AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015683

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015683.t1 MTR_8g104890 97.647 170 3 1 1 170 1 169 5.38e-123 343
MS.gene015683.t1 MTR_5g017650 60.227 176 50 3 1 156 1 176 4.81e-68 205
MS.gene015683.t1 MTR_8g104870 63.190 163 42 3 12 156 11 173 1.40e-65 199
MS.gene015683.t1 MTR_4g086330 50.602 166 71 2 14 170 34 197 2.85e-53 168
MS.gene015683.t1 MTR_8g104830 50.714 140 66 3 30 167 4 142 6.17e-43 140
MS.gene015683.t1 MTR_4g086320 56.667 120 51 1 25 144 42 160 1.45e-42 139
MS.gene015683.t1 MTR_2g101660 33.728 169 109 1 5 170 3 171 4.68e-31 110
MS.gene015683.t1 MTR_6g084940 43.066 137 74 3 34 170 17 149 1.39e-29 106
MS.gene015683.t1 MTR_1g075550 53.509 114 52 1 34 147 11 123 4.45e-26 97.1
MS.gene015683.t1 MTR_5g008240 39.416 137 68 4 21 142 27 163 4.01e-24 93.2
MS.gene015683.t1 MTR_5g008240 37.956 137 70 3 21 142 69 205 7.79e-24 93.6
MS.gene015683.t1 MTR_5g008240 37.956 137 70 3 21 142 93 229 9.69e-24 94.0
MS.gene015683.t1 MTR_2g101660 36.585 123 75 1 51 170 1 123 1.04e-23 90.5
MS.gene015683.t1 MTR_7g044840 31.655 139 65 3 28 137 53 190 5.10e-19 81.3
MS.gene015683.t1 MTR_0172s0050 32.414 145 64 4 29 140 57 200 1.02e-15 72.4
MS.gene015683.t1 MTR_3g408350 27.972 143 64 2 29 137 53 190 9.55e-15 69.7
MS.gene015683.t1 MTR_5g008240 40.741 108 49 4 50 142 38 145 1.34e-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.gene015683.t1 AT1G14870 64.626 147 49 3 26 170 7 152 4.68e-63 191
MS.gene015683.t1 AT5G35525 64.029 139 48 2 29 166 10 147 9.47e-60 183
MS.gene015683.t1 AT1G14870 68.067 119 38 0 26 144 7 125 2.07e-57 176
MS.gene015683.t1 AT1G14880 59.864 147 56 3 26 170 6 151 3.62e-55 171
MS.gene015683.t1 AT1G49030 48.428 159 71 4 5 160 66 216 1.10e-45 149
MS.gene015683.t1 AT1G68610 56.934 137 56 2 33 166 17 153 5.91e-45 145
MS.gene015683.t1 AT3G18470 50.388 129 59 1 32 160 2 125 1.06e-42 139
MS.gene015683.t1 AT3G18460 50.685 146 63 4 18 162 42 179 1.24e-42 140
MS.gene015683.t1 AT3G18450 46.358 151 74 3 10 160 33 176 2.10e-42 140
MS.gene015683.t1 AT1G58320 50.413 121 56 3 34 153 16 133 1.15e-36 124
MS.gene015683.t1 AT1G52200 39.535 172 94 4 9 170 19 190 6.11e-34 118
MS.gene015683.t1 AT1G52200 39.583 144 79 2 9 144 19 162 2.17e-28 104
MS.gene015683.t1 AT1G68630 38.298 141 82 2 26 162 16 155 3.10e-28 103
