGGCAGATTCTACTAGTCT+TGG 0.560428 4.3:+57529554 None:intergenic
GAATCTGCCACCTATTGCTA+AGG 0.568570 4.3:-57529542 MS.gene025030:CDS
CTTGTCAGCAGTAGTTGTCA+CGG 0.572052 4.3:-57529499 MS.gene025030:CDS
GATTCTACTAGTCTTGGCCA+TGG 0.580820 4.3:+57529560 None:intergenic
AGCTTTGGCTATAGCTCAAG+TGG 0.581117 4.3:-57528172 MS.gene025030:CDS
AGCTTTCTGCAGGAAGAAAG+AGG 0.586262 4.3:+57529041 None:intergenic
CCAAGAACCTTAGCAATAGG+TGG 0.626186 4.3:+57529535 None:intergenic
GACAACTACTGCTGACAAGG+TGG 0.681234 4.3:+57529503 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAAATGCTAAATTATTA+TGG - chr4.3:57529275-57529294 MS.gene025030:intron 15.0%
!!! ATTTTATATGATCAAACTTA+GGG + chr4.3:57529066-57529085 None:intergenic 15.0%
!!! GTTTTATTTTTATGGATTTA+AGG + chr4.3:57528996-57529015 None:intergenic 15.0%
!!! TATTTTATATGATCAAACTT+AGG + chr4.3:57529067-57529086 None:intergenic 15.0%
!! AAATGCTAAAATTGTAAAGT+CGG + chr4.3:57528744-57528763 None:intergenic 20.0%
!! ATGCTAAATTATTATGGTTA+TGG - chr4.3:57529281-57529300 MS.gene025030:intron 20.0%
!! CAAACATTATATGACTTAAA+TGG + chr4.3:57528803-57528822 None:intergenic 20.0%
!! GAACAAATATGTTTCAAATT+TGG + chr4.3:57528671-57528690 None:intergenic 20.0%
!!! ATGAGAAGGTTTTATTTTTA+TGG + chr4.3:57529004-57529023 None:intergenic 20.0%
!!! TATTTTTATGGATTTAAGGT+TGG + chr4.3:57528992-57529011 None:intergenic 20.0%
!!! TGTTCTTCATGTTTTTAAAA+TGG - chr4.3:57528686-57528705 MS.gene025030:intron 20.0%
!!! TTTAATTGATTTTTATGAGC+AGG - chr4.3:57529325-57529344 MS.gene025030:intron 20.0%
!!! TTTTCGTTTTTTCATTTCAT+TGG + chr4.3:57529257-57529276 None:intergenic 20.0%
! GACATAACTAGTATTCTAAT+AGG + chr4.3:57529111-57529130 None:intergenic 25.0%
! TATGAACTCTTTAACATAGT+TGG + chr4.3:57528845-57528864 None:intergenic 25.0%
! TATGTTAAAGAGTTCATACA+TGG - chr4.3:57528847-57528866 MS.gene025030:intron 25.0%
!! ATCACTTTAGAGATGAATTA+AGG + chr4.3:57528424-57528443 None:intergenic 25.0%
!! GTTAGTATATTTTGCTTCAA+AGG + chr4.3:57528117-57528136 None:intergenic 25.0%
!!! CTAACCAATGTATGATTTTT+TGG - chr4.3:57529179-57529198 MS.gene025030:intron 25.0%
!!! TCTTCATGTTTTTAAAATGG+AGG - chr4.3:57528689-57528708 MS.gene025030:intron 25.0%
AAAGTTCTTGCATGATAAAG+AGG + chr4.3:57528589-57528608 None:intergenic 30.0%
AACACGTCAAACAATAAACT+TGG + chr4.3:57529218-57529237 None:intergenic 30.0%
AACTCTATTGTAACTGTCTA+TGG - chr4.3:57528481-57528500 MS.gene025030:intron 30.0%
AACTCTTTAACATAGTTGGA+TGG + chr4.3:57528841-57528860 None:intergenic 30.0%
