AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034164

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034164.t1 MTR_4g008070 79.439 107 7 1 1 107 1 92 3.79e-57 173
MS.gene034164.t1 MTR_3g100050 53.659 82 24 3 1 79 164 234 1.46e-18 80.5
MS.gene034164.t1 MTR_5g066510 53.659 82 24 4 1 79 167 237 5.55e-18 78.6
MS.gene034164.t1 MTR_4g093730 49.367 79 33 2 1 79 140 211 6.72e-16 73.6
MS.gene034164.t1 MTR_3g100040 46.914 81 34 3 1 79 59 132 1.36e-15 71.6
MS.gene034164.t1 MTR_3g100040 46.914 81 34 3 1 79 163 236 1.52e-15 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034164.t1 AT1G51600 64.557 79 28 0 1 79 179 257 9.48e-30 110
MS.gene034164.t1 AT1G51600 64.557 79 28 0 1 79 179 257 9.48e-30 110
MS.gene034164.t1 AT3G21175 58.228 79 33 0 1 79 175 253 8.43e-27 102
MS.gene034164.t1 AT3G21175 58.228 79 33 0 1 79 173 251 9.05e-27 102
MS.gene034164.t1 AT4G24470 53.165 79 29 2 1 79 178 248 3.24e-20 85.1
MS.gene034164.t1 AT4G24470 53.165 79 29 2 1 79 178 248 3.83e-20 84.7
MS.gene034164.t1 AT4G24470 53.165 79 29 2 1 79 178 248 3.83e-20 84.7

Find 39 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGACTTCTGTGGGCAAATA+AGG 0.252080 4.3:+87463450 MS.gene034164:CDS
CAGAGGGTTCTTGGCCCTTC+AGG 0.272302 4.3:-87463418 None:intergenic
CAAGCATTGCAGAGGGTTCT+TGG 0.288221 4.3:-87463427 None:intergenic
TTCTGTTCGTAGCCATTGAC+TGG 0.328675 4.3:+87463896 MS.gene034164:intron
TTTAGGATGCAAAGAAATAA+AGG 0.333460 4.3:+87463052 None:intergenic
CGGAACAAGTGAAGGTTTGA+TGG 0.376343 4.3:+87463132 MS.gene034164:CDS
TCAGGTCCACGCCGCATCAT+TGG 0.388420 4.3:-87463400 None:intergenic
TTCCTGCAAATCTGAAAAGA+AGG 0.433348 4.3:-87463933 None:intergenic
CTTACACATTATCTTGCTGT+TGG 0.460419 4.3:-87463171 None:intergenic
AGACTCATCATGGTTGGACT+TGG 0.463495 4.3:-87463089 None:intergenic
TTACACATTATCTTGCTGTT+GGG 0.464252 4.3:-87463170 None:intergenic
TGGACTTGGCAGATGTAAAT+CGG 0.465549 4.3:-87463075 None:intergenic
CAGCCGATGCAGACTCATCA+TGG 0.498772 4.3:-87463099 None:intergenic
AATGGGAGGTAGTAGAAGAC+TGG 0.501501 4.3:+87463957 MS.gene034164:CDS
CAATGCTTGTGGACTTCTGT+GGG 0.512002 4.3:+87463441 MS.gene034164:CDS
GCAATGCTTGTGGACTTCTG+TGG 0.515681 4.3:+87463440 MS.gene034164:CDS
TAGATATGCCACTCTTAGCA+CGG 0.532965 4.3:-87464464 None:intergenic
ATGATGCGGCGTGGACCTGA+AGG 0.535411 4.3:+87463403 MS.gene034164:CDS
CCAGGTTTAATAGTGCTAGC+AGG 0.536807 4.3:-87464381 None:intergenic
AGAACCCTCTGCAATGCTTG+TGG 0.537519 4.3:+87463430 MS.gene034164:CDS