MS.gene015683.t1 AT2G40935 34.028 144 73 4 22 144 34 176 4.90e-22 88.2
MS.gene015683.t1 AT2G40935 34.028 144 73 4 22 144 34 176 4.90e-22 88.2
MS.gene015683.t1 AT2G40935 34.028 144 73 4 22 144 34 176 4.90e-22 88.2
MS.gene015683.t1 AT2G40935 34.028 144 73 4 22 144 34 176 4.90e-22 88.2
MS.gene015683.t1 AT2G40935 34.028 144 73 4 22 144 34 176 4.90e-22 88.2
MS.gene015683.t1 AT2G45010 33.103 145 66 4 28 142 9 152 9.41e-20 82.4
MS.gene015683.t1 AT2G45010 33.103 145 66 4 28 142 55 198 1.27e-19 82.8
MS.gene015683.t1 AT5G51400 30.921 152 73 5 19 140 47 196 1.41e-17 77.4
MS.gene015683.t1 AT2G40935 31.250 144 66 5 22 144 34 165 5.73e-16 72.0
MS.gene015683.t1 AT2G40935 35.345 116 53 4 50 144 38 152 1.32e-14 68.2
MS.gene015683.t1 AT2G40935 35.345 116 53 4 50 144 38 152 1.32e-14 68.2
MS.gene015683.t1 AT2G40935 35.345 116 53 4 50 144 38 152 1.32e-14 68.2

Find 48 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACCATTCCTGGTTGGCATT+AGG 0.310976 4.2:+1642379 None:intergenic
GCCACCAGCCACCGGTTTCC+CGG 0.332845 4.2:-1642422 MS.gene015683:CDS
CCTGGTTGGCATTAGGTTGT+TGG 0.349397 4.2:+1642386 None:intergenic
ATAGACCCGTGGACCATTCC+TGG 0.365914 4.2:+1642368 None:intergenic
CGTGGATTTGACATGGAACT+TGG 0.398558 4.2:-1641861 MS.gene015683:intron
GCCTACGTTCACCGGGAAAC+CGG 0.412709 4.2:+1642411 None:intergenic
ATTTGTTGTGTGACGGGTTG+TGG 0.418139 4.2:-1642020 MS.gene015683:CDS
TGGTGTCCATGCATCACCTT+TGG 0.421844 4.2:-1642202 MS.gene015683:CDS
TGTTGGTGGCCTACGTTCAC+CGG 0.423504 4.2:+1642403 None:intergenic
TTGCAGCTTGTGCTGTAAGC+GGG 0.457897 4.2:-1642058 MS.gene015683:intron
TACATTAATTTGTTGTGTGA+CGG 0.462544 4.2:-1642027 MS.gene015683:CDS
TGCTGGAGCTGTTGGTGCCA+TGG 0.464678 4.2:+1641444 None:intergenic
GTGGCTGATTGTACGGTTGT+TGG 0.466033 4.2:+1642440 None:intergenic
TGTTCAACTGCTGGAGCTGT+TGG 0.477230 4.2:+1641436 None:intergenic
CGAGTCATGTGTTCAACTGC+TGG 0.481564 4.2:+1641427 None:intergenic
ACATTAATTTGTTGTGTGAC+GGG 0.489462 4.2:-1642026 MS.gene015683:CDS
AAATGTGGCACAAGGGAACC+AGG 0.489547 4.2:-1641473 MS.gene015683:CDS
GGTTGGCATTAGGTTGTTGG+TGG 0.517094 4.2:+1642389 None:intergenic
GTGGCTGGTGGCTGATTGTA+CGG 0.517478 4.2:+1642433 None:intergenic
TTGGTGCCATGGCTACTCCC+TGG 0.530182 4.2:+1641455 None:intergenic
AACCTAATGCCAACCAGGAA+TGG 0.530457 4.2:-1642381 MS.gene015683:CDS
