AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1336610

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1336610 MtrunA17_Chr5g0405931 98.473 131 1 1 1 130 1 131 1.83e-93 265
Msa1336610 MtrunA17_Chr4g0065171 46.774 62 33 0 37 98 465 526 9.39e-16 72.4
Msa1336610 MtrunA17_Chr8g0369691 55.319 47 21 0 52 98 441 487 4.03e-15 70.5
Msa1336610 MtrunA17_Chr3g0138451 40.789 76 41 2 27 102 291 362 5.29e-14 67.0
Msa1336610 MtrunA17_Chr1g0148631 49.123 57 28 1 46 102 331 386 1.11e-13 66.2
Msa1336610 MtrunA17_Chr2g0325141 38.095 84 45 4 19 98 53 133 2.52e-13 62.8
Msa1336610 MtrunA17_Chr5g0408871 55.814 43 19 0 56 98 505 547 1.01e-12 63.5
Msa1336610 MtrunA17_Chr3g0112041 44.643 56 30 1 47 102 204 258 8.64e-12 60.5
Msa1336610 MtrunA17_Chr3g0123581 43.860 57 32 0 42 98 92 148 8.69e-12 58.5
Msa1336610 MtrunA17_Chr0c01g0489441 49.206 63 27 2 42 102 63 122 9.31e-12 58.5
Msa1336610 MtrunA17_Chr4g0039541 53.061 49 21 1 56 102 58 106 1.09e-11 57.8
Msa1336610 MtrunA17_Chr1g0209001 32.051 78 53 0 46 123 85 162 1.18e-11 58.5
Msa1336610 MtrunA17_Chr4g0031921 41.935 62 32 3 45 103 195 255 1.34e-11 60.1
Msa1336610 MtrunA17_Chr8g0391751 35.135 74 47 1 28 101 257 329 1.40e-11 60.1
Msa1336610 MtrunA17_Chr3g0124531 50.000 48 24 0 51 98 64 111 2.50e-11 57.8
Msa1336610 MtrunA17_Chr3g0104311 44.776 67 36 1 50 115 52 118 2.55e-11 57.0
Msa1336610 MtrunA17_Chr5g0427771 50.000 56 27 1 46 101 50 104 2.75e-11 57.0
Msa1336610 MtrunA17_Chr4g0031911 40.323 62 33 3 45 103 195 255 3.04e-11 58.9
Msa1336610 MtrunA17_Chr5g0427781 47.273 55 29 0 47 101 50 104 3.47e-11 57.0
Msa1336610 MtrunA17_Chr5g0425981 49.091 55 27 1 47 101 49 102 3.91e-11 56.6
Msa1336610 MtrunA17_Chr5g0437361 39.535 86 38 4 22 104 77 151 4.21e-11 57.4
Msa1336610 MtrunA17_Chr3g0104301 44.776 67 36 1 50 115 52 118 4.43e-11 56.6
Msa1336610 MtrunA17_Chr3g0104321 44.776 67 36 1 50 115 52 118 4.43e-11 56.6
Msa1336610 MtrunA17_Chr4g0057351 44.828 58 30 2 56 113 316 371 4.94e-11 58.5
Msa1336610 MtrunA17_Chr5g0417501 42.857 56 31 1 52 107 111 165 5.95e-11 57.8
Msa1336610 MtrunA17_Chr1g0203541 52.083 48 21 2 56 102 136 182 6.82e-11 57.4
Msa1336610 MtrunA17_Chr8g0348551 33.028 109 59 2 4 98 27 135 7.09e-11 56.6
Msa1336610 MtrunA17_Chr3g0102761 40.000 90 47 4 14 98 241 328 9.38e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1336610 AT3G51325.1 47.945 73 29 2 56 127 26 90 2.31e-16 69.3
Msa1336610 AT5G45290.1 54.902 51 23 0 48 98 482 532 1.06e-14 69.7
Msa1336610 AT5G45290.2 53.846 52 23 1 48 98 482 533 2.08e-13 65.9
Msa1336610 AT4G32600.1 36.782 87 51 2 16 102 326 408 4.35e-13 65.1
Msa1336610 AT4G32600.2 36.782 87 51 2 16 102 326 408 4.35e-13 65.1
Msa1336610 AT4G26580.1 38.636 88 43 3 14 98 251 330 4.47e-12 62.0
Msa1336610 AT4G26580.2 38.636 88 43 3 14 98 251 330 4.47e-12 62.0
Msa1336610 AT5G06490.1 39.362 94 47 4 8 100 89 173 2.52e-11 58.5
Msa1336610 AT1G53820.1 50.847 59 26 3 56 112 120 177 3.07e-11 59.7
Msa1336610 AT1G80400.1 51.064 47 22 1 56 102 355 400 5.07e-11 59.3
Msa1336610 AT5G55970.2 50.000 50 24 1 49 98 290 338 5.38e-11 58.9
Msa1336610 AT5G55970.1 50.000 50 24 1 49 98 290 338 5.38e-11 58.9
Msa1336610 AT1G26800.1 32.857 70 46 1 54 123 111 179 5.90e-11 57.8
Msa1336610 AT4G09560.1 47.727 44 23 0 55 98 233 276 9.92e-11 58.2

