AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1079950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1079950 MtrunA17_Chr7g0265391 50.935 214 54 6 24 186 202 415 3.26e-48 165
Msa1079950 MtrunA17_Chr3g0112391 41.379 116 56 3 82 186 299 413 3.87e-16 75.5
Msa1079950 MtrunA17_Chr3g0125471 37.273 110 63 3 81 186 323 430 3.90e-13 67.0
Msa1079950 MtrunA17_Chr2g0333181 36.471 85 54 0 95 179 15 99 4.11e-12 63.5
Msa1079950 MtrunA17_Chr3g0125461 33.945 109 68 2 81 186 406 513 5.89e-12 63.5
Msa1079950 MtrunA17_Chr1g0209361 43.243 74 42 0 107 180 330 403 1.15e-11 62.8
Msa1079950 MtrunA17_Chr5g0403051 32.075 106 70 1 74 179 286 389 2.81e-11 61.6
Msa1079950 MtrunA17_Chr3g0125491 36.036 111 63 3 81 186 19 126 2.91e-11 61.2
Msa1079950 MtrunA17_Chr1g0148491 33.577 137 70 4 66 186 275 406 2.92e-11 61.6
Msa1079950 MtrunA17_Chr8g0340091 26.875 160 100 4 31 179 438 591 3.52e-11 61.2
Msa1079950 MtrunA17_Chr1g0148511 33.628 113 72 1 77 186 380 492 3.55e-11 61.2
Msa1079950 MtrunA17_Chr2g0279661 36.000 100 59 2 90 186 403 500 5.72e-11 60.5
Msa1079950 MtrunA17_Chr1g0148501 39.759 83 47 1 107 186 417 499 5.89e-11 60.5
Msa1079950 MtrunA17_Chr1g0148461 31.579 114 73 2 76 186 395 506 7.70e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1079950 AT5G02070.1 41.935 93 51 2 88 179 332 422 3.15e-14 70.5
Msa1079950 AT4G28670.1 44.444 72 40 0 108 179 319 390 4.60e-13 67.0
Msa1079950 AT3G53840.1 38.384 99 55 2 91 186 328 423 6.46e-13 66.6
Msa1079950 AT4G11470.1 44.444 72 40 0 108 179 327 398 1.46e-11 62.8
Msa1079950 AT4G11480.4 45.833 72 39 0 108 179 309 380 1.56e-11 62.8
Msa1079950 AT4G11480.1 45.833 72 39 0 108 179 309 380 1.58e-11 62.8
Msa1079950 AT4G11480.2 45.833 72 39 0 108 179 312 383 1.72e-11 62.4
Msa1079950 AT4G11470.2 44.444 72 40 0 108 179 332 403 1.83e-11 62.4
Msa1079950 AT4G11480.3 45.833 72 39 0 108 179 312 383 1.98e-11 62.4
Msa1079950 AT3G53590.1 30.275 109 72 1 75 179 572 680 6.95e-11 60.8

Find 49 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTAGTTGAAACATCGTATA+AGG 0.293758 7_2:-79222681 None:intergenic
TCTTAGGAAGTGGTTGCTTT+GGG 0.308970 7_2:+79222745 Msa1079950:CDS
GTCCTTATACATCCTTCATT+TGG 0.312776 7_2:+79222377 Msa1079950:CDS
TTGGGGTCCTATCAATCATT+GGG 0.318862 7_2:+79222354 Msa1079950:CDS
ATCTTAGGAAGTGGTTGCTT+TGG 0.331108 7_2:+79222744 Msa1079950:CDS
AGGCCTCCTTTCCCTTGATT+AGG 0.331464 7_2:-79222414 None:intergenic
TTCATGTTTCCATGGATTCC+CGG 0.336174 7_2:+79222307 None:intergenic
CTTGATTAGGAGGTTTGTCT+TGG 0.339137 7_2:-79222401 None:intergenic
TGCTTTCTTCTCATTGGTCC+TGG 0.340759 7_2:+79222571 Msa1079950:CDS
CTTGGGGTCCTATCAATCAT+TGG 0.347173 7_2:+79222353 Msa1079950:CDS
CATTTCGGTTAGGAAGGTTC+CGG 0.376652 7_2:-79222326 None:intergenic
