AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066098


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066098.t1 MTR_4g107840 96.098 205 8 0 8 212 40 244 2.43e-144 402
MS.gene066098.t1 MTR_8g469150 40.566 212 117 3 3 212 72 276 1.46e-46 155
MS.gene066098.t1 MTR_7g009330 41.176 204 111 3 11 212 81 277 7.47e-46 153
MS.gene066098.t1 MTR_8g469150 40.306 196 109 2 3 196 72 261 4.33e-43 146
MS.gene066098.t1 MTR_6g011390 37.209 215 122 4 2 212 73 278 4.50e-42 143
MS.gene066098.t1 MTR_5g015580 27.358 212 145 3 3 212 72 276 1.88e-25 100
MS.gene066098.t1 MTR_1g018205 25.943 212 148 3 3 212 73 277 1.58e-21 89.7
MS.gene066098.t1 MTR_4g128300 29.016 193 129 2 22 212 93 279 3.50e-21 89.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066098.t1 AT3G01280 41.951 205 110 3 10 212 79 276 6.00e-49 161
MS.gene066098.t1 AT5G15090 36.275 204 119 4 11 212 80 274 1.05e-38 135
MS.gene066098.t1 AT5G15090 36.275 204 119 4 11 212 80 274 1.05e-38 135
MS.gene066098.t1 AT5G57490 30.189 212 137 4 3 212 72 274 9.50e-29 108
MS.gene066098.t1 AT5G67500 30.189 212 139 3 3 212 72 276 8.22e-28 106
MS.gene066098.t1 AT5G67500 30.189 212 139 3 3 212 99 303 1.08e-27 107
MS.gene066098.t1 AT5G67500 29.064 203 135 3 3 203 72 267 3.16e-23 95.1
MS.gene066098.t1 AT3G49920 34.127 126 82 1 87 212 102 226 1.10e-15 73.2

Find 58 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCCGGCGAAATGGATTT+TGG 0.152016 8.4:-19354826 MS.gene066098:CDS
ACTGGATGCATTGGATTATT+AGG 0.191506 8.4:-19355416 MS.gene066098:CDS
CTCTCATTCAACAAGGATTT+TGG 0.192793 8.4:-19354867 MS.gene066098:CDS
CGAGCCTTTAGCAATGTTTC+AGG 0.209136 8.4:+19354916 None:intergenic
TTGCAATGGCCGTCTGGGTT+AGG 0.244222 8.4:+19355007 None:intergenic
AATAGATTCACTGGGATTAC+TGG 0.244615 8.4:-19355434 MS.gene066098:CDS
CTTGTGTTGCAATGGCCGTC+TGG 0.310688 8.4:+19355001 None:intergenic
TGCAATGGCCGTCTGGGTTA+GGG 0.312768 8.4:+19355008 None:intergenic
AAGAAATTCTACCTGGATTC+AGG 0.317980 8.4:-19355624 MS.gene066098:CDS
GACCCTGTTGTAAAATTATC+AGG 0.320742 8.4:-19355374 MS.gene066098:CDS
ACAGAATGCTTGTTCCTAAA+AGG 0.329840 8.4:+19355351 None:intergenic
GGGGTTTACTTCATGATAAA+TGG 0.338544 8.4:+19355029 None:intergenic
TAGAATTTCTTGAACTGTAA+TGG 0.369739 8.4:+19355636 None:intergenic
AAAGGCTCGCTTTGACAGTT+CGG 0.382952 8.4:-19354902 MS.gene066098:CDS
TGTAACTATGGCCGGCGAAA+TGG 0.408333 8.4:-19354833 MS.gene066098:CDS
AAGGCTCGCTTTGACAGTTC+GGG 0.409065 8.4:-19354901 MS.gene066098:CDS
AATGGTACCTTCCCGGAGTC+TGG 0.421783 8.4:+19355580 None:intergenic
ACCAAGTTGACTGCTGGCTT+CGG 0.424833 8.4:-19355284 MS.gene066098:CDS
GCAAGGCAACATTGGCTCCT+AGG 0.425523 8.4:+19355327 None:intergenic