Find 20 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTGTTGATTGGTCTTCTT+TGG 0.177595 tig0001300:-27658 None:intergenic
TCACTTATCTTCAATTTAAT+TGG 0.181614 tig0001300:+27571 Msa1336610:CDS
AAATTGCATCATTGTTTGTT+TGG 0.299867 tig0001300:-27606 None:intergenic
AATTGCATCATTGTTTGTTT+GGG 0.352553 tig0001300:-27605 None:intergenic
ATTGTTGATTGGTCTTCTTT+GGG 0.387292 tig0001300:-27657 None:intergenic
TCAGTGAAGAGATGCTAATA+TGG 0.395360 tig0001300:+27890 Msa1336610:CDS
ACAAGGTTTGTGTAGATAGT+TGG 0.401789 tig0001300:+27785 Msa1336610:CDS
TGTTTGTTTGGGTCTCTGCC+AGG 0.416786 tig0001300:-27594 None:intergenic
TGTGTAGATAGTTGGCTAAA+GGG 0.434937 tig0001300:+27793 Msa1336610:CDS
TTGTGTAGATAGTTGGCTAA+AGG 0.452426 tig0001300:+27792 Msa1336610:CDS
ATTGAGGTGGCAACAATGTA+AGG 0.461304 tig0001300:-27631 None:intergenic
AGATTCTGATGATTGTTGAT+TGG 0.465917 tig0001300:-27668 None:intergenic
GGTCTTCTTTGGGACAATTG+AGG 0.479027 tig0001300:-27647 None:intergenic
TATCTTCAATTTAATTGGCC+TGG 0.483741 tig0001300:+27576 Msa1336610:CDS
TCTTCAACAACAAATGATGT+TGG 0.485848 tig0001300:+27688 Msa1336610:CDS
CTTCTTTGGGACAATTGAGG+TGG 0.552904 tig0001300:-27644 None:intergenic
AGATAAGTGATACAAAGCCT+TGG 0.557913 tig0001300:-27558 None:intergenic
TTGTGAAATTCGTGTGAACA+AGG 0.580501 tig0001300:-27766 None:intergenic
AAAATCAAGATGACACTCCA+AGG 0.592008 tig0001300:+27541 None:intergenic
TTGTTCACACGAATTTCACA+AGG 0.650344 tig0001300:+27768 Msa1336610:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCACTTATCTTCAATTTAAT+TGG + tig0001300:27571-27590 Msa1336610:CDS 20.0%
! AATTGCATCATTGTTTGTTT+GGG - tig0001300:27608-27627 None:intergenic 25.0%
! AAATTGCATCATTGTTTGTT+TGG - tig0001300:27609-27628 None:intergenic 25.0%
!! TTTTCTTCTTTTCATATAGC+TGG + tig0001300:27913-27932 Msa1336610:CDS 25.0%
TATCTTCAATTTAATTGGCC+TGG + tig0001300:27576-27595 Msa1336610:CDS 30.0%
!! ATTGTTGATTGGTCTTCTTT+GGG - tig0001300:27660-27679 None:intergenic 30.0%
AGATTCTGATGATTGTTGAT+TGG - tig0001300:27671-27690 None:intergenic 30.0%
TCTTCAACAACAAATGATGT+TGG + tig0001300:27688-27707 Msa1336610:CDS 30.0%
AGATAAGTGATACAAAGCCT+TGG - tig0001300:27561-27580 None:intergenic 35.0%