CCTAACCGAAATGATTCCTT+GGG 0.396408 7_2:+79222336 Msa1079950:CDS
ATTTCGGTTAGGAAGGTTCC+GGG 0.406196 7_2:-79222325 None:intergenic
TCCTAACCGAAATGATTCCT+TGG 0.416883 7_2:+79222335 Msa1079950:CDS
GGCCAAATGAAGGATGTATA+AGG 0.421343 7_2:-79222379 None:intergenic
TAAGGACCCCAATGATTGAT+AGG 0.431828 7_2:-79222361 None:intergenic
AAGGAGGCCTACAGATTAGA+TGG 0.436707 7_2:+79222427 Msa1079950:CDS
TTTGTAATAGTGATTCTGTT+GGG 0.443696 7_2:+79222541 Msa1079950:CDS
TTGATTAGGAGGTTTGTCTT+GGG 0.449448 7_2:-79222400 None:intergenic
AAACCTCATTATGCACTAGT+TGG 0.453543 7_2:-79222845 None:intergenic
CCTCCTTTCCCTTGATTAGG+AGG 0.457119 7_2:-79222411 None:intergenic
AGGACCCCAAGGAATCATTT+CGG 0.460312 7_2:-79222341 None:intergenic
TTGTGTCCTGCATACAGGTT+CGG 0.477664 7_2:-79222460 None:intergenic
GTTTGTCTTGGGCCAAATGA+AGG 0.485193 7_2:-79222389 None:intergenic
GCAATCACAAGAACCTAGTC+AGG 0.491400 7_2:+79222883 Msa1079950:CDS
CAAGACAAACCTCCTAATCA+AGG 0.492062 7_2:+79222402 Msa1079950:CDS
CCCAAGGAATCATTTCGGTT+AGG 0.515040 7_2:-79222336 None:intergenic
CTTTGTAATAGTGATTCTGT+TGG 0.515279 7_2:+79222540 Msa1079950:CDS
GTTCTTCAAACGTTCTAAGC+AGG 0.520014 7_2:+79222611 Msa1079950:CDS
CACAACAGCATCTTAGGAAG+TGG 0.538457 7_2:+79222735 Msa1079950:CDS
AGGAATCATTTCGGTTAGGA+AGG 0.542384 7_2:-79222332 None:intergenic
AGGAAGGTTCCGGGAATCCA+TGG 0.558955 7_2:-79222316 None:intergenic
AACCTCATTATGCACTAGTT+GGG 0.559284 7_2:-79222844 None:intergenic
CTTAGGAAGTGGTTGCTTTG+GGG 0.590416 7_2:+79222746 Msa1079950:CDS
GCAGAAATCAAGCGCTGGAG+AGG 0.590846 7_2:+79222653 Msa1079950:CDS
AAACCTCCTAATCAAGGGAA+AGG 0.593579 7_2:+79222408 Msa1079950:CDS
GTCCTGCATACAGGTTCGGA+TGG 0.599275 7_2:-79222456 None:intergenic
CCTCCTAATCAAGGGAAAGG+AGG 0.600002 7_2:+79222411 Msa1079950:CDS
GAAGAGACCATCTAATCTGT+AGG 0.600659 7_2:-79222434 None:intergenic
CACCCAACTAGTGCATAATG+AGG 0.609291 7_2:+79222842 Msa1079950:CDS
CAGCGATGATGACAAAGACC+AGG 0.610654 7_2:-79222589 None:intergenic
GCTGTCAAGAAAGCGAGAGT+TGG 0.613643 7_2:+79222807 Msa1079950:CDS
CAAACGTTCTAAGCAGGTCA+AGG 0.618563 7_2:+79222617 Msa1079950:CDS
ATTGTGCAGAAATCAAGCGC+TGG 0.624625 7_2:+79222648 Msa1079950:CDS
ATTCTACATAAAGCCTGACT+AGG 0.632184 7_2:-79222896 None:intergenic
AAGACAAACCTCCTAATCAA+GGG 0.634691 7_2:+79222403 Msa1079950:CDS
TGGGGTCCTATCAATCATTG+GGG 0.639790 7_2:+79222355 Msa1079950:CDS
CAATGATTGATAGGACCCCA+AGG 0.669612 7_2:-79222352 None:intergenic
CTAACCGAAATGATTCCTTG+GGG 0.702534 7_2:+79222337 Msa1079950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTGTAATAGTGATTCTGTT+GGG + chr7_2:79222541-79222560 Msa1079950:CDS 25.0%
CTTTGTAATAGTGATTCTGT+TGG + chr7_2:79222540-79222559 Msa1079950:CDS 30.0%
GTTAGTTGAAACATCGTATA+AGG - chr7_2:79222684-79222703 None:intergenic 30.0%