ACAAAGTAATGGTACCTTCC+CGG 0.441553 8.4:+19355573 None:intergenic
AGCTTGTCACTCAAGGAAAC+TGG 0.442221 8.4:-19354970 MS.gene066098:CDS
ACTGGGATTACTGGATGCAT+TGG 0.448328 8.4:-19355425 MS.gene066098:CDS
CAGGGTCATATGCTCCATCT+TGG 0.460843 8.4:+19355390 None:intergenic
ACAAGGTCAATGAAGCTTCA+AGG 0.465289 8.4:+19355246 None:intergenic
GCCATGGAGACTCCAACCTT+TGG 0.474824 8.4:+19354784 None:intergenic
CAGTACTTGAATAGATTCAC+TGG 0.475573 8.4:-19355443 MS.gene066098:CDS
AACTTGGTTATCGATCTTGT+TGG 0.497298 8.4:+19355299 None:intergenic
TTTGACAGTTCGGGCAAAGT+AGG 0.498953 8.4:-19354892 MS.gene066098:CDS
GCAATGGCCGTCTGGGTTAG+GGG 0.501382 8.4:+19355009 None:intergenic
CAAGGCAACATTGGCTCCTA+GGG 0.505987 8.4:+19355328 None:intergenic
GCCGAAGCCAGCAGTCAACT+TGG 0.507792 8.4:+19355283 None:intergenic
TTGTGTTGCAATGGCCGTCT+GGG 0.533482 8.4:+19355002 None:intergenic
GGAACAAGCATTCTGTCCCT+AGG 0.535981 8.4:-19355344 MS.gene066098:CDS
AAGGAAACTGGTGTCACCAT+TGG 0.538400 8.4:-19354958 MS.gene066098:CDS
AAATGTACCGTACCAGACTC+CGG 0.544121 8.4:-19355592 MS.gene066098:CDS
CAATGGCCGTCTGGGTTAGG+GGG 0.545151 8.4:+19355010 None:intergenic
TTGAAAACAGTCCTGAATCC+AGG 0.545165 8.4:+19355613 None:intergenic
ACAGTTCAAGAAATTCTACC+TGG 0.548340 8.4:-19355631 MS.gene066098:CDS
TCGATAACCAAGTTGACTGC+TGG 0.549363 8.4:-19355290 MS.gene066098:CDS
GGCCCCAAAATCCATTTCGC+CGG 0.561250 8.4:+19354822 None:intergenic
CGATCTTGTTGGTATGTGCA+AGG 0.562305 8.4:+19355310 None:intergenic
AACCTTTGGAATCTTATCAT+CGG 0.566666 8.4:+19354798 None:intergenic
AAATGCATGCTGAGCACCAA+TGG 0.571123 8.4:+19354942 None:intergenic
GGATTATTAGGAAACCAAGA+TGG 0.572580 8.4:-19355404 MS.gene066098:CDS
TCCAAAGGTTGGAGTCTCCA+TGG 0.577690 8.4:-19354785 MS.gene066098:CDS
ATGCTTCACTTGTGTTGCAA+TGG 0.577920 8.4:+19354993 None:intergenic
GATGATAAGATTCCAAAGGT+TGG 0.579129 8.4:-19354796 MS.gene066098:CDS
AGATTAGGGTCTTAGAGCCA+TGG 0.589733 8.4:+19354768 None:intergenic
AATGTACCGTACCAGACTCC+GGG 0.592748 8.4:-19355591 MS.gene066098:CDS
CTTTGGAATCTTATCATCGG+TGG 0.598433 8.4:+19354801 None:intergenic
GAAGCATAGCTTGTCACTCA+AGG 0.598774 8.4:-19354977 MS.gene066098:CDS
TACCTTCCCGGAGTCTGGTA+CGG 0.603084 8.4:+19355585 None:intergenic
GGTCAATGAAGCTTCAAGGA+AGG 0.612698 8.4:+19355250 None:intergenic
AGTACTTGAATAGATTCACT+GGG 0.614520 8.4:-19355442 MS.gene066098:CDS
TGGTATGTGCAAGGCAACAT+TGG 0.624437 8.4:+19355319 None:intergenic
CACCGATGATAAGATTCCAA+AGG 0.660499 8.4:-19354800 MS.gene066098:CDS
TACCGTACCAGACTCCGGGA+AGG 0.677553 8.4:-19355587 MS.gene066098:intron
GTAGGTGCTCTCATTCAACA+AGG 0.711960 8.4:-19354874 MS.gene066098:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATATTTCATATTATGC+AGG - chr8.4:19355358-19355377 MS.gene066098:CDS 15.0%
