AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1432610

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1432610 MtrunA17_Chr1g0190231 97.802 182 4 0 1 182 1 182 1.88e-133 370
Msa1432610 MtrunA17_Chr5g0431211 79.433 141 28 1 31 170 28 168 2.91e-83 245
Msa1432610 MtrunA17_Chr7g0274631 64.865 185 47 6 1 182 1 170 3.33e-79 233
Msa1432610 MtrunA17_Chr1g0167411 83.200 125 21 0 40 164 65 189 4.12e-79 234
Msa1432610 MtrunA17_Chr4g0051251 73.333 135 36 0 35 169 41 175 3.59e-76 228
Msa1432610 MtrunA17_Chr1g0187671 79.710 138 28 0 32 169 45 182 8.04e-74 220
Msa1432610 MtrunA17_Chr7g0261381 81.203 133 25 0 37 169 61 193 1.19e-71 215
Msa1432610 MtrunA17_Chr3g0105921 63.736 182 63 2 1 179 1 182 1.35e-70 213
Msa1432610 MtrunA17_Chr1g0183761 81.538 130 24 0 40 169 45 174 2.86e-70 212
Msa1432610 MtrunA17_Chr2g0325831 68.056 144 46 0 20 163 3 146 4.41e-70 209
Msa1432610 MtrunA17_Chr2g0283861 63.462 156 45 2 20 163 3 158 1.42e-69 209
Msa1432610 MtrunA17_Chr4g0041141 69.630 135 41 0 29 163 18 152 2.13e-69 208
Msa1432610 MtrunA17_Chr2g0315791 76.000 125 30 0 39 163 32 156 2.83e-69 208
Msa1432610 MtrunA17_Chr8g0379061 68.800 125 39 0 39 163 84 208 2.87e-52 167
Msa1432610 MtrunA17_Chr1g0211641 82.222 45 8 0 33 77 64 108 1.81e-23 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1432610 AT3G04510.1 75.000 176 37 2 1 176 1 169 2.30e-78 232
Msa1432610 AT1G07090.1 64.881 168 56 2 13 177 1 168 3.26e-78 232
Msa1432610 AT5G28490.1 73.964 169 29 2 1 169 1 154 3.75e-78 231
Msa1432610 AT5G58500.1 71.528 144 39 2 39 180 18 161 8.30e-75 223
Msa1432610 AT2G31160.1 71.098 173 42 3 7 172 16 187 4.82e-73 219
Msa1432610 AT3G23290.2 85.714 126 18 0 39 164 47 172 1.61e-71 214
Msa1432610 AT2G42610.1 71.852 135 36 1 31 163 14 148 1.29e-67 204
Msa1432610 AT2G42610.2 71.852 135 36 1 31 163 14 148 1.29e-67 204
Msa1432610 AT1G78815.1 68.800 125 39 0 39 163 39 163 2.71e-65 199
Msa1432610 AT4G18610.1 56.522 161 69 1 4 163 1 161 9.26e-63 192
Msa1432610 AT1G16910.1 63.910 133 48 0 36 168 19 151 4.06e-61 187

Find 58 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTGTTAGGATTTATTTA+AGG 0.161002 tig0027132:-17212 Msa1432610:CDS
TGTTCCAGTCTCTTCTCTTT+TGG 0.228365 tig0027132:+17508 None:intergenic
GGACAAGGAGCTGGTGGATT+AGG 0.248534 tig0027132:+17342 None:intergenic
CGCTCTCATCGGTCGTCTTC+GGG 0.260569 tig0027132:-17286 Msa1432610:CDS