GTCCTTATACATCCTTCATT+TGG + chr7_2:79222377-79222396 Msa1079950:CDS 35.0%
TTGATTAGGAGGTTTGTCTT+GGG - chr7_2:79222403-79222422 None:intergenic 35.0%
AAGACAAACCTCCTAATCAA+GGG + chr7_2:79222403-79222422 Msa1079950:CDS 35.0%
! CTCTTTTGCTTTCTTCTCAT+TGG + chr7_2:79222565-79222584 Msa1079950:CDS 35.0%
! TTTTCACACAACAGCATCTT+AGG + chr7_2:79222729-79222748 Msa1079950:CDS 35.0%
AACCTCATTATGCACTAGTT+GGG - chr7_2:79222847-79222866 None:intergenic 35.0%
AAACCTCATTATGCACTAGT+TGG - chr7_2:79222848-79222867 None:intergenic 35.0%
ATTCTACATAAAGCCTGACT+AGG - chr7_2:79222899-79222918 None:intergenic 35.0%
AGGAATCATTTCGGTTAGGA+AGG - chr7_2:79222335-79222354 None:intergenic 40.0%
TCCTAACCGAAATGATTCCT+TGG + chr7_2:79222335-79222354 Msa1079950:CDS 40.0%
CCTAACCGAAATGATTCCTT+GGG + chr7_2:79222336-79222355 Msa1079950:CDS 40.0%
CTAACCGAAATGATTCCTTG+GGG + chr7_2:79222337-79222356 Msa1079950:CDS 40.0%
TTGGGGTCCTATCAATCATT+GGG + chr7_2:79222354-79222373 Msa1079950:CDS 40.0%
TAAGGACCCCAATGATTGAT+AGG - chr7_2:79222364-79222383 None:intergenic 40.0%
GGCCAAATGAAGGATGTATA+AGG - chr7_2:79222382-79222401 None:intergenic 40.0%
CTTGATTAGGAGGTTTGTCT+TGG - chr7_2:79222404-79222423 None:intergenic 40.0%
CAAGACAAACCTCCTAATCA+AGG + chr7_2:79222402-79222421 Msa1079950:CDS 40.0%
AAACCTCCTAATCAAGGGAA+AGG + chr7_2:79222408-79222427 Msa1079950:CDS 40.0%
GAAGAGACCATCTAATCTGT+AGG - chr7_2:79222437-79222456 None:intergenic 40.0%
! GTTCTTCAAACGTTCTAAGC+AGG + chr7_2:79222611-79222630 Msa1079950:CDS 40.0%
ATCTTAGGAAGTGGTTGCTT+TGG + chr7_2:79222744-79222763 Msa1079950:CDS 40.0%
! TCTTAGGAAGTGGTTGCTTT+GGG + chr7_2:79222745-79222764 Msa1079950:CDS 40.0%
ATTTCGGTTAGGAAGGTTCC+GGG - chr7_2:79222328-79222347 None:intergenic 45.0%
CATTTCGGTTAGGAAGGTTC+CGG - chr7_2:79222329-79222348 None:intergenic 45.0%
CCCAAGGAATCATTTCGGTT+AGG - chr7_2:79222339-79222358 None:intergenic 45.0%
AGGACCCCAAGGAATCATTT+CGG - chr7_2:79222344-79222363 None:intergenic 45.0%
CAATGATTGATAGGACCCCA+AGG - chr7_2:79222355-79222374 None:intergenic 45.0%
CTTGGGGTCCTATCAATCAT+TGG + chr7_2:79222353-79222372 Msa1079950:CDS 45.0%
TGGGGTCCTATCAATCATTG+GGG + chr7_2:79222355-79222374 Msa1079950:CDS 45.0%
GTTTGTCTTGGGCCAAATGA+AGG - chr7_2:79222392-79222411 None:intergenic 45.0%
AAGGAGGCCTACAGATTAGA+TGG + chr7_2:79222427-79222446 Msa1079950:CDS 45.0%
TTGTGTCCTGCATACAGGTT+CGG - chr7_2:79222463-79222482 None:intergenic 45.0%
AACCTGTATGCAGGACACAA+TGG + chr7_2:79222463-79222482 Msa1079950:intron 45.0%
ACCTGTATGCAGGACACAAT+GGG + chr7_2:79222464-79222483 Msa1079950:intron 45.0%
TGCATCGTCTCTACCAAAAG+GGG - chr7_2:79222512-79222531 None:intergenic 45.0%
GTGCATCGTCTCTACCAAAA+GGG - chr7_2:79222513-79222532 None:intergenic 45.0%
AGTGCATCGTCTCTACCAAA+AGG - chr7_2:79222514-79222533 None:intergenic 45.0%
