AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1383060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1383060 MtrunA17_Chr1g0160761 79.310 145 27 1 1 145 1 142 2.07e-72 228
Msa1383060 MtrunA17_Chr1g0160711 85.714 126 17 1 21 145 17 142 5.12e-70 222
Msa1383060 MtrunA17_Chr1g0160561 57.143 147 54 4 2 147 7 145 2.08e-47 162
Msa1383060 MtrunA17_Chr1g0160721 62.069 145 45 3 1 145 12 146 5.56e-47 160
Msa1383060 MtrunA17_Chr1g0160661 57.241 145 52 3 1 145 27 161 7.45e-43 147
Msa1383060 MtrunA17_Chr1g0160701 65.672 134 32 6 17 145 32 156 1.17e-42 149
Msa1383060 MtrunA17_Chr1g0157881 44.643 112 53 3 33 143 60 163 4.30e-21 88.6
Msa1383060 MtrunA17_Chr1g0157991 39.189 148 71 5 12 145 16 158 5.15e-21 88.2
Msa1383060 MtrunA17_Chr1g0157791 47.107 121 52 5 7 120 6 121 6.37e-21 87.8
Msa1383060 MtrunA17_Chr1g0157961 47.009 117 51 5 24 134 33 144 9.34e-21 85.9
Msa1383060 MtrunA17_Chr1g0158151 45.161 124 59 5 1 120 1 119 1.09e-20 87.0
Msa1383060 MtrunA17_Chr1g0158191 47.368 114 46 5 24 128 24 132 5.61e-20 85.1
Msa1383060 MtrunA17_Chr1g0158061 50.495 101 39 4 33 127 35 130 9.47e-20 82.8
Msa1383060 MtrunA17_Chr1g0158761 42.149 121 63 4 1 119 1 116 4.17e-18 79.7
Msa1383060 MtrunA17_Chr1g0157861 40.870 115 59 3 33 146 45 151 9.39e-17 75.9
Msa1383060 MtrunA17_Chr3g0088331 40.000 125 60 6 21 138 34 150 9.99e-17 74.7
Msa1383060 MtrunA17_Chr1g0158411 39.474 114 59 3 30 138 51 159 1.40e-16 75.5
Msa1383060 MtrunA17_Chr1g0158541 38.931 131 65 5 5 125 16 141 1.06e-15 72.8
Msa1383060 MtrunA17_Chr1g0157911 44.944 89 43 2 33 120 42 125 2.01e-15 72.0
Msa1383060 MtrunA17_Chr1g0158041 46.154 104 44 4 33 129 36 134 4.03e-15 71.2
Msa1383060 MtrunA17_Chr1g0158461 34.752 141 76 4 1 134 17 148 4.39e-15 70.5
Msa1383060 MtrunA17_Chr1g0158121 45.263 95 45 3 24 116 29 118 5.86e-15 67.0
Msa1383060 MtrunA17_Chr6g0467711 41.228 114 56 3 33 145 48 151 7.40e-15 70.5
Msa1383060 MtrunA17_Chr1g0158661 42.553 94 48 2 27 119 33 121 1.49e-14 69.7
Msa1383060 MtrunA17_Chr1g0158631 42.391 92 47 2 27 117 33 119 2.38e-14 68.9
Msa1383060 MtrunA17_Chr1g0158331 34.426 122 70 3 1 117 17 133 3.98e-14 68.2
Msa1383060 MtrunA17_Chr1g0158301 33.577 137 71 6 1 126 16 143 9.95e-13 64.3
Msa1383060 MtrunA17_Chr1g0158731 35.246 122 67 4 4 118 8 124 1.05e-12 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCCTCCTTATTATTCTTT+AGG 0.151819 tig0020564:+50738 Msa1383060:CDS
TCCCTCCTTATTATTCTTTA+GGG 0.210688 tig0020564:+50739 Msa1383060:CDS