CTCATGTGATTGCAAAATTT+GGG + chr4.3:57529458-57529477 None:intergenic 30.0%
TACATAAATGCTATGAAGCA+TGG - chr4.3:57528184-57528203 MS.gene025030:CDS 30.0%
TCAAACAATTCCTACTTTCT+AGG - chr4.3:57528443-57528462 MS.gene025030:intron 30.0%
TCAGCCAAAAAATCATACAT+TGG + chr4.3:57529186-57529205 None:intergenic 30.0%
TCTCATGTGATTGCAAAATT+TGG + chr4.3:57529459-57529478 None:intergenic 30.0%
TTATGACATTACCATATCCA+TGG + chr4.3:57528560-57528579 None:intergenic 30.0%
TTCAGTGTAATTACAAGTGT+CGG + chr4.3:57528273-57528292 None:intergenic 30.0%
! AAATTTTGCAATCACATGAG+AGG - chr4.3:57529458-57529477 MS.gene025030:CDS 30.0%
! AAGTTTTTCTCAAAAGGAGA+GGG + chr4.3:57529559-57529578 None:intergenic 30.0%
! GCATTTTTGTTAGTTGAGTT+AGG - chr4.3:57528758-57528777 MS.gene025030:intron 30.0%
! TGTAACTGTCTATGGATTTT+TGG - chr4.3:57528489-57528508 MS.gene025030:intron 30.0%
AATGGAGTTCACTTACTTCA+AGG + chr4.3:57528147-57528166 None:intergenic 35.0%
ATGGAAACAATTATGCTGCT+TGG - chr4.3:57529411-57529430 MS.gene025030:intron 35.0%
GAATACTAGTTATGTCTCGA+TGG - chr4.3:57529115-57529134 MS.gene025030:intron 35.0%
! ACATTGGTTAGTCACACATT+GGG + chr4.3:57529170-57529189 None:intergenic 35.0%
! CAAGTTTTTCTCAAAAGGAG+AGG + chr4.3:57529560-57529579 None:intergenic 35.0%
! TACATTGGTTAGTCACACAT+TGG + chr4.3:57529171-57529190 None:intergenic 35.0%
! TCACAAAGTACCTAGAAAGT+AGG + chr4.3:57528456-57528475 None:intergenic 35.0%
!! TATGGATTTAAGGTTGGTGA+TGG + chr4.3:57528986-57529005 None:intergenic 35.0%
!!! TGAAGAAGCTAGCTTTTTCA+TGG + chr4.3:57528088-57528107 None:intergenic 35.0%
ATAGCTCAAGTGGCAAAGAA+TGG - chr4.3:57529392-57529411 MS.gene025030:intron 40.0%
GTAAAGTCGGACGTTATGAT+CGG + chr4.3:57528731-57528750 None:intergenic 40.0%
TAAAGTCGGACGTTATGATC+GGG + chr4.3:57528730-57528749 None:intergenic 40.0%
TTGGGAACTGAACCACAAAT+CGG + chr4.3:57529440-57529459 None:intergenic 40.0%
AAAGTCGGACGTTATGATCG+GGG + chr4.3:57528729-57528748 None:intergenic 45.0%
AGCGTGTTTGAGAGATGAGA+AGG + chr4.3:57529018-57529037 None:intergenic 45.0%
AGCTTTCTGCAGGAAGAAAG+AGG + chr4.3:57528516-57528535 None:intergenic 45.0%
AGGCCAAGAACCTTAGCAAT+AGG + chr4.3:57528025-57528044 None:intergenic 45.0%
AGGGTCAAGGACAGTATGAA+TGG + chr4.3:57529540-57529559 None:intergenic 45.0%
CACGTATATGCTATGAAGCG+AGG + chr4.3:57528365-57528384 None:intergenic 45.0%
CCAAGAACCTTAGCAATAGG+TGG + chr4.3:57528022-57528041 None:intergenic 45.0%
CCACCTATTGCTAAGGTTCT+TGG - chr4.3:57528019-57528038 MS.gene025030:CDS 45.0%
