AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0351870

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0351870 MtrunA17_Chr3g0087041 86.905 168 11 1 1 157 1 168 3.01e-80 235
Msa0351870 MtrunA17_Chr3g0087041 76.000 75 14 1 37 107 102 176 2.61e-21 85.5
Msa0351870 MtrunA17_Chr3g0087151 84.177 158 14 1 1 158 1 147 2.94e-72 218
Msa0351870 MtrunA17_Chr3g0087151 67.742 124 23 5 39 155 132 245 2.92e-27 102
Msa0351870 MtrunA17_Chr3g0087151 69.298 114 22 4 32 143 144 246 6.83e-27 101
Msa0351870 MtrunA17_Chr3g0087231 57.488 207 38 4 1 157 1 207 4.51e-54 174
Msa0351870 MtrunA17_Chr3g0087231 57.047 149 30 3 40 156 148 294 1.41e-29 110
Msa0351870 MtrunA17_Chr3g0087231 66.129 124 37 3 35 158 189 307 3.06e-28 107
Msa0351870 MtrunA17_Chr3g0087231 74.468 94 21 2 49 142 247 337 7.85e-26 100
Msa0351870 MtrunA17_Chr3g0087231 70.833 96 22 3 36 128 242 334 1.16e-20 87.0
Msa0351870 MtrunA17_Chr3g0087231 65.517 87 20 3 37 115 254 338 1.64e-15 72.8
Msa0351870 MtrunA17_Chr3g0087211 56.604 212 37 4 1 157 1 212 1.78e-53 173
Msa0351870 MtrunA17_Chr3g0087211 56.757 148 30 3 40 155 153 298 5.00e-28 107
Msa0351870 MtrunA17_Chr3g0087211 58.940 151 26 5 39 157 198 344 1.80e-26 102
Msa0351870 MtrunA17_Chr3g0087211 71.000 100 26 2 49 148 252 348 1.22e-25 100
Msa0351870 MtrunA17_Chr3g0087211 57.143 147 35 5 37 158 169 312 6.28e-22 90.5
Msa0351870 MtrunA17_Chr3g0087211 70.103 97 26 2 46 142 260 353 4.58e-21 88.2
Msa0351870 MtrunA17_Chr3g0087211 68.605 86 22 3 35 120 273 353 1.41e-14 70.1
Msa0351870 MtrunA17_Chr3g0087211 64.474 76 22 2 37 109 281 354 6.12e-12 62.8
Msa0351870 MtrunA17_Chr3g0087161 54.206 107 44 2 1 107 1 102 1.99e-26 97.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0351870 AT5G09530.1 64.029 139 36 4 28 157 32 165 2.81e-34 124
Msa0351870 AT5G09530.1 59.722 144 32 5 35 155 100 240 3.60e-28 107
Msa0351870 AT5G09530.1 64.754 122 35 4 37 155 91 207 1.27e-25 100
Msa0351870 AT5G09530.1 60.870 138 37 5 32 158 179 310 4.19e-25 99.8
Msa0351870 AT5G09530.1 55.333 150 38 6 37 157 201 350 5.67e-22 91.3
Msa0351870 AT5G09530.1 65.138 109 30 5 37 142 262 365 3.95e-21 89.0
Msa0351870 AT5G09530.1 53.896 154 36 6 35 157 171 320 5.68e-21 88.2
Msa0351870 AT5G09530.1 58.462 130 33 7 37 155 240 359 5.26e-20 85.9
Msa0351870 AT5G09530.1 60.465 86 26 2 37 119 290 370 7.00e-15 71.2
Msa0351870 AT5G09520.1 52.273 132 53 3 7 138 9 130 1.32e-29 105