!!! ATTTTTCTGATAAATTTAGT+CGG + chr8.4:19355240-19355259 None:intergenic 15.0%
!! AATTTATCAGAAAAATGGAT+AGG - chr8.4:19355244-19355263 MS.gene066098:intron 20.0%
!! GACTAAATTTATCAGAAAAA+TGG - chr8.4:19355239-19355258 MS.gene066098:intron 20.0%
!! TGATACTATACATAGTATAT+AGG + chr8.4:19354896-19354915 None:intergenic 20.0%
! TAGAATTTCTTGAACTGTAA+TGG + chr8.4:19354805-19354824 None:intergenic 25.0%
! TATAGGTAAGTACAAAGTAA+TGG + chr8.4:19354879-19354898 None:intergenic 25.0%
! TATGAATTCATTGTGATTTG+AGG + chr8.4:19354965-19354984 None:intergenic 25.0%
! TCAAATCACAATGAATTCAT+AGG - chr8.4:19354964-19354983 MS.gene066098:CDS 25.0%
!!! TATGATGGATATATCTTACA+AGG + chr8.4:19355212-19355231 None:intergenic 25.0%
AATCACAATGAATTCATAGG+TGG - chr8.4:19354967-19354986 MS.gene066098:CDS 30.0%
AGTACTTGAATAGATTCACT+GGG - chr8.4:19354996-19355015 MS.gene066098:CDS 30.0%
ATTTAGTCGGTAGTTTATGA+TGG + chr8.4:19355227-19355246 None:intergenic 30.0%
! GTAAAATTATCAGGCCTTTT+AGG - chr8.4:19355073-19355092 MS.gene066098:intron 30.0%
! TTTTCCTGAAACATTGCTAA+AGG - chr8.4:19355518-19355537 MS.gene066098:intron 30.0%
!! AACCTTTGGAATCTTATCAT+CGG + chr8.4:19355643-19355662 None:intergenic 30.0%
!!! AGATTTTTTGTAACTATGGC+CGG - chr8.4:19355597-19355616 MS.gene066098:CDS 30.0%
!!! GCAGAGATTTTTTGTAACTA+TGG - chr8.4:19355593-19355612 MS.gene066098:CDS 30.0%
AACTTGGTTATCGATCTTGT+TGG + chr8.4:19355142-19355161 None:intergenic 35.0%
AAGAAATTCTACCTGGATTC+AGG - chr8.4:19354814-19354833 MS.gene066098:CDS 35.0%
AATAGATTCACTGGGATTAC+TGG - chr8.4:19355004-19355023 MS.gene066098:CDS 35.0%
ACAGAATGCTTGTTCCTAAA+AGG + chr8.4:19355090-19355109 None:intergenic 35.0%
ACAGTTCAAGAAATTCTACC+TGG - chr8.4:19354807-19354826 MS.gene066098:CDS 35.0%
ACTGGATGCATTGGATTATT+AGG - chr8.4:19355022-19355041 MS.gene066098:CDS 35.0%
CAGTACTTGAATAGATTCAC+TGG - chr8.4:19354995-19355014 MS.gene066098:CDS 35.0%
GACCCTGTTGTAAAATTATC+AGG - chr8.4:19355064-19355083 MS.gene066098:intron 35.0%
GATGATAAGATTCCAAAGGT+TGG - chr8.4:19355642-19355661 MS.gene066098:CDS 35.0%
GGATTATTAGGAAACCAAGA+TGG - chr8.4:19355034-19355053 MS.gene066098:CDS 35.0%
GGGGTTTACTTCATGATAAA+TGG + chr8.4:19355412-19355431 None:intergenic 35.0%
! AGGCCTGATAATTTTACAAC+AGG + chr8.4:19355070-19355089 None:intergenic 35.0%
! CTCTCATTCAACAAGGATTT+TGG - chr8.4:19355571-19355590 MS.gene066098:intron 35.0%
! GGCCTGATAATTTTACAACA+GGG + chr8.4:19355069-19355088 None:intergenic 35.0%
ACAAAGTAATGGTACCTTCC+CGG + chr8.4:19354868-19354887 None:intergenic 40.0%
ACAAGGTCAATGAAGCTTCA+AGG + chr8.4:19355195-19355214 None:intergenic 40.0%