CTTGTCAGCAGTAGTTGTCA+CGG - chr4.3:57528055-57528074 MS.gene025030:CDS 45.0%
GAATCTGCCACCTATTGCTA+AGG - chr4.3:57528012-57528031 MS.gene025030:CDS 45.0%
GAGTTCACTTACTTCAAGGC+AGG + chr4.3:57528143-57528162 None:intergenic 45.0%
GCTTTAGTCGCTAGTGTCAT+TGG - chr4.3:57529482-57529501 MS.gene025030:CDS 45.0%
TATGAAGCATGGACACTCCT+CGG - chr4.3:57528195-57528214 MS.gene025030:CDS 45.0%
TCGATGGAGATTGAGTCTAC+AGG - chr4.3:57529131-57529150 MS.gene025030:intron 45.0%
TTCTCAAAAGGAGAGGGTCA+AGG + chr4.3:57529553-57529572 None:intergenic 45.0%
! AGCTTTGGCTATAGCTCAAG+TGG - chr4.3:57529382-57529401 MS.gene025030:intron 45.0%
! GTGGCAGATTCTACTAGTCT+TGG + chr4.3:57528003-57528022 None:intergenic 45.0%
!! TACAAGTGTCGGTGTCGTAT+CGG + chr4.3:57528262-57528281 None:intergenic 45.0%
!! AATAATTTAAATAAAACAAA+TGG + chr4.3:57528165-57528184 None:intergenic 5.0%
ACAGACACAGACACCAGACA+CGG + chr4.3:57528340-57528359 None:intergenic 50.0%
ACTTGTGGTCGCCATGGATA+TGG - chr4.3:57528546-57528565 MS.gene025030:intron 50.0%
CGTGACAACTACTGCTGACA+AGG + chr4.3:57528057-57528076 None:intergenic 50.0%
CTCAAGCATCTCTGCAGCTT+TGG - chr4.3:57529367-57529386 MS.gene025030:intron 50.0%
GACAACTACTGCTGACAAGG+TGG + chr4.3:57528054-57528073 None:intergenic 50.0%
! GCTAAGGTTCTTGGCCTTCT+CGG - chr4.3:57528028-57528047 MS.gene025030:CDS 50.0%
! TTCCTGCAGAAAGCTTGCTC+TGG - chr4.3:57528521-57528540 MS.gene025030:intron 50.0%
GATTAGGCGTGTCCTGGTGT+CGG - chr4.3:57528217-57528236 MS.gene025030:intron 55.0%
GCATGGACACTCCTCGGATT+AGG - chr4.3:57528201-57528220 MS.gene025030:CDS 55.0%
! AAGCTTGCTCTGGCGACTTG+TGG - chr4.3:57528531-57528550 MS.gene025030:intron 55.0%
!! GCTGCTTGGCTACCGATTTG+TGG - chr4.3:57529425-57529444 MS.gene025030:intron 55.0%
!! TGTCGGTGTCGTATCGGTGT+CGG + chr4.3:57528256-57528275 None:intergenic 55.0%
ACCAGGACACGCCTAATCCG+AGG + chr4.3:57528215-57528234 None:intergenic 60.0%
CACAGACACCAGACACGGCA+TGG + chr4.3:57528335-57528354 None:intergenic 60.0%
CGCCAGAGCAAGCTTTCTGC+AGG + chr4.3:57528526-57528545 None:intergenic 60.0%
GTCAGTGTCCATGCCGTGTC+TGG - chr4.3:57528324-57528343 MS.gene025030:intron 60.0%
TGCTGACAAGGTGGCCGAGA+AGG + chr4.3:57528045-57528064 None:intergenic 60.0%
! TCCTCGGATTAGGCGTGTCC+TGG - chr4.3:57528211-57528230 MS.gene025030:intron 60.0%
CACGACACGTGTCCGACACC+AGG + chr4.3:57528232-57528251 None:intergenic 65.0%
CTGGCGACTTGTGGTCGCCA+TGG - chr4.3:57528540-57528559 MS.gene025030:intron 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 57527996 57529580 57527996 ID=MS.gene025030