Find 56 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGGGTATCTTTGGAATTTC+TGG 0.088558 3_1:-19336604 None:intergenic
AGCTCAGGTTTGGGCAATTC+AGG 0.197717 3_1:-19336556 None:intergenic
TCAGGTACCTTAGGCAATTC+TGG 0.231204 3_1:-19336397 None:intergenic
AATTCAGGGGCATTAAATTT+AGG 0.233034 3_1:-19336646 None:intergenic
TCAGGTACTTTAGGTAATTC+TGG 0.242157 3_1:-19336430 None:intergenic
AATTCTGGCTTTGGCAATTC+AGG 0.265103 3_1:-19336415 None:intergenic
GACTTTAGGTAGCTCAGGTT+TGG 0.265600 3_1:-19336566 None:intergenic
TTTGGCAATTCGGGTATCTT+TGG 0.268546 3_1:-19336613 None:intergenic
TTTGGAAGTTCAGGTACTTT+AGG 0.279783 3_1:-19336439 None:intergenic
TTTATTTCATGCTCGGGTTT+TGG 0.288588 3_1:-19336670 None:intergenic
ATAGACAATTCGGGGACTTT+AGG 0.311738 3_1:-19336580 None:intergenic
AGTATAGCTAGAATCATTAA+TGG 0.316206 3_1:-19336244 None:intergenic
TTAGGCAATTCAGGAATCTT+AGG 0.318033 3_1:-19336373 None:intergenic
AGCTCGGGCTTTGGAAGTTC+AGG 0.341805 3_1:-19336448 None:intergenic
TTAGGCAACTCAGGAACTTT+GGG 0.343639 3_1:-19336511 None:intergenic
AAGTCGGACTTTGGCAATTC+GGG 0.351787 3_1:-19336622 None:intergenic
ATAGGTGGAAAATCAAGTTT+TGG 0.353325 3_1:-19336334 None:intergenic
ACTTTGGGAAACTCGGGTTT+TGG 0.357337 3_1:-19336496 None:intergenic
TTTAGGCAACTCAGGAACTT+TGG 0.360297 3_1:-19336512 None:intergenic
TATTATTTATTTATATTGAA+TGG 0.364195 3_1:-19336704 None:intergenic
ACTTTAGGTAGCTCAGGTTT+GGG 0.365399 3_1:-19336565 None:intergenic
AATTTCTGGCATAGACAATT+CGG 0.365865 3_1:-19336590 None:intergenic
GGAAGCTCAGGCTTTGGTAT+AGG 0.376080 3_1:-19336352 None:intergenic
TAAGTCGGACTTTGGCAATT+CGG 0.380730 3_1:-19336623 None:intergenic
AATTCTGGCTTAGGCAATTC+AGG 0.383466 3_1:-19336382 None:intergenic
CTCAGGAACTTTGGGAAACT+CGG 0.389158 3_1:-19336503 None:intergenic
ACTTTAGGTAATTCTGGCTT+TGG 0.389572 3_1:-19336424 None:intergenic
ATCTTAGGAAGCTCAGGCTT+TGG 0.394512 3_1:-19336358 None:intergenic
ATTTCTGGCATAGACAATTC+GGG 0.397522 3_1:-19336589 None:intergenic
AACTTAGGTAGCTCGGGCTT+TGG 0.403695 3_1:-19336457 None:intergenic
CAAATTATTTATTTCATGCT+CGG 0.406441 3_1:-19336677 None:intergenic
AGAGTATTACAATGGTTGTC+GGG 0.440611 3_1:+19336275 Msa0351870:CDS
TTTGGCAATTCAGGTACCTT+AGG 0.442441 3_1:-19336406 None:intergenic
AAATTATTTATTTCATGCTC+GGG 0.443514 3_1:-19336676 None:intergenic
AATTTAGGTAAGTCGGACTT+TGG 0.460942 3_1:-19336631 None:intergenic
TCAGGAATCTTAGGAAGCTC+AGG 0.462216 3_1:-19336364 None:intergenic