AACCATCCTTGTCCTTTCTT+TGG 0.263470 tig0027132:-17369 Msa1432610:CDS
ATCTTCATCCTCCATGGATT+TGG 0.293649 tig0027132:-17649 None:intergenic
ACGCTCTCATCGGTCGTCTT+CGG 0.308665 tig0027132:-17287 Msa1432610:CDS
CTCAACTATCTTGACCAGTT+TGG 0.334013 tig0027132:-17408 Msa1432610:CDS
TTCTGTTAGGATTTATTTAA+GGG 0.334103 tig0027132:-17211 Msa1432610:CDS
CGTCCTGAGACTAACCCTTT+TGG 0.356884 tig0027132:-17240 Msa1432610:CDS
GACAAGGAGCTGGTGGATTA+GGG 0.371455 tig0027132:+17343 None:intergenic
GTTGTAGATACCTTAGGTTT+AGG 0.383180 tig0027132:+17129 None:intergenic
TCCATGGATTTGGTTTCATC+AGG 0.387953 tig0027132:-17639 Msa1432610:CDS
TGATGTTGAACTTCCACTTC+CGG 0.415099 tig0027132:+17557 None:intergenic
GTCATTGAAGATCCACTTGT+TGG 0.419117 tig0027132:+17591 None:intergenic
TCCACTTCCGGTGCTATTGT+TGG 0.438537 tig0027132:+17569 None:intergenic
AGAGTGGTGGACGGTGGTTT+CGG 0.448012 tig0027132:+17469 None:intergenic
ACAAGGATGGTTGTGAACTT+TGG 0.448409 tig0027132:+17380 None:intergenic
GTGTTAGCTATGAAAAGAAA+AGG 0.462297 tig0027132:-17158 Msa1432610:CDS
GCAGTGGTTGTAGATACCTT+AGG 0.484827 tig0027132:+17123 None:intergenic
GGACATGGGAACCGCTACAT+AGG 0.494340 tig0027132:+17439 None:intergenic
ACCAACAATAGCACCGGAAG+TGG 0.495122 tig0027132:-17570 Msa1432610:CDS
CTAACAGAACGAGAACCAAA+AGG 0.506615 tig0027132:+17225 None:intergenic
CATGTCCTCTTCGTCAAGCG+TGG 0.509192 tig0027132:-17320 Msa1432610:CDS
ATGTCCTCTTCGTCAAGCGT+GGG 0.521066 tig0027132:-17319 Msa1432610:CDS
CACGCTTGACGAAGAGGACA+TGG 0.538595 tig0027132:+17321 None:intergenic
GAACCAAAAGGGTTAGTCTC+AGG 0.546578 tig0027132:+17237 None:intergenic
AAGGAAGAGGCCTAAACCTA+AGG 0.549128 tig0027132:-17139 Msa1432610:CDS
TTGTTGGACTCTCTACACTC+TGG 0.549585 tig0027132:+17607 None:intergenic
AAAACCAAAAGAGAAGAGAC+TGG 0.553636 tig0027132:-17512 Msa1432610:CDS
GGATTAGGGATGCCAAAGAA+AGG 0.556995 tig0027132:+17357 None:intergenic
AGAGGACATGGACAAGGAGC+TGG 0.558895 tig0027132:+17333 None:intergenic
TCCTGATGAAACCAAATCCA+TGG 0.559307 tig0027132:+17638 None:intergenic
TAACAGAACGAGAACCAAAA+GGG 0.559474 tig0027132:+17226 None:intergenic
AAGGTATCTACAACCACTGC+TGG 0.564271 tig0027132:-17120 Msa1432610:CDS
GACATGGGAACCGCTACATA+GGG 0.570761 tig0027132:+17440 None:intergenic
CTACCCCACGCTTGACGAAG+AGG 0.572444 tig0027132:+17315 None:intergenic
GGTAGTCTCGACGCTCTCAT+CGG 0.573996 tig0027132:-17297 Msa1432610:CDS