ATGCTTCACTTGTGTTGCAA+TGG + chr8.4:19355448-19355467 None:intergenic 40.0%
CACCGATGATAAGATTCCAA+AGG - chr8.4:19355638-19355657 MS.gene066098:CDS 40.0%
TTGAAAACAGTCCTGAATCC+AGG + chr8.4:19354828-19354847 None:intergenic 40.0%
!! CTTTGGAATCTTATCATCGG+TGG + chr8.4:19355640-19355659 None:intergenic 40.0%
AAAGGCTCGCTTTGACAGTT+CGG - chr8.4:19355536-19355555 MS.gene066098:intron 45.0%
AAATGCATGCTGAGCACCAA+TGG + chr8.4:19355499-19355518 None:intergenic 45.0%
AAATGTACCGTACCAGACTC+CGG - chr8.4:19354846-19354865 MS.gene066098:CDS 45.0%
ACTGGGATTACTGGATGCAT+TGG - chr8.4:19355013-19355032 MS.gene066098:CDS 45.0%
AGCTTGTCACTCAAGGAAAC+TGG - chr8.4:19355468-19355487 MS.gene066098:intron 45.0%
CGAGCCTTTAGCAATGTTTC+AGG + chr8.4:19355525-19355544 None:intergenic 45.0%
CGATCTTGTTGGTATGTGCA+AGG + chr8.4:19355131-19355150 None:intergenic 45.0%
GGTCAATGAAGCTTCAAGGA+AGG + chr8.4:19355191-19355210 None:intergenic 45.0%
GTAGGTGCTCTCATTCAACA+AGG - chr8.4:19355564-19355583 MS.gene066098:intron 45.0%
TGGTATGTGCAAGGCAACAT+TGG + chr8.4:19355122-19355141 None:intergenic 45.0%
TTTGACAGTTCGGGCAAAGT+AGG - chr8.4:19355546-19355565 MS.gene066098:intron 45.0%
! GAAGCATAGCTTGTCACTCA+AGG - chr8.4:19355461-19355480 MS.gene066098:intron 45.0%
! TCGATAACCAAGTTGACTGC+TGG - chr8.4:19355148-19355167 MS.gene066098:intron 45.0%
!! AAGGAAACTGGTGTCACCAT+TGG - chr8.4:19355480-19355499 MS.gene066098:intron 45.0%
AAGGCTCGCTTTGACAGTTC+GGG - chr8.4:19355537-19355556 MS.gene066098:intron 50.0%
AATGTACCGTACCAGACTCC+GGG - chr8.4:19354847-19354866 MS.gene066098:CDS 50.0%
AGTAAACCCCCTAACCCAGA+CGG - chr8.4:19355422-19355441 MS.gene066098:CDS 50.0%
CAGGGTCATATGCTCCATCT+TGG + chr8.4:19355051-19355070 None:intergenic 50.0%
GGAACAAGCATTCTGTCCCT+AGG - chr8.4:19355094-19355113 MS.gene066098:intron 50.0%
TCCAAAGGTTGGAGTCTCCA+TGG - chr8.4:19355653-19355672 MS.gene066098:CDS 50.0%
TGTAACTATGGCCGGCGAAA+TGG - chr8.4:19355605-19355624 MS.gene066098:CDS 50.0%
TTGTGTTGCAATGGCCGTCT+GGG + chr8.4:19355439-19355458 None:intergenic 50.0%
!! ACCAAGTTGACTGCTGGCTT+CGG - chr8.4:19355154-19355173 MS.gene066098:intron 50.0%
!! ATGGCCGGCGAAATGGATTT+TGG - chr8.4:19355612-19355631 MS.gene066098:CDS 50.0%
!! CAAGGCAACATTGGCTCCTA+GGG + chr8.4:19355113-19355132 None:intergenic 50.0%
!! TGGCCGGCGAAATGGATTTT+GGG - chr8.4:19355613-19355632 MS.gene066098:CDS 50.0%
AATGGTACCTTCCCGGAGTC+TGG + chr8.4:19354861-19354880 None:intergenic 55.0%
CTTGTGTTGCAATGGCCGTC+TGG + chr8.4:19355440-19355459 None:intergenic 55.0%
GCCATGGAGACTCCAACCTT+TGG + chr8.4:19355657-19355676 None:intergenic 55.0%
GGCCCCAAAATCCATTTCGC+CGG + chr8.4:19355619-19355638 None:intergenic 55.0%