AACATTAAACTTAGGTAGCT+CGG 0.462347 3_1:-19336464 None:intergenic
TCGGGGACTTTAGGTAGCTC+AGG 0.467048 3_1:-19336571 None:intergenic
TTGGGCAATTCAGGGAACTT+AGG 0.475381 3_1:-19336547 None:intergenic
GACAACCATTGTAATACTCT+TGG 0.484545 3_1:-19336272 None:intergenic
ACCTTAGGCAATTCTGGCTT+AGG 0.484577 3_1:-19336391 None:intergenic
GGCATTAAATTTAGGTAAGT+CGG 0.487607 3_1:-19336638 None:intergenic
AATTCAGGAACATTAAACTT+AGG 0.490699 3_1:-19336472 None:intergenic
ACATTAAACTTAGGTAGCTC+GGG 0.491103 3_1:-19336463 None:intergenic
TTCAGGGAACTTAGGCAACT+CGG 0.499436 3_1:-19336539 None:intergenic
GCTCAGGTTTGGGCAATTCA+GGG 0.523757 3_1:-19336555 None:intergenic
AAGAGTATTACAATGGTTGT+CGG 0.526376 3_1:+19336274 Msa0351870:CDS
TCAGGAACTTTGGGAAACTC+GGG 0.528389 3_1:-19336502 None:intergenic
AGCTCAGGCTTTGGTATAGG+TGG 0.530445 3_1:-19336349 None:intergenic
TGACAAATTGATGTAAGCCA+TGG 0.548467 3_1:-19336209 None:intergenic
TCAGGGAACTTAGGCAACTC+GGG 0.565240 3_1:-19336538 None:intergenic
TTTCTGGCATAGACAATTCG+GGG 0.611978 3_1:-19336588 None:intergenic
GCCTAAGCCAGAATTGCCTA+AGG 0.613699 3_1:+19336390 Msa0351870:CDS
GAGTATTACAATGGTTGTCG+GGG 0.633099 3_1:+19336276 Msa0351870:CDS
GTCAGCCAAGAGTATTACAA+TGG 0.663719 3_1:+19336267 Msa0351870:CDS
TCTAGAGTCGAACATACCTG+AGG 0.701502 3_1:+19336309 Msa0351870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTTATTTCATGCTC+GGG - chr3_1:19336679-19336698 None:intergenic 20.0%
!! CAAATTATTTATTTCATGCT+CGG - chr3_1:19336680-19336699 None:intergenic 20.0%
! AGTATAGCTAGAATCATTAA+TGG - chr3_1:19336247-19336266 None:intergenic 25.0%
! AATTCAGGAACATTAAACTT+AGG - chr3_1:19336475-19336494 None:intergenic 25.0%
!! AAGAGTATTACAATGGTTGT+CGG + chr3_1:19336274-19336293 Msa0351870:CDS 30.0%
! ATAGGTGGAAAATCAAGTTT+TGG - chr3_1:19336337-19336356 None:intergenic 30.0%
AACATTAAACTTAGGTAGCT+CGG - chr3_1:19336467-19336486 None:intergenic 30.0%
!! AATTTCTGGCATAGACAATT+CGG - chr3_1:19336593-19336612 None:intergenic 30.0%
GGCATTAAATTTAGGTAAGT+CGG - chr3_1:19336641-19336660 None:intergenic 30.0%
!! AATTCAGGGGCATTAAATTT+AGG - chr3_1:19336649-19336668 None:intergenic 30.0%
GACAACCATTGTAATACTCT+TGG - chr3_1:19336275-19336294 None:intergenic 35.0%
! AGAGTATTACAATGGTTGTC+GGG + chr3_1:19336275-19336294 Msa0351870:CDS 35.0%
!!! AAATCAAGTTTTGGAACCTC+AGG - chr3_1:19336328-19336347 None:intergenic 35.0%
TTAGGCAATTCAGGAATCTT+AGG - chr3_1:19336376-19336395 None:intergenic 35.0%