ATGAATTGCGGAACAAGTGA+AGG 0.546961 4.3:+87463124 MS.gene034164:CDS
AAGACTGGGCGTACAACCTA+AGG 0.553754 4.3:+87463972 MS.gene034164:CDS
TCTGTTCGTAGCCATTGACT+GGG 0.562926 4.3:+87463897 MS.gene034164:intron
TGAAACATAAGCCCAGTCAA+TGG 0.568944 4.3:-87463908 None:intergenic
AGATATGCCACTCTTAGCAC+GGG 0.573650 4.3:-87464463 None:intergenic
CCTGCTAGCACTATTAAACC+TGG 0.574351 4.3:+87464381 MS.gene034164:CDS
CGATGCAGACTCATCATGGT+TGG 0.584481 4.3:-87463095 None:intergenic
CAACCATGATGAGTCTGCAT+CGG 0.601385 4.3:+87463096 MS.gene034164:CDS
TGATGCGGCGTGGACCTGAA+GGG 0.602634 4.3:+87463404 MS.gene034164:CDS
AACAAATTGCAGAGTCCTAG+CGG 0.614428 4.3:+87464417 MS.gene034164:CDS
ATTGCAGAGTCCTAGCGGAT+CGG 0.615186 4.3:+87464422 MS.gene034164:CDS
AGAAGTGCACGCCAATGATG+CGG 0.629029 4.3:+87463389 MS.gene034164:CDS
ATGGGAGGTAGTAGAAGACT+GGG 0.636419 4.3:+87463958 MS.gene034164:CDS
ATTCAAACCCGTGCTAAGAG+TGG 0.636777 4.3:+87464456 MS.gene034164:CDS
GCATCGGCTGAAATGAATTG+CGG 0.643791 4.3:+87463112 MS.gene034164:CDS
GAAGTCCACAAGCATTGCAG+AGG 0.650799 4.3:-87463435 None:intergenic
TGCACGCCAATGATGCGGCG+TGG 0.659677 4.3:+87463394 MS.gene034164:CDS
AAGTCCACAAGCATTGCAGA+GGG 0.669436 4.3:-87463434 None:intergenic
GGTTTGATGGCAGACAACGA+TGG 0.718774 4.3:+87463145 MS.gene034164:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAATTTTTTTATTTTATA+CGG - chr4.3:87463604-87463623 None:intergenic 0.0%
!! ATTAACCAATAATAATTGTA+TGG - chr4.3:87463538-87463557 None:intergenic 15.0%
!! CCATTTATCAAATAATATAA+AGG - chr4.3:87463324-87463343 None:intergenic 15.0%
!! CCTTTATATTATTTGATAAA+TGG + chr4.3:87463321-87463340 MS.gene034164:intron 15.0%
!! GTATTCTAATCTATATATTA+TGG + chr4.3:87463236-87463255 MS.gene034164:intron 15.0%
!! TATTGACAAAATTAAGAAGT+TGG + chr4.3:87464178-87464197 MS.gene034164:intron 20.0%
!!! CTTGAAAATAAAGTCTTATT+TGG + chr4.3:87463271-87463290 MS.gene034164:intron 20.0%
!!! TTATTGGTTAATCATGATTT+TGG + chr4.3:87463546-87463565 MS.gene034164:intron 20.0%
! ATAAAGGACAATTTCAGTAT+AGG - chr4.3:87463308-87463327 None:intergenic 25.0%
! ATATGCATAAGTTGTTAGTT+GGG + chr4.3:87464025-87464044 MS.gene034164:intron 25.0%
! ATCAAAAGCTTAAACTAACT+TGG - chr4.3:87464310-87464329 None:intergenic 25.0%
! TATATGCATAAGTTGTTAGT+TGG + chr4.3:87464024-87464043 MS.gene034164:intron 25.0%
! TTATGTTTATTAATTCCACC+TGG + chr4.3:87463708-87463727 MS.gene034164:intron 25.0%
! TTGCTCCATACAATTATTAT+TGG + chr4.3:87463530-87463549 MS.gene034164:intron 25.0%