CATTATTCTCCTCACATAAT+AGG 0.233904 tig0020564:-50596 None:intergenic
CAACTTCACCATACGACTAT+TGG 0.252740 tig0020564:+50686 Msa1383060:CDS
CTCTTGTCACCACATTCTTC+TGG 0.284196 tig0020564:-50567 None:intergenic
TAAAGCCCTAAAGAATAATA+AGG 0.353798 tig0020564:-50744 None:intergenic
TAACAGCACGACAAGGGTTA+AGG 0.424277 tig0020564:-50433 None:intergenic
TTTCGTATCCATTAAAAGCT+AGG 0.462412 tig0020564:-50800 None:intergenic
GTATCCATTAAAAGCTAGGT+AGG 0.522243 tig0020564:-50796 None:intergenic
TAAAGAATAATAAGGAGGGA+TGG 0.555369 tig0020564:-50736 None:intergenic
ATTGAAATCCAATAGTCGTA+TGG 0.568248 tig0020564:-50694 None:intergenic
GCCCTAAAGAATAATAAGGA+GGG 0.574069 tig0020564:-50740 None:intergenic
TTCTCGTACAACAAAGTGCA+TGG 0.590113 tig0020564:+50468 Msa1383060:CDS
ATTAAAAGCTAGGTAGGGTG+AGG 0.606952 tig0020564:-50790 None:intergenic
AACAAGAGTCATGTTCAAGA+AGG 0.614007 tig0020564:+50499 Msa1383060:CDS
CAGAAGAATGTGGTGACAAG+AGG 0.621774 tig0020564:+50568 Msa1383060:CDS
AGCCCTAAAGAATAATAAGG+AGG 0.622034 tig0020564:-50741 None:intergenic
TATCCATTAAAAGCTAGGTA+GGG 0.625375 tig0020564:-50795 None:intergenic
GTATTATTAACAGCACGACA+AGG 0.626342 tig0020564:-50440 None:intergenic
TATGAATTTGAAGAATACCA+TGG 0.632125 tig0020564:+50633 Msa1383060:CDS
TATTATTAACAGCACGACAA+GGG 0.643162 tig0020564:-50439 None:intergenic
GAGTCATGTTCAAGAAGGTG+CGG 0.657869 tig0020564:+50504 Msa1383060:CDS
GAGGTACAACCTATTATGTG+AGG 0.678478 tig0020564:+50587 Msa1383060:CDS
AAAGACAGTCCAGAAGAATG+TGG 0.689791 tig0020564:+50558 Msa1383060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGTACATAATATTTTCCA+TGG - tig0020564:50653-50672 None:intergenic 20.0%
! TATGAATTTGAAGAATACCA+TGG + tig0020564:50633-50652 Msa1383060:CDS 25.0%
! TAAAGCCCTAAAGAATAATA+AGG - tig0020564:50747-50766 None:intergenic 25.0%
TATTATTAACAGCACGACAA+GGG - tig0020564:50442-50461 None:intergenic 30.0%
CATTATTCTCCTCACATAAT+AGG - tig0020564:50599-50618 None:intergenic 30.0%
ATTGAAATCCAATAGTCGTA+TGG - tig0020564:50697-50716 None:intergenic 30.0%
TAAAGAATAATAAGGAGGGA+TGG - tig0020564:50739-50758 None:intergenic 30.0%
ATCCCTCCTTATTATTCTTT+AGG + tig0020564:50738-50757 Msa1383060:CDS 30.0%
TCCCTCCTTATTATTCTTTA+GGG + tig0020564:50739-50758 Msa1383060:CDS 30.0%
TATCCATTAAAAGCTAGGTA+GGG - tig0020564:50798-50817 None:intergenic 30.0%
TTTCGTATCCATTAAAAGCT+AGG - tig0020564:50803-50822 None:intergenic 30.0%
GTATTATTAACAGCACGACA+AGG - tig0020564:50443-50462 None:intergenic 35.0%