chr4.3 mRNA 57527996 57529580 57527996 ID=MS.gene025030.t1;Parent=MS.gene025030
chr4.3 exon 57529426 57529580 57529426 ID=MS.gene025030.t1.exon1;Parent=MS.gene025030.t1
chr4.3 CDS 57529426 57529580 57529426 ID=cds.MS.gene025030.t1;Parent=MS.gene025030.t1
chr4.3 exon 57529009 57529111 57529009 ID=MS.gene025030.t1.exon2;Parent=MS.gene025030.t1
chr4.3 CDS 57529009 57529111 57529009 ID=cds.MS.gene025030.t1;Parent=MS.gene025030.t1
chr4.3 exon 57527996 57528229 57527996 ID=MS.gene025030.t1.exon3;Parent=MS.gene025030.t1
chr4.3 CDS 57527996 57528229 57527996 ID=cds.MS.gene025030.t1;Parent=MS.gene025030.t1
Gene Sequence

>MS.gene025030

ATGGCCAAGACTAGTAGAATCTGCCACCTATTGCTAAGGTTCTTGGCCTTCTCGGCCACCTTGTCAGCAGTAGTTGTCACGGTTTCTAGCCATGAAAAAGCTAGCTTCTTCACTGTTTCCTTTGAAGCAAAATATACTAACTCTCCTGCCTTGAAGTAAGTGAACTCCATTTGTTTTATTTAAATTATTACATAAATGCTATGAAGCATGGACACTCCTCGGATTAGGCGTGTCCTGGTGTCGGACACGTGTCGTGTCCGACACCGATACGACACCGACACTTGTAATTACACTGAATTATGTCATTTTTTTCAAATTGTGTCGACGTGTCAGTGTCCATGCCGTGTCTGGTGTCTGTGTCTGTATCCTCGCTTCATAGCATATACGTGTAACTAACTAATTTCTTTTGTTCAACAAAATTGTTTCCTTAATTCATCTCTAAAGTGATCAAACAATTCCTACTTTCTAGGTACTTTGTGATTGCAAACTCTATTGTAACTGTCTATGGATTTTTGGTCCTCTTTCTTCCTGCAGAAAGCTTGCTCTGGCGACTTGTGGTCGCCATGGATATGGTAATGTCATAAAGTTAACCTCTTTATCATGCAAGAACTTTTGTACAAGTTTTGTTTCACAAATCGTTAAAATTTGTAACTTGTTTTAATTTATGTTAAGCCAAATTTGAAACATATTTGTTCTTCATGTTTTTAAAATGGAGGTGTTGAAGTTTGAACCCCGATCATAACGTCCGACTTTACAATTTTAGCATTTTTGTTAGTTGAGTTAGGACTTATGAGACTAAATTGACCATTTAAGTCATATAATGTTTGCATAGTTAGTATTTTCCATCCAACTATGTTAAAGAGTTCATACATGGTTGTTAAATGTAGACGTCGTATGTTGTATGTTCAGTTGAGAAAAAAATAATTTAATTAGATTTTTTATCAAAAAACTCAAAATAATTAAAAAAAAAAAATCATCATCTTCACTCCATCACCAACCTTAAATCCATAAAAATAAAACCTTCTCATCTCTCAAACACGCTTAAATATGATGTTTTCAATAAATAACCCTAAGTTTGATCATATAAAATAAAATAATGATTCTAATAAAAACCTATTAGAATACTAGTTATGTCTCGATGGAGATTGAGTCTACAGGAAAAGATTATACTCCCAATGTGTGACTAACCAATGTATGATTTTTTGGCTGAGAGATGTATCCAAGTTTATTGTTTGACGTGTTAAAAAATATATCATCTCCAATGAAATGAAAAAACGAAAAAGAAATGCTAAATTATTATGGTTATGGAACTATAATATTACTTATTGCTTTAATTGATTTTTATGAGCAGGTGTTGACAATGTTACTCATCTCAAGCATCTCTGCAGCTTTGGCTATAGCTCAAGTGGCAAAGAATGGAAACAATTATGCTGCTTGGCTACCGATTTGTGGTTCAGTTCCCAAATTTTGCAATCACATGAGAGGAGCTTTAGTCGCTAGTGTCATTGGAGTCATTATATATTTGATTCTTCTGTTGCATTCCATTCATACTGTCCTTGACCCTCTCCTTTTGAGAAAAACTTGA
Protein sequence

>MS.gene025030.t1

MAKTSRICHLLLRFLAFSATLSAVVVTVSSHEKASFFTVSFEAKYTNSPALKYFVIANSIVTVYGFLVLFLPAESLLWRLVVAMDMVLTMLLISSISAALAIAQVAKNGNNYAAWLPICGSVPKFCNHMRGALVASVIGVIIYLILLLHSIHTVLDPLLLRKT