!!! ACTGGTTTATTTTTGAACAA+GGG + chr4.3:87463197-87463216 MS.gene034164:intron 25.0%
AAATGTGAAGATGCATAAAC+AGG - chr4.3:87463812-87463831 None:intergenic 30.0%
AAGATAATGTGTAAGTAGAC+TGG + chr4.3:87463179-87463198 MS.gene034164:intron 30.0%
AATGTGAAGATGCATAAACA+GGG - chr4.3:87463811-87463830 None:intergenic 30.0%
ACAAAATTAAGAAGTTGGAG+AGG + chr4.3:87464183-87464202 MS.gene034164:intron 30.0%
ACAATTCCATCCAATATTGA+TGG + chr4.3:87464079-87464098 MS.gene034164:intron 30.0%
ATAATTGTATGGAGCAACAT+TGG - chr4.3:87463527-87463546 None:intergenic 30.0%
CAAAATTAAGAAGTTGGAGA+GGG + chr4.3:87464184-87464203 MS.gene034164:intron 30.0%
CAACTTATGCATATAACCTT+AGG - chr4.3:87464019-87464038 None:intergenic 30.0%
CCTCAACAAAAAAAAACCTA+AGG + chr4.3:87464000-87464019 MS.gene034164:intron 30.0%
TATGCATAAGTTGTTAGTTG+GGG + chr4.3:87464026-87464045 MS.gene034164:intron 30.0%
TCACAATGACAGATAAATGA+GGG - chr4.3:87463647-87463666 None:intergenic 30.0%
TCATTGTGAATGTGTTAAAG+TGG + chr4.3:87463658-87463677 MS.gene034164:intron 30.0%
TTCACAATGACAGATAAATG+AGG - chr4.3:87463648-87463667 None:intergenic 30.0%
TTCAGATTTGCAGGAAAAAT+GGG + chr4.3:87463940-87463959 MS.gene034164:CDS 30.0%
TTTCAACTCATATCAGTTGT+AGG + chr4.3:87463350-87463369 MS.gene034164:intron 30.0%
TTTCAGATTTGCAGGAAAAA+TGG + chr4.3:87463939-87463958 MS.gene034164:CDS 30.0%
! TTTTGTTGAGGTATAACCTT+AGG - chr4.3:87463991-87464010 None:intergenic 30.0%
!! AAGCACTTTAGGAATGATTT+TGG + chr4.3:87464136-87464155 MS.gene034164:intron 30.0%
!! TTACACATTATCTTGCTGTT+GGG - chr4.3:87463173-87463192 None:intergenic 30.0%
!!! CCTTAGGTTTTTTTTTGTTG+AGG - chr4.3:87464003-87464022 None:intergenic 30.0%
!!! GACTGGTTTATTTTTGAACA+AGG + chr4.3:87463196-87463215 MS.gene034164:intron 30.0%
AACGAAGAACTTACTCATGA+TGG + chr4.3:87464208-87464227 MS.gene034164:intron 35.0%
AGACGAGAAGAAACAATGAA+GGG - chr4.3:87463778-87463797 None:intergenic 35.0%
AGATAAATGAGGGGAAAAAG+TGG - chr4.3:87463637-87463656 None:intergenic 35.0%
AGCAACATTGGAAAAACGAA+AGG - chr4.3:87463515-87463534 None:intergenic 35.0%
ATTCCATCCAATATTGATGG+TGG + chr4.3:87464082-87464101 MS.gene034164:intron 35.0%
CACAATGACAGATAAATGAG+GGG - chr4.3:87463646-87463665 None:intergenic 35.0%
CCTGTAATATTGAGCCAATT+CGG + chr4.3:87463571-87463590 MS.gene034164:intron 35.0%
TGCTTCATCTTCTACTGAAT+CGG + chr4.3:87463855-87463874 MS.gene034164:intron 35.0%
TTCCTGCAAATCTGAAAAGA+AGG - chr4.3:87463936-87463955 None:intergenic 35.0%