TACCTTCCCGGAGTCTGGTA+CGG + chr8.4:19354856-19354875 None:intergenic 55.0%
TGCAATGGCCGTCTGGGTTA+GGG + chr8.4:19355433-19355452 None:intergenic 55.0%
TTGCAATGGCCGTCTGGGTT+AGG + chr8.4:19355434-19355453 None:intergenic 55.0%
!! GCAAGGCAACATTGGCTCCT+AGG + chr8.4:19355114-19355133 None:intergenic 55.0%
!! GGCCGGCGAAATGGATTTTG+GGG - chr8.4:19355614-19355633 MS.gene066098:CDS 55.0%
GCCGAAGCCAGCAGTCAACT+TGG + chr8.4:19355158-19355177 None:intergenic 60.0%
TACCGTACCAGACTCCGGGA+AGG - chr8.4:19354851-19354870 MS.gene066098:CDS 60.0%
! CAATGGCCGTCTGGGTTAGG+GGG + chr8.4:19355431-19355450 None:intergenic 60.0%
! GCAATGGCCGTCTGGGTTAG+GGG + chr8.4:19355432-19355451 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 19354771 19355689 19354771 ID=MS.gene066098
chr8.4 mRNA 19354771 19355689 19354771 ID=MS.gene066098.t1;Parent=MS.gene066098
chr8.4 exon 19355588 19355689 19355588 ID=MS.gene066098.t1.exon1;Parent=MS.gene066098.t1
chr8.4 CDS 19355588 19355689 19355588 ID=cds.MS.gene066098.t1;Parent=MS.gene066098.t1
chr8.4 exon 19355248 19355474 19355248 ID=MS.gene066098.t1.exon2;Parent=MS.gene066098.t1
chr8.4 CDS 19355248 19355474 19355248 ID=cds.MS.gene066098.t1;Parent=MS.gene066098.t1
chr8.4 exon 19354771 19355080 19354771 ID=MS.gene066098.t1.exon3;Parent=MS.gene066098.t1
chr8.4 CDS 19354771 19355080 19354771 ID=cds.MS.gene066098.t1;Parent=MS.gene066098.t1
Gene Sequence

>MS.gene066098

ATGTCTGACTGTAGTGCTTTTGCTGCTGTATCCATTACAGTTCAAGAAATTCTACCTGGATTCAGGACTGTTTTCAAATGTACCGTACCAGACTCCGGGAAGGTACCATTACTTTGTACTTACCTATATACTATGTATAGTATCATCTTTAATAGTTTTAGTGTTTTTTTGTTCATTGCATCTGAGTATTTCCTCAAATCACAATGAATTCATAGGTGGAACTACAGTACTTGAATAGATTCACTGGGATTACTGGATGCATTGGATTATTAGGAAACCAAGATGGAGCATATGACCCTGTTGTAAAATTATCAGGCCTTTTAGGAACAAGCATTCTGTCCCTAGGAGCCAATGTTGCCTTGCACATACCAACAAGATCGATAACCAAGTTGACTGCTGGCTTCGGCTTAAACACTGCCTTCCTTGAAGCTTCATTGACCTTGTAAGATATATCCATCATAAACTACCGACTAAATTTATCAGAAAAATGGATAGGAATATCAATTAGTGATCTCTAAACTAACTTTAGCATTTAATTAATCATTACTGCTTAGTGTTCTGCTACTGTTTCTTTTGTCGAGCTTGAATTAAATATTTCATATTATGCAGGCATGACAGCTTTGACACTCTAAAAGCGACCATTTATCATGAAGTAAACCCCCTAACCCAGACGGCCATTGCAACACAAGTGAAGCATAGCTTGTCACTCAAGGAAACTGGTGTCACCATTGGTGCTCAGCATGCATTTTTTCCTGAAACATTGCTAAAGGCTCGCTTTGACAGTTCGGGCAAAGTAGGTGCTCTCATTCAACAAGGATTTTGGCAGAGATTTTTTGTAACTATGGCCGGCGAAATGGATTTTGGGGCCACCGATGATAAGATTCCAAAGGTTGGAGTCTCCATGGCTCTAAGACCCTAA

Protein sequence

>MS.gene066098.t1

MSDCSAFAAVSITVQEILPGFRTVFKCTVPDSGKVELQYLNRFTGITGCIGLLGNQDGAYDPVVKLSGLLGTSILSLGANVALHIPTRSITKLTAGFGLNTAFLEASLTLHDSFDTLKATIYHEVNPLTQTAIATQVKHSLSLKETGVTIGAQHAFFPETLLKARFDSSGKVGALIQQGFWQRFFVTMAGEMDFGATDDKIPKVGVSMALRP