AGTTGAGAAACTCAAGGACA+TGG 0.576269 tig0027132:+17424 None:intergenic
GCTATGAAAAGAAAAGGAAG+AGG 0.585681 tig0027132:-17152 Msa1432610:CDS
GGAACCGCTACATAGGGCTA+AGG 0.607722 tig0027132:+17446 None:intergenic
AGTGTAGAGAGTCCAACAAG+TGG 0.618422 tig0027132:-17603 Msa1432610:CDS
CTACATAGGGCTAAGGAGAG+TGG 0.621558 tig0027132:+17453 None:intergenic
TCAATGACCAACAATAGCAC+CGG 0.625940 tig0027132:-17576 Msa1432610:CDS
GTCTTAACTAGCACCAGCAG+TGG 0.629792 tig0027132:+17107 None:intergenic
GGGCTAAGGAGAGTGGTGGA+CGG 0.632875 tig0027132:+17460 None:intergenic
CTAAGGAGAGTGGTGGACGG+TGG 0.639457 tig0027132:+17463 None:intergenic
CAAGATAGTTGAGAAACTCA+AGG 0.640517 tig0027132:+17418 None:intergenic
GGACATGGACAAGGAGCTGG+TGG 0.641101 tig0027132:+17336 None:intergenic
TGTCCTCTTCGTCAAGCGTG+GGG 0.649722 tig0027132:-17318 Msa1432610:CDS
TGCCAAAGAAAGGACAAGGA+TGG 0.651402 tig0027132:+17367 None:intergenic
TGACGAAGAGGACATGGACA+AGG 0.652351 tig0027132:+17327 None:intergenic
CATAGGGCTAAGGAGAGTGG+TGG 0.653546 tig0027132:+17456 None:intergenic
CTCTCCTTAGCCCTATGTAG+CGG 0.658117 tig0027132:-17450 Msa1432610:CDS
GTTGAGAAACTCAAGGACAT+GGG 0.658451 tig0027132:+17425 None:intergenic
CGGGCTGCTTACGAAGAGAA+CGG 0.659740 tig0027132:-17267 Msa1432610:CDS
GGGATGCCAAAGAAAGGACA+AGG 0.667842 tig0027132:+17363 None:intergenic
GCTGCTTACGAAGAGAACGG+TGG 0.749462 tig0027132:-17264 Msa1432610:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGTTAGGATTTATTTAA+GGG - tig0027132:17535-17554 Msa1432610:CDS 20.0%
!!! TTCTCTTTTGGTTTTCATAA+CGG + tig0027132:17229-17248 None:intergenic 25.0%
! GTTCTGTTAGGATTTATTTA+AGG - tig0027132:17534-17553 Msa1432610:CDS 25.0%
!! GATTTTCAAGCAAAATCTAG+AGG - tig0027132:17566-17585 Msa1432610:CDS 30.0%
GTGTTAGCTATGAAAAGAAA+AGG - tig0027132:17588-17607 Msa1432610:CDS 30.0%
! TTTTCATAACGGCTTGAAGT+TGG + tig0027132:17218-17237 None:intergenic 35.0%
AAAACCAAAAGAGAAGAGAC+TGG - tig0027132:17234-17253 Msa1432610:CDS 35.0%
CAAGATAGTTGAGAAACTCA+AGG + tig0027132:17331-17350 None:intergenic 35.0%
!!! GAACTTTGGTTTTTCCAAAC+TGG + tig0027132:17355-17374 None:intergenic 35.0%
TAACAGAACGAGAACCAAAA+GGG + tig0027132:17523-17542 None:intergenic 35.0%
GCTATGAAAAGAAAAGGAAG+AGG - tig0027132:17594-17613 Msa1432610:CDS 35.0%
GTTGTAGATACCTTAGGTTT+AGG + tig0027132:17620-17639 None:intergenic 35.0%