TTGCAACATACGTGAAATGA+AGG + chr4.3:87464105-87464124 MS.gene034164:intron 35.0%
! ATATTGAGCCAATTCGGTTT+TGG + chr4.3:87463577-87463596 MS.gene034164:intron 35.0%
! CGAATTGGCTCAATATTACA+GGG - chr4.3:87463573-87463592 None:intergenic 35.0%
! CTTACACATTATCTTGCTGT+TGG - chr4.3:87463174-87463193 None:intergenic 35.0%
! GTTAAAGTGGCATACTGATT+TGG + chr4.3:87463671-87463690 MS.gene034164:intron 35.0%
!!! AGGTTTTTCTGAAGCACTTT+AGG + chr4.3:87464125-87464144 MS.gene034164:intron 35.0%
!!! TTGTTTTTGCTTTTTCTGCC+AGG - chr4.3:87464402-87464421 None:intergenic 35.0%
AACAAATTGCAGAGTCCTAG+CGG + chr4.3:87464417-87464436 MS.gene034164:CDS 40.0%
ACAATGAAGGGGAAGATGAA+TGG - chr4.3:87463766-87463785 None:intergenic 40.0%
AGATTTGCAGGAAAAATGGG+AGG + chr4.3:87463943-87463962 MS.gene034164:CDS 40.0%
ATGAATTGCGGAACAAGTGA+AGG + chr4.3:87463124-87463143 MS.gene034164:CDS 40.0%
CAACCACCATCAATATTGGA+TGG - chr4.3:87464088-87464107 None:intergenic 40.0%
CTGTGGGCAAATAAGGTAAA+CGG + chr4.3:87463457-87463476 MS.gene034164:intron 40.0%
CTTCTTCTTCCTCTTGGTTT+AGG + chr4.3:87463735-87463754 MS.gene034164:intron 40.0%
GACGAGAAGAAACAATGAAG+GGG - chr4.3:87463777-87463796 None:intergenic 40.0%
GAGACGAGAAGAAACAATGA+AGG - chr4.3:87463779-87463798 None:intergenic 40.0%
GTTGCAACCACCATCAATAT+TGG - chr4.3:87464092-87464111 None:intergenic 40.0%
TAGATATGCCACTCTTAGCA+CGG - chr4.3:87464467-87464486 None:intergenic 40.0%
TATACGGACCAAAACCGAAT+TGG - chr4.3:87463588-87463607 None:intergenic 40.0%
TCATCTTCTACTGAATCGGA+TGG + chr4.3:87463859-87463878 MS.gene034164:intron 40.0%
TGAAACATAAGCCCAGTCAA+TGG - chr4.3:87463911-87463930 None:intergenic 40.0%
TGGACTTGGCAGATGTAAAT+CGG - chr4.3:87463078-87463097 None:intergenic 40.0%
TGTGGGCAAATAAGGTAAAC+GGG + chr4.3:87463458-87463477 MS.gene034164:intron 40.0%
! CCGAATTGGCTCAATATTAC+AGG - chr4.3:87463574-87463593 None:intergenic 40.0%
! TGCCTTCTTTTCAGATTTGC+AGG + chr4.3:87463931-87463950 MS.gene034164:CDS 40.0%
!! TGATGGCTTTGATGATGTCT+TGG + chr4.3:87464225-87464244 MS.gene034164:intron 40.0%
AATGGGAGGTAGTAGAAGAC+TGG + chr4.3:87463957-87463976 MS.gene034164:CDS 45.0%
AGACTCATCATGGTTGGACT+TGG - chr4.3:87463092-87463111 None:intergenic 45.0%
AGAGGAAGAAGAAGAATGCC+AGG - chr4.3:87463729-87463748 None:intergenic 45.0%
AGATATGCCACTCTTAGCAC+GGG - chr4.3:87464466-87464485 None:intergenic 45.0%
ATGGGAGGTAGTAGAAGACT+GGG + chr4.3:87463958-87463977 MS.gene034164:CDS 45.0%