!! ACTTTAGGTAATTCTGGCTT+TGG - chr3_1:19336427-19336446 None:intergenic 35.0%
TCAGGTACTTTAGGTAATTC+TGG - chr3_1:19336433-19336452 None:intergenic 35.0%
TTTGGAAGTTCAGGTACTTT+AGG - chr3_1:19336442-19336461 None:intergenic 35.0%
ACATTAAACTTAGGTAGCTC+GGG - chr3_1:19336466-19336485 None:intergenic 35.0%
!! ATTTCTGGCATAGACAATTC+GGG - chr3_1:19336592-19336611 None:intergenic 35.0%
AATTTAGGTAAGTCGGACTT+TGG - chr3_1:19336634-19336653 None:intergenic 35.0%
! TTTATTTCATGCTCGGGTTT+TGG - chr3_1:19336673-19336692 None:intergenic 35.0%
!! GTCAGCCAAGAGTATTACAA+TGG + chr3_1:19336267-19336286 Msa0351870:CDS 40.0%
GAGTATTACAATGGTTGTCG+GGG + chr3_1:19336276-19336295 Msa0351870:CDS 40.0%
!! AATTCTGGCTTAGGCAATTC+AGG - chr3_1:19336385-19336404 None:intergenic 40.0%
TTTGGCAATTCAGGTACCTT+AGG - chr3_1:19336409-19336428 None:intergenic 40.0%
!! AATTCTGGCTTTGGCAATTC+AGG - chr3_1:19336418-19336437 None:intergenic 40.0%
TTAGGCAACTCAGGAACTTT+GGG - chr3_1:19336514-19336533 None:intergenic 40.0%
TTTAGGCAACTCAGGAACTT+TGG - chr3_1:19336515-19336534 None:intergenic 40.0%
! TTAGGCAACTCGGGAATTTT+AGG - chr3_1:19336532-19336551 None:intergenic 40.0%
ACTTTAGGTAGCTCAGGTTT+GGG - chr3_1:19336568-19336587 None:intergenic 40.0%
ATAGACAATTCGGGGACTTT+AGG - chr3_1:19336583-19336602 None:intergenic 40.0%
! TTTCTGGCATAGACAATTCG+GGG - chr3_1:19336591-19336610 None:intergenic 40.0%
!! TCGGGTATCTTTGGAATTTC+TGG - chr3_1:19336607-19336626 None:intergenic 40.0%
TTTGGCAATTCGGGTATCTT+TGG - chr3_1:19336616-19336635 None:intergenic 40.0%
TAAGTCGGACTTTGGCAATT+CGG - chr3_1:19336626-19336645 None:intergenic 40.0%
! TCTAGAGTCGAACATACCTG+AGG + chr3_1:19336309-19336328 Msa0351870:CDS 45.0%
ATCTTAGGAAGCTCAGGCTT+TGG - chr3_1:19336361-19336380 None:intergenic 45.0%
TCAGGAATCTTAGGAAGCTC+AGG - chr3_1:19336367-19336386 None:intergenic 45.0%
!! ACCTTAGGCAATTCTGGCTT+AGG - chr3_1:19336394-19336413 None:intergenic 45.0%
TCAGGTACCTTAGGCAATTC+TGG - chr3_1:19336400-19336419 None:intergenic 45.0%
!! AACTCGGGTTTTGGCAATTC+AGG - chr3_1:19336490-19336509 None:intergenic 45.0%
!! ACTTTGGGAAACTCGGGTTT+TGG - chr3_1:19336499-19336518 None:intergenic 45.0%
! TCAGGAACTTTGGGAAACTC+GGG - chr3_1:19336505-19336524 None:intergenic 45.0%
! CTCAGGAACTTTGGGAAACT+CGG - chr3_1:19336506-19336525 None:intergenic 45.0%
! TCGGGAATTTTAGGCAACTC+AGG - chr3_1:19336523-19336542 None:intergenic 45.0%