GTCATTGAAGATCCACTTGT+TGG + tig0027132:17158-17177 None:intergenic 40.0%
TCAATGACCAACAATAGCAC+CGG - tig0027132:17170-17189 Msa1432610:CDS 40.0%
TGATGTTGAACTTCCACTTC+CGG + tig0027132:17192-17211 None:intergenic 40.0%
! TGTTCCAGTCTCTTCTCTTT+TGG + tig0027132:17241-17260 None:intergenic 40.0%
GTTGAGAAACTCAAGGACAT+GGG + tig0027132:17324-17343 None:intergenic 40.0%
AGTTGAGAAACTCAAGGACA+TGG + tig0027132:17325-17344 None:intergenic 40.0%
CTCAACTATCTTGACCAGTT+TGG - tig0027132:17338-17357 Msa1432610:CDS 40.0%
ACAAGGATGGTTGTGAACTT+TGG + tig0027132:17369-17388 None:intergenic 40.0%
AACCATCCTTGTCCTTTCTT+TGG - tig0027132:17377-17396 Msa1432610:CDS 40.0%
CTAACAGAACGAGAACCAAA+AGG + tig0027132:17524-17543 None:intergenic 40.0%
!!! CTTTTGGTTCTCGTTCTGTT+AGG - tig0027132:17522-17541 Msa1432610:CDS 40.0%
TTGTTGGACTCTCTACACTC+TGG + tig0027132:17142-17161 None:intergenic 45.0%
AGTGTAGAGAGTCCAACAAG+TGG - tig0027132:17143-17162 Msa1432610:CDS 45.0%
TGCCAAAGAAAGGACAAGGA+TGG + tig0027132:17382-17401 None:intergenic 45.0%
GGATTAGGGATGCCAAAGAA+AGG + tig0027132:17392-17411 None:intergenic 45.0%
!! GAACCAAAAGGGTTAGTCTC+AGG + tig0027132:17512-17531 None:intergenic 45.0%
AAGGAAGAGGCCTAAACCTA+AGG - tig0027132:17607-17626 Msa1432610:CDS 45.0%
GCAGTGGTTGTAGATACCTT+AGG + tig0027132:17626-17645 None:intergenic 45.0%
! AAGGTATCTACAACCACTGC+TGG - tig0027132:17626-17645 Msa1432610:CDS 45.0%
! ACCAACAATAGCACCGGAAG+TGG - tig0027132:17176-17195 Msa1432610:CDS 50.0%
!! TCCACTTCCGGTGCTATTGT+TGG + tig0027132:17180-17199 None:intergenic 50.0%
CTACATAGGGCTAAGGAGAG+TGG + tig0027132:17296-17315 None:intergenic 50.0%
CTCTCCTTAGCCCTATGTAG+CGG - tig0027132:17296-17315 Msa1432610:CDS 50.0%
GACATGGGAACCGCTACATA+GGG + tig0027132:17309-17328 None:intergenic 50.0%
GGGATGCCAAAGAAAGGACA+AGG + tig0027132:17386-17405 None:intergenic 50.0%
!! GACAAGGAGCTGGTGGATTA+GGG + tig0027132:17406-17425 None:intergenic 50.0%
TGACGAAGAGGACATGGACA+AGG + tig0027132:17422-17441 None:intergenic 50.0%
ATGTCCTCTTCGTCAAGCGT+GGG - tig0027132:17427-17446 Msa1432610:CDS 50.0%
! CGTCCTGAGACTAACCCTTT+TGG - tig0027132:17506-17525 Msa1432610:CDS 50.0%
!! AGAGTGGTGGACGGTGGTTT+CGG + tig0027132:17280-17299 None:intergenic 55.0%
CATAGGGCTAAGGAGAGTGG+TGG + tig0027132:17293-17312 None:intergenic 55.0%
GGAACCGCTACATAGGGCTA+AGG + tig0027132:17303-17322 None:intergenic 55.0%