ATGGTCGAACCTAAACCAAG+AGG - chr4.3:87463747-87463766 None:intergenic 45.0%
ATTCAAACCCGTGCTAAGAG+TGG + chr4.3:87464456-87464475 MS.gene034164:CDS 45.0%
CAACCATGATGAGTCTGCAT+CGG + chr4.3:87463096-87463115 MS.gene034164:CDS 45.0%
CAATGCTTGTGGACTTCTGT+GGG + chr4.3:87463441-87463460 MS.gene034164:CDS 45.0%
CCAGGTTTAATAGTGCTAGC+AGG - chr4.3:87464384-87464403 None:intergenic 45.0%
CCTGCTAGCACTATTAAACC+TGG + chr4.3:87464381-87464400 MS.gene034164:CDS 45.0%
CGGAACAAGTGAAGGTTTGA+TGG + chr4.3:87463132-87463151 MS.gene034164:CDS 45.0%
GGCATTCTTCTTCTTCCTCT+TGG + chr4.3:87463729-87463748 MS.gene034164:intron 45.0%
TGGACTTCTGTGGGCAAATA+AGG + chr4.3:87463450-87463469 MS.gene034164:CDS 45.0%
TTCTGTTCGTAGCCATTGAC+TGG + chr4.3:87463896-87463915 MS.gene034164:intron 45.0%
! AAGTCCACAAGCATTGCAGA+GGG - chr4.3:87463437-87463456 None:intergenic 45.0%
! TCTGTTCGTAGCCATTGACT+GGG + chr4.3:87463897-87463916 MS.gene034164:intron 45.0%
!! GCATCGGCTGAAATGAATTG+CGG + chr4.3:87463112-87463131 MS.gene034164:CDS 45.0%
AAGACTGGGCGTACAACCTA+AGG + chr4.3:87463972-87463991 MS.gene034164:CDS 50.0%
AGAACCCTCTGCAATGCTTG+TGG + chr4.3:87463430-87463449 MS.gene034164:CDS 50.0%
CGATGCAGACTCATCATGGT+TGG - chr4.3:87463098-87463117 None:intergenic 50.0%
GCAATGCTTGTGGACTTCTG+TGG + chr4.3:87463440-87463459 MS.gene034164:CDS 50.0%
GGAAGAAGAAGAATGCCAGG+TGG - chr4.3:87463726-87463745 None:intergenic 50.0%
! AGAAGTGCACGCCAATGATG+CGG + chr4.3:87463389-87463408 MS.gene034164:CDS 50.0%
! ATTGCAGAGTCCTAGCGGAT+CGG + chr4.3:87464422-87464441 MS.gene034164:CDS 50.0%
! CAAGCATTGCAGAGGGTTCT+TGG - chr4.3:87463430-87463449 None:intergenic 50.0%
! CACTCATTTTCCGATCCGCT+AGG - chr4.3:87464435-87464454 None:intergenic 50.0%
! GAAGTCCACAAGCATTGCAG+AGG - chr4.3:87463438-87463457 None:intergenic 50.0%
! GGTTTGATGGCAGACAACGA+TGG + chr4.3:87463145-87463164 MS.gene034164:CDS 50.0%
CAGCCGATGCAGACTCATCA+TGG - chr4.3:87463102-87463121 None:intergenic 55.0%
ATGATGCGGCGTGGACCTGA+AGG + chr4.3:87463403-87463422 MS.gene034164:CDS 60.0%
CAGAGGGTTCTTGGCCCTTC+AGG - chr4.3:87463421-87463440 None:intergenic 60.0%
TCAGGTCCACGCCGCATCAT+TGG - chr4.3:87463403-87463422 None:intergenic 60.0%
TGATGCGGCGTGGACCTGAA+GGG + chr4.3:87463404-87463423 MS.gene034164:CDS 60.0%
TGCACGCCAATGATGCGGCG+TGG + chr4.3:87463394-87463413 MS.gene034164:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 87463058 87464503 87463058 ID=MS.gene034164
chr4.3 mRNA 87463058 87464503 87463058 ID=MS.gene034164.t1;Parent=MS.gene034164