GCCAACCAGGAATGGTCCAC+GGG 0.546652 4.2:-1642373 MS.gene015683:CDS
GTTGGTGGCCTACGTTCACC+GGG 0.550874 4.2:+1642404 None:intergenic
TTCACCGGGAAACCGGTGGC+TGG 0.551343 4.2:+1642418 None:intergenic
ACCGGGAAACCGGTGGCTGG+TGG 0.560600 4.2:+1642421 None:intergenic
TACAATCAGCCACCAGCCAC+CGG 0.567328 4.2:-1642430 MS.gene015683:CDS
ATTGCAGCTTGTGCTGTAAG+CGG 0.567979 4.2:-1642059 MS.gene015683:intron
AAATTGGCTATAGGGTGGCA+TGG 0.569669 4.2:-1641496 MS.gene015683:intron
CCAACAACCTAATGCCAACC+AGG 0.574274 4.2:-1642386 MS.gene015683:CDS
TGGCATGGAAATGTGGCACA+AGG 0.574561 4.2:-1641481 MS.gene015683:CDS
TGCCAACCAGGAATGGTCCA+CGG 0.582618 4.2:-1642374 MS.gene015683:CDS
TGCAGCTTGTGCTGTAAGCG+GGG 0.590429 4.2:-1642057 MS.gene015683:intron
AATCTCAGCAATTCGTCCAA+AGG 0.597233 4.2:+1642186 None:intergenic
ATTCGTCCAAAGGTGATGCA+TGG 0.598061 4.2:+1642196 None:intergenic
TGAAAACCGTGGATTTGACA+TGG 0.599587 4.2:-1641868 MS.gene015683:CDS
ACCCGTGGACCATTCCTGGT+TGG 0.600890 4.2:+1642372 None:intergenic
AATTGCTGAGATTGTTGACA+AGG 0.603304 4.2:-1642176 MS.gene015683:CDS
TATAGGGTGGCATGGAAATG+TGG 0.605383 4.2:-1641488 MS.gene015683:intron
AGGGAACCAGGGAGTAGCCA+TGG 0.614002 4.2:-1641461 MS.gene015683:CDS
CAAGTTCCATGTCAAATCCA+CGG 0.615456 4.2:+1641862 None:intergenic
TACGTTCACCGGGAAACCGG+TGG 0.615540 4.2:+1642414 None:intergenic
AATGTGGCACAAGGGAACCA+GGG 0.650557 4.2:-1641472 MS.gene015683:CDS
GGCATGGAAATGTGGCACAA+GGG 0.652763 4.2:-1641480 MS.gene015683:CDS
TGAACTAAGCAATCACAACA+AGG 0.663046 4.2:+1641936 None:intergenic
ATTGCTGAGATTGTTGACAA+GGG 0.678367 4.2:-1642175 MS.gene015683:CDS
ACCGGTTTCCCGGTGAACGT+AGG 0.680377 4.2:-1642412 MS.gene015683:CDS
TATCGTGAGCTTGAAAACCG+TGG 0.692905 4.2:-1641879 MS.gene015683:CDS
GAAGCAGTCAAATAGACCCG+TGG 0.701710 4.2:+1642357 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTATTAAAATTTAGAAG+AGG + chr4.2:1641621-1641640 None:intergenic 10.0%
!! TAGTTATATATCATTATTAA+TGG + chr4.2:1641766-1641785 None:intergenic 10.0%
!!! TAAATTTCATTTCATTTTTT+AGG - chr4.2:1641648-1641667 MS.gene015683:intron 10.0%
!!! TCTCTTAAATTTTTTATTTA+AGG - chr4.2:1642167-1642186 MS.gene015683:CDS 10.0%
!!! ATCTTAATTCTTTTATCTTT+TGG - chr4.2:1642082-1642101 MS.gene015683:intron 15.0%
!! CTTGTAAGATATTCATTAAT+TGG - chr4.2:1641739-1641758 MS.gene015683:intron 20.0%
!! TTAGAAGAGGAATTAATTAA+TGG + chr4.2:1641608-1641627 None:intergenic 20.0%