GGACATGGGAACCGCTACAT+AGG + tig0027132:17310-17329 None:intergenic 55.0%
!! GGACAAGGAGCTGGTGGATT+AGG + tig0027132:17407-17426 None:intergenic 55.0%
AGAGGACATGGACAAGGAGC+TGG + tig0027132:17416-17435 None:intergenic 55.0%
CACGCTTGACGAAGAGGACA+TGG + tig0027132:17428-17447 None:intergenic 55.0%
CATGTCCTCTTCGTCAAGCG+TGG - tig0027132:17426-17445 Msa1432610:CDS 55.0%
TGTCCTCTTCGTCAAGCGTG+GGG - tig0027132:17428-17447 Msa1432610:CDS 55.0%
GGTAGTCTCGACGCTCTCAT+CGG - tig0027132:17449-17468 Msa1432610:CDS 55.0%
ACGCTCTCATCGGTCGTCTT+CGG - tig0027132:17459-17478 Msa1432610:CDS 55.0%
CGGGCTGCTTACGAAGAGAA+CGG - tig0027132:17479-17498 Msa1432610:CDS 55.0%
GCTGCTTACGAAGAGAACGG+TGG - tig0027132:17482-17501 Msa1432610:CDS 55.0%
!! CTAAGGAGAGTGGTGGACGG+TGG + tig0027132:17286-17305 None:intergenic 60.0%
! GGGCTAAGGAGAGTGGTGGA+CGG + tig0027132:17289-17308 None:intergenic 60.0%
GGACATGGACAAGGAGCTGG+TGG + tig0027132:17413-17432 None:intergenic 60.0%
CTACCCCACGCTTGACGAAG+AGG + tig0027132:17434-17453 None:intergenic 60.0%
CGCTCTCATCGGTCGTCTTC+GGG - tig0027132:17460-17479 Msa1432610:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0027132 gene 17110 17658 17110 ID=Msa1432610;Name=Msa1432610
tig0027132 mRNA 17110 17658 17110 ID=Msa1432610-mRNA-1;Parent=Msa1432610;Name=Msa1432610-mRNA-1;_AED=0.34;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|182
tig0027132 exon 17110 17658 17110 ID=Msa1432610-mRNA-1:exon:8211;Parent=Msa1432610-mRNA-1
tig0027132 CDS 17110 17658 17110 ID=Msa1432610-mRNA-1:cds;Parent=Msa1432610-mRNA-1
Gene Sequence

>Msa1432610

ATGGATTTGGTTTCATCAGGATCAACAAACCAGAGTGTAGAGAGTCCAACAAGTGGATCTTCAATGACCAACAATAGCACCGGAAGTGGAAGTTCAACATCAACTCCAACTTCAAGCCGTTATGAAAACCAAAAGAGAAGAGACTGGAACACATTCTGTCAGTATCTCCGAAACCACCGTCCACCACTCTCCTTAGCCCTATGTAGCGGTTCCCATGTCCTTGAGTTTCTCAACTATCTTGACCAGTTTGGAAAAACCAAAGTTCACAACCATCCTTGTCCTTTCTTTGGCATCCCTAATCCACCAGCTCCTTGTCCATGTCCTCTTCGTCAAGCGTGGGGTAGTCTCGACGCTCTCATCGGTCGTCTTCGGGCTGCTTACGAAGAGAACGGTGGTCGTCCTGAGACTAACCCTTTTGGTTCTCGTTCTGTTAGGATTTATTTAAGGGATGTTCGTGATTTTCAAGCAAAATCTAGAGGTGTTAGCTATGAAAAGAAAAGGAAGAGGCCTAAACCTAAGGTATCTACAACCACTGCTGGTGCTAGTTAA
Protein sequence

>Msa1432610

MDLVSSGSTNQSVESPTSGSSMTNNSTGSGSSTSTPTSSRYENQKRRDWNTFCQYLRNHRPPLSLALCSGSHVLEFLNYLDQFGKTKVHNHPCPFFGIPNPPAPCPCPLRQAWGSLDALIGRLRAAYEENGGRPETNPFGSRSVRIYLRDVRDFQAKSRGVSYEKKRKRPKPKVSTTTAGAS*