TGCTTTCTTCTCATTGGTCC+TGG + chr7_2:79222571-79222590 Msa1079950:CDS 45.0%
! CAAACGTTCTAAGCAGGTCA+AGG + chr7_2:79222617-79222636 Msa1079950:CDS 45.0%
ATTGTGCAGAAATCAAGCGC+TGG + chr7_2:79222648-79222667 Msa1079950:CDS 45.0%
CACAACAGCATCTTAGGAAG+TGG + chr7_2:79222735-79222754 Msa1079950:CDS 45.0%
! CTTAGGAAGTGGTTGCTTTG+GGG + chr7_2:79222746-79222765 Msa1079950:CDS 45.0%
CACCCAACTAGTGCATAATG+AGG + chr7_2:79222842-79222861 Msa1079950:CDS 45.0%
GCAATCACAAGAACCTAGTC+AGG + chr7_2:79222883-79222902 Msa1079950:CDS 45.0%
CCTCCTTTCCCTTGATTAGG+AGG - chr7_2:79222414-79222433 None:intergenic 50.0%
CCTCCTAATCAAGGGAAAGG+AGG + chr7_2:79222411-79222430 Msa1079950:CDS 50.0%
AGGCCTCCTTTCCCTTGATT+AGG - chr7_2:79222417-79222436 None:intergenic 50.0%
TTCCATCCGAACCTGTATGC+AGG + chr7_2:79222454-79222473 Msa1079950:intron 50.0%
TCCCATTGTGTCCTGCATAC+AGG - chr7_2:79222468-79222487 None:intergenic 50.0%
! GAGACTCGATGTTCCCCTTT+TGG + chr7_2:79222496-79222515 Msa1079950:intron 50.0%
CAGCGATGATGACAAAGACC+AGG - chr7_2:79222592-79222611 None:intergenic 50.0%
GCTGTCAAGAAAGCGAGAGT+TGG + chr7_2:79222807-79222826 Msa1079950:CDS 50.0%
GTCCTGCATACAGGTTCGGA+TGG - chr7_2:79222459-79222478 None:intergenic 55.0%
!! GCAGAAATCAAGCGCTGGAG+AGG + chr7_2:79222653-79222672 Msa1079950:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 79222318 79222932 79222318 ID=Msa1079950;Name=Msa1079950
chr7_2 mRNA 79222318 79222932 79222318 ID=Msa1079950-mRNA-1;Parent=Msa1079950;Name=Msa1079950-mRNA-1;_AED=0.37;_eAED=0.38;_QI=0|0|0|1|0|0|2|0|186
chr7_2 exon 79222318 79222467 79222318 ID=Msa1079950-mRNA-1:exon:19939;Parent=Msa1079950-mRNA-1
chr7_2 exon 79222522 79222932 79222522 ID=Msa1079950-mRNA-1:exon:19940;Parent=Msa1079950-mRNA-1
chr7_2 CDS 79222318 79222467 79222318 ID=Msa1079950-mRNA-1:cds;Parent=Msa1079950-mRNA-1
chr7_2 CDS 79222522 79222932 79222522 ID=Msa1079950-mRNA-1:cds;Parent=Msa1079950-mRNA-1
Gene Sequence

>Msa1079950

ATGGATTCCCGGAACCTTCCTAACCGAAATGATTCCTTGGGGTCCTATCAATCATTGGGGTCCTTATACATCCTTCATTTGGCCCAAGACAAACCTCCTAATCAAGGGAAAGGAGGCCTACAGATTAGATGGTCTCTTCCATCCGAACCTAGACGATGCACTCTTTTGCTTTGTAATAGTGATTCTGTTGGGACTCTTTTGCTTTCTTCTCATTGGTCCTGGTCTTTGTCATCATCGCTGTTCTTCAAACGTTCTAAGCAGGTCAAGGAAAGAGAAATTGTGCAGAAATCAAGCGCTGGAGAGGAGAAACCTTATACGATGTTTCAACTAACACAGTTGAACAAAGTAACAAACTGTTTTTCACACAACAGCATCTTAGGAAGTGGTTGCTTTGGGGAAGTTTACTATGATGAACTAGAAGATGAAACACATGTAGCTGTCAAGAAAGCGAGAGTTGGTAAACTTAAAAGCACCCAACTAGTGCATAATGAGGTTTCAGTTCTTTCACGATGCAATCACAAGAACCTAGTCAGGCTTTATGTAGAATCTGAGCAGCCTTGA
Protein sequence

>Msa1079950

MDSRNLPNRNDSLGSYQSLGSLYILHLAQDKPPNQGKGGLQIRWSLPSEPRRCTLLLCNSDSVGTLLLSSHWSWSLSSSLFFKRSKQVKEREIVQKSSAGEEKPYTMFQLTQLNKVTNCFSHNSILGSGCFGEVYYDELEDETHVAVKKARVGKLKSTQLVHNEVSVLSRCNHKNLVRLYVESEQP*