TTCAGGGAACTTAGGCAACT+CGG - chr3_1:19336542-19336561 None:intergenic 45.0%
TTGGGCAATTCAGGGAACTT+AGG - chr3_1:19336550-19336569 None:intergenic 45.0%
GACTTTAGGTAGCTCAGGTT+TGG - chr3_1:19336569-19336588 None:intergenic 45.0%
AAGTCGGACTTTGGCAATTC+GGG - chr3_1:19336625-19336644 None:intergenic 45.0%
! AGCTCAGGCTTTGGTATAGG+TGG - chr3_1:19336352-19336371 None:intergenic 50.0%
! GGAAGCTCAGGCTTTGGTAT+AGG - chr3_1:19336355-19336374 None:intergenic 50.0%
GCCTAAGCCAGAATTGCCTA+AGG + chr3_1:19336390-19336409 Msa0351870:CDS 50.0%
AACTTAGGTAGCTCGGGCTT+TGG - chr3_1:19336460-19336479 None:intergenic 50.0%
TCAGGGAACTTAGGCAACTC+GGG - chr3_1:19336541-19336560 None:intergenic 50.0%
GCTCAGGTTTGGGCAATTCA+GGG - chr3_1:19336558-19336577 None:intergenic 50.0%
AGCTCAGGTTTGGGCAATTC+AGG - chr3_1:19336559-19336578 None:intergenic 50.0%
!! CTCGGGTTTTGGCAATTCAG+GGG - chr3_1:19336488-19336507 None:intergenic 50.0%
!! GCTCGGGTTTTGGCAATTCA+GGG - chr3_1:19336663-19336682 None:intergenic 50.0%
!! TGCTCGGGTTTTGGCAATTC+AGG - chr3_1:19336664-19336683 None:intergenic 50.0%
!! AGCTCGGGCTTTGGAAGTTC+AGG - chr3_1:19336451-19336470 None:intergenic 55.0%
TCGGGGACTTTAGGTAGCTC+AGG - chr3_1:19336574-19336593 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 19336211 19336720 19336211 ID=Msa0351870;Name=Msa0351870
chr3_1 mRNA 19336211 19336720 19336211 ID=Msa0351870-mRNA-1;Parent=Msa0351870;Name=Msa0351870-mRNA-1;_AED=0.42;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|169
chr3_1 exon 19336211 19336720 19336211 ID=Msa0351870-mRNA-1:exon:4543;Parent=Msa0351870-mRNA-1
chr3_1 CDS 19336211 19336720 19336211 ID=Msa0351870-mRNA-1:cds;Parent=Msa0351870-mRNA-1
Gene Sequence

>Msa0351870

ATGGCTTACATCAATTTGTCAAAAATTATTTTTCCATTAATGATTCTAGCTATACTGTCAGCCAAGAGTATTACAATGGTTGTCGGGGCACGCAATCTTCTAGAGTCGAACATACCTGAGGTTCCAAAACTTGATTTTCCACCTATACCAAAGCCTGAGCTTCCTAAGATTCCTGAATTGCCTAAGCCAGAATTGCCTAAGGTACCTGAATTGCCAAAGCCAGAATTACCTAAAGTACCTGAACTTCCAAAGCCCGAGCTACCTAAGTTTAATGTTCCTGAATTGCCAAAACCCGAGTTTCCCAAAGTTCCTGAGTTGCCTAAAATTCCCGAGTTGCCTAAGTTCCCTGAATTGCCCAAACCTGAGCTACCTAAAGTCCCCGAATTGTCTATGCCAGAAATTCCAAAGATACCCGAATTGCCAAAGTCCGACTTACCTAAATTTAATGCCCCTGAATTGCCAAAACCCGAGCATGAAATAAATAATTTGATAACCATTCAATATAAATAA
Protein sequence

>Msa0351870

MAYINLSKIIFPLMILAILSAKSITMVVGARNLLESNIPEVPKLDFPPIPKPELPKIPELPKPELPKVPELPKPELPKVPELPKPELPKFNVPELPKPEFPKVPELPKIPELPKFPELPKPELPKVPELSMPEIPKIPELPKSDLPKFNAPELPKPEHEINNLITIQYK*