!! GATTGTTGATTGGTCTTCTT+TGG - tig0001300:27661-27680 None:intergenic 35.0%
TTGTGAAATTCGTGTGAACA+AGG - tig0001300:27769-27788 None:intergenic 35.0%
TTGTTCACACGAATTTCACA+AGG + tig0001300:27768-27787 Msa1336610:CDS 35.0%
ACAAGGTTTGTGTAGATAGT+TGG + tig0001300:27785-27804 Msa1336610:CDS 35.0%
TTGTGTAGATAGTTGGCTAA+AGG + tig0001300:27792-27811 Msa1336610:CDS 35.0%
TGTGTAGATAGTTGGCTAAA+GGG + tig0001300:27793-27812 Msa1336610:CDS 35.0%
CTTCAACTCCCATTGAAAAA+CGG - tig0001300:27843-27862 None:intergenic 35.0%
TCAGTGAAGAGATGCTAATA+TGG + tig0001300:27890-27909 Msa1336610:CDS 35.0%
ATTGAGGTGGCAACAATGTA+AGG - tig0001300:27634-27653 None:intergenic 40.0%
!!! TCCATTGTGCCGTTTTTCAA+TGG + tig0001300:27831-27850 Msa1336610:CDS 40.0%
!!! CCATTGTGCCGTTTTTCAAT+GGG + tig0001300:27832-27851 Msa1336610:CDS 40.0%
!! CTTCTTTGGGACAATTGAGG+TGG - tig0001300:27647-27666 None:intergenic 45.0%
!! GGTCTTCTTTGGGACAATTG+AGG - tig0001300:27650-27669 None:intergenic 45.0%
CCCATTGAAAAACGGCACAA+TGG - tig0001300:27835-27854 None:intergenic 45.0%
TGTTTGTTTGGGTCTCTGCC+AGG - tig0001300:27597-27616 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0001300 gene 27550 27942 27550 ID=Msa1336610;Name=Msa1336610
tig0001300 mRNA 27550 27942 27550 ID=Msa1336610-mRNA-1;Parent=Msa1336610;Name=Msa1336610-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|130
tig0001300 exon 27550 27942 27550 ID=Msa1336610-mRNA-1:exon:774;Parent=Msa1336610-mRNA-1
tig0001300 CDS 27550 27942 27550 ID=Msa1336610-mRNA-1:cds;Parent=Msa1336610-mRNA-1
Gene Sequence

>Msa1336610

ATGACACTCCAAGGCTTTGTATCACTTATCTTCAATTTAATTGGCCTGGCAGAGACCCAAACAAACAATGATGCAATTTTACCTTACATTGTTGCCACCTCAATTGTCCCAAAGAAGACCAATCAACAATCATCAGAATCTTCAACAACAAATGATGTTGGTTTGTGTTGTGTATGCTTGTCAATGTTAAACAACAAAGATGAAATTCGTGTGCTTCCTTGTTCACACGAATTTCACAAGGTTTGTGTAGATAGTTGGCTAAAGGGTCATCATAAAACATGTCCATTGTGCCGTTTTTCAATGGGAGTTGAAGAAAAGTCTCATCATCGTGCTGAAATGTTCAGTGAAGAGATGCTAATATGGTTTTCTTCTTTTCATATAGCTGGTATGTAA
Protein sequence

>Msa1336610

MTLQGFVSLIFNLIGLAETQTNNDAILPYIVATSIVPKKTNQQSSESSTTNDVGLCCVCLSMLNNKDEIRVLPCSHEFHKVCVDSWLKGHHKTCPLCRFSMGVEEKSHHRAEMFSEEMLIWFSSFHIAGM*