chr4.3 exon 87463058 87463188 87463058 ID=MS.gene034164.t1.exon1;Parent=MS.gene034164.t1
chr4.3 CDS 87463058 87463188 87463058 ID=cds.MS.gene034164.t1;Parent=MS.gene034164.t1
chr4.3 exon 87463366 87463471 87463366 ID=MS.gene034164.t1.exon2;Parent=MS.gene034164.t1
chr4.3 CDS 87463366 87463471 87463366 ID=cds.MS.gene034164.t1;Parent=MS.gene034164.t1
chr4.3 exon 87463908 87463993 87463908 ID=MS.gene034164.t1.exon3;Parent=MS.gene034164.t1
chr4.3 CDS 87463908 87463993 87463908 ID=cds.MS.gene034164.t1;Parent=MS.gene034164.t1
chr4.3 exon 87464365 87464503 87464365 ID=MS.gene034164.t1.exon4;Parent=MS.gene034164.t1
chr4.3 CDS 87464365 87464503 87464365 ID=cds.MS.gene034164.t1;Parent=MS.gene034164.t1
Gene Sequence

>MS.gene034164

ATGCAAAGAAATAAAGGCCGATTTACATCTGCCAAGTCCAACCATGATGAGTCTGCATCGGCTGAAATGAATTGCGGAACAAGTGAAGGTTTGATGGCAGACAACGATGGATCCCAACAGCAAGATAATGTGTAAGTAGACTGGTTTATTTTTGAACAAGGGAAGAAAAACTGAATGAGTATTCTAATCTATATATTATGGTTGACTTGATAGCTTGAAAATAAAGTCTTATTTGGAAAGATTTCAACCTATACTGAAATTGTCCTTTATATTATTTGATAAATGGTCTTTCTTTCAACTCATATCAGTTGTAGGCATTGTAACATCAGTGAGAAGTGCACGCCAATGATGCGGCGTGGACCTGAAGGGCCAAGAACCCTCTGCAATGCTTGTGGACTTCTGTGGGCAAATAAGGTAAACGGGAACTATGTTAATTATTCATGTCAATTGTTATCCTTTCGTTTTTCCAATGTTGCTCCATACAATTATTATTGGTTAATCATGATTTTGGTCCCTGTAATATTGAGCCAATTCGGTTTTGGTCCGTATAAAATAAAAAAATTATATTACATTTCTCCACTTTTTCCCCTCATTTATCTGTCATTGTGAATGTGTTAAAGTGGCATACTGATTTGGAATATATCATTATTTTATGTTTATTAATTCCACCTGGCATTCTTCTTCTTCCTCTTGGTTTAGGTTCGACCATTCATCTTCCCCTTCATTGTTTCTTCTCGTCTCTACTTCAAACCCTGTTTATGCATCTTCACATTTCTGCTTCATCGTCATCACGTTTCTGCTTCATCTTCTACTGAATCGGATGGCTAATGTTAACGATTTCTGTTCGTAGCCATTGACTGGGCTTATGTTTCATGCCTTCTTTTCAGATTTGCAGGAAAAATGGGAGGTAGTAGAAGACTGGGCGTACAACCTAAGGTTATACCTCAACAAAAAAAAACCTAAGGTTATATGCATAAGTTGTTAGTTGGGGTGATGAATTTGACGTTGTTAATGAATAAATACAATTCCATCCAATATTGATGGTGGTTGCAACATACGTGAAATGAAGGTTTTTCTGAAGCACTTTAGGAATGATTTTGGAAAAGAATTTGTCAAAGAATATTGACAAAATTAAGAAGTTGGAGAGGGAAACGAAGAACTTACTCATGATGGCTTTGATGATGTCTTGGATTTTTACAAGTCAATGTAATTTGTTGTGTATTTTAATTTTTTTTATGTCTGTAACAATCCAAGTTAGTTTAAGCTTTTGATGTTGTTGATGTTAAATGTTATGTATGCTTTGTGAGTTATGTAAGTTTTGAACCTGCTAGCACTATTAAACCTGGCAGAAAAAGCAAAAACAAATTGCAGAGTCCTAGCGGATCGGAAAATGAGTGCATTCAAACCCGTGCTAAGAGTGGCATATCTAAAGCTTATAAATCATGA
Protein sequence

>MS.gene034164.t1

MQRNKGRFTSAKSNHDESASAEMNCGTSEGLMADNDGSQQQDNVCRHCNISEKCTPMMRRGPEGPRTLCNACGLLWANKPLTGLMFHAFFSDLQEKWEVVEDWAYNLSYVSFEPASTIKPGRKSKNKLQSPSGSENECIQTRAKSGISKAYKS