!!! ATTTATTTGAAATTGGCTAT+AGG - chr4.2:1642381-1642400 MS.gene015683:CDS 20.0%
!!! TTTATTTGAAATTGGCTATA+GGG - chr4.2:1642382-1642401 MS.gene015683:CDS 20.0%
! AAGAGGAATTAATTAATGGA+CGG + chr4.2:1641604-1641623 None:intergenic 25.0%
! GTTCTAATTACCACTTAATT+TGG - chr4.2:1641577-1641596 MS.gene015683:intron 25.0%
!! ATTGTTGTCTCATTTTGTTA+CGG + chr4.2:1641913-1641932 None:intergenic 25.0%
!!! TACATTAATTTGTTGTGTGA+CGG - chr4.2:1641859-1641878 MS.gene015683:intron 25.0%
! TAACATACAAGTTTTGCAGT+CGG + chr4.2:1641556-1641575 None:intergenic 30.0%
! TCGACAATTCAATGTTTCTA+TGG - chr4.2:1642125-1642144 MS.gene015683:intron 30.0%
!! ACATTAATTTGTTGTGTGAC+GGG - chr4.2:1641860-1641879 MS.gene015683:intron 30.0%
!!! TTTTAGGTTGCATAACGTTT+TGG - chr4.2:1641664-1641683 MS.gene015683:intron 30.0%
AATTGCTGAGATTGTTGACA+AGG - chr4.2:1641710-1641729 MS.gene015683:intron 35.0%
ATTGCTGAGATTGTTGACAA+GGG - chr4.2:1641711-1641730 MS.gene015683:intron 35.0%
TGAACTAAGCAATCACAACA+AGG + chr4.2:1641953-1641972 None:intergenic 35.0%
! ATTTGAAATTGGCTATAGGG+TGG - chr4.2:1642385-1642404 MS.gene015683:CDS 35.0%
! GGTTGTTGGAATTTTGAACT+TGG + chr4.2:1641435-1641454 None:intergenic 35.0%
! TGTTGGAATTTTGAACTTGG+AGG + chr4.2:1641432-1641451 None:intergenic 35.0%
AATCTCAGCAATTCGTCCAA+AGG + chr4.2:1641703-1641722 None:intergenic 40.0%
AATGGACGGTCCAAATTAAG+TGG + chr4.2:1641590-1641609 None:intergenic 40.0%
ATTTGTACCATTGTCGCATC+TGG - chr4.2:1642315-1642334 MS.gene015683:intron 40.0%
CAAGTTCCATGTCAAATCCA+CGG + chr4.2:1642027-1642046 None:intergenic 40.0%
TGAAAACCGTGGATTTGACA+TGG - chr4.2:1642018-1642037 MS.gene015683:CDS 40.0%
AAATTGGCTATAGGGTGGCA+TGG - chr4.2:1642390-1642409 MS.gene015683:CDS 45.0%
AACCTAATGCCAACCAGGAA+TGG - chr4.2:1641505-1641524 MS.gene015683:intron 45.0%
AACTCATCCAGATGCGACAA+TGG + chr4.2:1642325-1642344 None:intergenic 45.0%
ATTCGTCCAAAGGTGATGCA+TGG + chr4.2:1641693-1641712 None:intergenic 45.0%
ATTGCAGCTTGTGCTGTAAG+CGG - chr4.2:1641827-1641846 MS.gene015683:intron 45.0%
CGTGGATTTGACATGGAACT+TGG - chr4.2:1642025-1642044 MS.gene015683:CDS 45.0%
TATAGGGTGGCATGGAAATG+TGG - chr4.2:1642398-1642417 MS.gene015683:CDS 45.0%
TATCGTGAGCTTGAAAACCG+TGG - chr4.2:1642007-1642026 MS.gene015683:CDS 45.0%
!! ATTTGTTGTGTGACGGGTTG+TGG - chr4.2:1641866-1641885 MS.gene015683:CDS 45.0%