AACAAGAGTCATGTTCAAGA+AGG + tig0020564:50499-50518 Msa1383060:CDS 35.0%
! ATAACATTAGCCCTCCTTTT+AGG + tig0020564:50532-50551 Msa1383060:CDS 35.0%
! TGTCTTTTAGCCTAAAAGGA+GGG - tig0020564:50545-50564 None:intergenic 35.0%
GCCCTAAAGAATAATAAGGA+GGG - tig0020564:50743-50762 None:intergenic 35.0%
AGCCCTAAAGAATAATAAGG+AGG - tig0020564:50744-50763 None:intergenic 35.0%
GTATCCATTAAAAGCTAGGT+AGG - tig0020564:50799-50818 None:intergenic 35.0%
TTCTCGTACAACAAAGTGCA+TGG + tig0020564:50468-50487 Msa1383060:CDS 40.0%
! CTGTCTTTTAGCCTAAAAGG+AGG - tig0020564:50546-50565 None:intergenic 40.0%
! GGACTGTCTTTTAGCCTAAA+AGG - tig0020564:50549-50568 None:intergenic 40.0%
AAAGACAGTCCAGAAGAATG+TGG + tig0020564:50558-50577 Msa1383060:CDS 40.0%
GAGGTACAACCTATTATGTG+AGG + tig0020564:50587-50606 Msa1383060:CDS 40.0%
CAACTTCACCATACGACTAT+TGG + tig0020564:50686-50705 Msa1383060:CDS 40.0%
ATTAAAAGCTAGGTAGGGTG+AGG - tig0020564:50793-50812 None:intergenic 40.0%
!! TCACCCTACCTAGCTTTTAA+TGG + tig0020564:50792-50811 Msa1383060:CDS 40.0%
TAACAGCACGACAAGGGTTA+AGG - tig0020564:50436-50455 None:intergenic 45.0%
GAGTCATGTTCAAGAAGGTG+CGG + tig0020564:50504-50523 Msa1383060:CDS 45.0%
CTCTTGTCACCACATTCTTC+TGG - tig0020564:50570-50589 None:intergenic 45.0%
CAGAAGAATGTGGTGACAAG+AGG + tig0020564:50568-50587 Msa1383060:CDS 45.0%
Chromosome Type Strat End Strand Name
tig0020564 gene 50426 50869 50426 ID=Msa1383060;Name=Msa1383060
tig0020564 mRNA 50426 50869 50426 ID=Msa1383060-mRNA-1;Parent=Msa1383060;Name=Msa1383060-mRNA-1;_AED=0.21;_eAED=0.23;_QI=0|-1|0|1|-1|1|1|0|147
tig0020564 exon 50426 50869 50426 ID=Msa1383060-mRNA-1:exon:8432;Parent=Msa1383060-mRNA-1
tig0020564 CDS 50426 50869 50426 ID=Msa1383060-mRNA-1:cds;Parent=Msa1383060-mRNA-1
Gene Sequence

>Msa1383060

ATGTCTTCCTTAACCCTTGTCGTGCTGTTAATAATACTGATATTCTCGTACAACAAAGTGCATGGTGATGAACAACAAGAGTCATGTTCAAGAAGGTGCGGTGTTCATAACATTAGCCCTCCTTTTAGGCTAAAAGACAGTCCAGAAGAATGTGGTGACAAGAGGTACAACCTATTATGTGAGGAGAATAATGAATTGATTTTGTACTATGAATTTGAAGAATACCATGGAAAATATTATGTACAATCAATTAATTACAACAACTTCACCATACGACTATTGGATTTCAATCTTGCTTCTTCTAATAATTCCATCCCTCCTTATTATTCTTTAGGGCTTTATAATTTCAGTTCTAACTTCATCACCTCACCCTACCTAGCTTTTAATGGATACGAAAACTACACTCATCATATATTGACGAAATCTATGTTATATTATATGTGA
Protein sequence

>Msa1383060

MSSLTLVVLLIILIFSYNKVHGDEQQESCSRRCGVHNISPPFRLKDSPEECGDKRYNLLCEENNELILYYEFEEYHGKYYVQSINYNNFTIRLLDFNLASSNNSIPPYYSLGLYNFSSNFITSPYLAFNGYENYTHHILTKSMLYYM*