!!! TTAATTTATTTATTTGAAAT+TGG - chr4.2:1642374-1642393 MS.gene015683:CDS 5.0%
AAATGTGGCACAAGGGAACC+AGG - chr4.2:1642413-1642432 MS.gene015683:CDS 50.0%
AATGTGGCACAAGGGAACCA+GGG - chr4.2:1642414-1642433 MS.gene015683:CDS 50.0%
CCAACAACCTAATGCCAACC+AGG - chr4.2:1641500-1641519 MS.gene015683:intron 50.0%
CGAGTCATGTGTTCAACTGC+TGG + chr4.2:1642462-1642481 None:intergenic 50.0%
GAAGCAGTCAAATAGACCCG+TGG + chr4.2:1641532-1641551 None:intergenic 50.0%
GACCATTCCTGGTTGGCATT+AGG + chr4.2:1641510-1641529 None:intergenic 50.0%
GGCATGGAAATGTGGCACAA+GGG - chr4.2:1642406-1642425 MS.gene015683:CDS 50.0%
GTGGCTGATTGTACGGTTGT+TGG + chr4.2:1641449-1641468 None:intergenic 50.0%
TGGCATGGAAATGTGGCACA+AGG - chr4.2:1642405-1642424 MS.gene015683:CDS 50.0%
TGGTGTCCATGCATCACCTT+TGG - chr4.2:1641684-1641703 MS.gene015683:intron 50.0%
TGTTCAACTGCTGGAGCTGT+TGG + chr4.2:1642453-1642472 None:intergenic 50.0%
TTGCAGCTTGTGCTGTAAGC+GGG - chr4.2:1641828-1641847 MS.gene015683:intron 50.0%
! CCTGGTTGGCATTAGGTTGT+TGG + chr4.2:1641503-1641522 None:intergenic 50.0%
! GGTTGGCATTAGGTTGTTGG+TGG + chr4.2:1641500-1641519 None:intergenic 50.0%
ATAGACCCGTGGACCATTCC+TGG + chr4.2:1641521-1641540 None:intergenic 55.0%
GTGGCTGGTGGCTGATTGTA+CGG + chr4.2:1641456-1641475 None:intergenic 55.0%
TACAATCAGCCACCAGCCAC+CGG - chr4.2:1641456-1641475 MS.gene015683:CDS 55.0%
TGCAGCTTGTGCTGTAAGCG+GGG - chr4.2:1641829-1641848 MS.gene015683:intron 55.0%
TGCCAACCAGGAATGGTCCA+CGG - chr4.2:1641512-1641531 MS.gene015683:intron 55.0%
!! TGTTGGTGGCCTACGTTCAC+CGG + chr4.2:1641486-1641505 None:intergenic 55.0%
ACCCGTGGACCATTCCTGGT+TGG + chr4.2:1641517-1641536 None:intergenic 60.0%
AGGGAACCAGGGAGTAGCCA+TGG - chr4.2:1642425-1642444 MS.gene015683:CDS 60.0%
GCCAACCAGGAATGGTCCAC+GGG - chr4.2:1641513-1641532 MS.gene015683:intron 60.0%
GCCTACGTTCACCGGGAAAC+CGG + chr4.2:1641478-1641497 None:intergenic 60.0%
TACGTTCACCGGGAAACCGG+TGG + chr4.2:1641475-1641494 None:intergenic 60.0%
! ACCGGTTTCCCGGTGAACGT+AGG - chr4.2:1641474-1641493 MS.gene015683:CDS 60.0%
!! GTTGGTGGCCTACGTTCACC+GGG + chr4.2:1641485-1641504 None:intergenic 60.0%
!! TGCTGGAGCTGTTGGTGCCA+TGG + chr4.2:1642445-1642464 None:intergenic 60.0%
!! TTGGTGCCATGGCTACTCCC+TGG + chr4.2:1642434-1642453 None:intergenic 60.0%
TTCACCGGGAAACCGGTGGC+TGG + chr4.2:1641471-1641490 None:intergenic 65.0%
ACCGGGAAACCGGTGGCTGG+TGG + chr4.2:1641468-1641487 None:intergenic 70.0%
!! GCCACCAGCCACCGGTTTCC+CGG - chr4.2:1641464-1641483 MS.gene015683:CDS 70.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 1641423 1642485 1641423 ID=MS.gene015683
chr4.2 mRNA 1641423 1642485 1641423 ID=MS.gene015683.t1;Parent=MS.gene015683
chr4.2 exon 1642341 1642485 1642341 ID=MS.gene015683.t1.exon1;Parent=MS.gene015683.t1
chr4.2 CDS 1642341 1642485 1642341 ID=cds.MS.gene015683.t1;Parent=MS.gene015683.t1
chr4.2 exon 1642167 1642238 1642167 ID=MS.gene015683.t1.exon2;Parent=MS.gene015683.t1
chr4.2 CDS 1642167 1642238 1642167 ID=cds.MS.gene015683.t1;Parent=MS.gene015683.t1
chr4.2 exon 1641862 1642074 1641862 ID=MS.gene015683.t1.exon3;Parent=MS.gene015683.t1
chr4.2 CDS 1641862 1642074 1641862 ID=cds.MS.gene015683.t1;Parent=MS.gene015683.t1
chr4.2 exon 1641423 1641505 1641423 ID=MS.gene015683.t1.exon4;Parent=MS.gene015683.t1
chr4.2 CDS 1641423 1641505 1641423 ID=cds.MS.gene015683.t1;Parent=MS.gene015683.t1
Gene Sequence

>MS.gene015683

ATGAATCCTCCAAGTTCAAAATTCCAACAACCGTACAATCAGCCACCAGCCACCGGTTTCCCGGTGAACGTAGGCCACCAACAACCTAATGCCAACCAGGAATGGTCCACGGGTCTATTTGACTGCTTCTCCGACTGCAAAACTTGTATGTTATGTTCTAATTACCACTTAATTTGGACCGTCCATTAATTAATTCCTCTTCTAAATTTTAATAATTATATATACTAAATTTCATTTCATTTTTTAGGTTGCATAACGTTTTGGTGTCCATGCATCACCTTTGGACGAATTGCTGAGATTGTTGACAAGGGATCAACTTGTAAGATATTCATTAATTGGTCCATTAATAATGATATATAACTATTATATTATACATGTATTAATTATTATATTGTTTGAATTATATTGCAGCTTGTGCTGTAAGCGGGGCTCTATATACATTAATTTGTTGTGTGACGGGTTGTGGTTGTTTATACTCGTGCATCTACCGTAACAAAATGAGACAACAATACATGCTCAAAGACACTCCTTGTTGTGATTGCTTAGTTCATTGTTGTTGTGAATCATGTGCATTATGTCAAGAATATCGTGAGCTTGAAAACCGTGGATTTGACATGGAACTTGGTATGTATATAGTACTATTATTTTGCTCTTCAATAATCTTAATTCTTTTATCTTTTGGTATTCAGTTTTATTCTTTAGTCGACAATTCAATGTTTCTATGGTGCTCTACTTTTAAACGATTCTCTTAAATTTTTTATTTAAGGTCATAGAAATTAAATCACTTTGAAATATATTAGTATTGTACTAGTCAACTTTAATCTTTGAAATTTTCAACGAGAGAGCGATGAGATAAACATGAGTAGAAATAGTTTAAGACACATATTATTTAATTTGTACCATTGTCGCATCTGGATGAGTTTTTTTAATTTTTTTATTACTTGAATCTGTTTAATTTATTTATTTGAAATTGGCTATAGGGTGGCATGGAAATGTGGCACAAGGGAACCAGGGAGTAGCCATGGCACCAACAGCTCCAGCAGTTGAACACATGACTCGTTGA
Protein sequence

>MS.gene015683.t1

MNPPSSKFQQPYNQPPATGFPVNVGHQQPNANQEWSTGLFDCFSDCKTCCITFWCPCITFGRIAEIVDKGSTSCAVSGALYTLICCVTGCGCLYSCIYRNKMRQQYMLKDTPCCDCLVHCCCESCALCQEYRELENRGFDMELGWHGNVAQGNQGVAMAPTAPAVEHMTR