AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0627870

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627870 MtrunA17_Chr8g0382931 94.089 203 5 1 1 196 1 203 1.69e-141 392
Msa0627870 MtrunA17_Chr5g0446491 79.487 117 22 1 13 129 10 124 6.36e-63 192
Msa0627870 MtrunA17_Chr2g0290491 80.702 114 20 1 24 137 13 124 2.03e-62 191
Msa0627870 MtrunA17_Chr3g0102351 87.879 99 12 0 25 123 24 122 3.18e-60 186
Msa0627870 MtrunA17_Chr7g0263601 75.439 114 28 0 13 126 11 124 1.05e-59 184
Msa0627870 MtrunA17_Chr8g0384451 76.636 107 25 0 27 133 39 145 1.13e-56 178
Msa0627870 MtrunA17_Chr1g0185911 71.681 113 30 1 23 133 24 136 1.86e-54 171
Msa0627870 MtrunA17_Chr4g0076321 74.312 109 28 0 17 125 8 116 1.71e-53 167
Msa0627870 MtrunA17_Chr1g0195851 69.307 101 31 0 22 122 30 130 1.44e-48 157
Msa0627870 MtrunA17_Chr2g0296321 65.385 104 36 0 22 125 60 163 5.78e-47 154
Msa0627870 MtrunA17_Chr4g0076381 64.948 97 34 0 27 123 57 153 3.81e-46 152
Msa0627870 MtrunA17_Chr4g0067091 62.963 108 40 0 12 119 6 113 8.58e-46 150
Msa0627870 MtrunA17_Chr1g0165041 62.745 102 38 0 27 128 5 106 1.08e-44 146
Msa0627870 MtrunA17_Chr1g0191981 61.957 92 35 0 28 119 4 95 6.04e-39 130
Msa0627870 MtrunA17_Chr1g0159271 55.294 85 38 0 42 126 1 85 4.99e-27 99.0
Msa0627870 MtrunA17_Chr5g0446601 44.330 97 51 1 24 117 17 113 1.33e-21 87.4
Msa0627870 MtrunA17_Chr1g0158951 53.125 64 30 0 58 121 19 82 1.66e-18 77.0
Msa0627870 MtrunA17_Chr1g0159291 40.789 76 45 0 33 108 7 82 1.48e-17 73.9
Msa0627870 MtrunA17_Chr2g0307551 32.143 84 57 0 22 105 5 88 5.38e-14 66.6
Msa0627870 MtrunA17_Chr4g0062271 33.766 77 51 0 29 105 12 88 2.04e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627870 AT4G14540.1 81.818 110 20 0 24 133 17 126 3.79e-64 195
Msa0627870 AT5G47640.1 85.859 99 14 0 25 123 24 122 6.71e-60 186
Msa0627870 AT2G13570.1 74.576 118 29 1 8 125 17 133 1.99e-59 185
Msa0627870 AT3G53340.5 68.800 125 28 2 14 133 21 139 1.94e-56 176
Msa0627870 AT3G53340.1 68.800 125 28 2 14 133 21 139 1.94e-56 176
Msa0627870 AT2G37060.2 71.552 116 28 1 27 137 29 144 4.71e-56 175
Msa0627870 AT2G37060.3 71.552 116 28 1 27 137 29 144 4.71e-56 175
Msa0627870 AT2G37060.1 71.552 116 28 1 27 137 29 144 4.71e-56 175
Msa0627870 AT2G38880.3 69.643 112 34 0 14 125 7 118 8.06e-55 171
Msa0627870 AT3G53340.4 75.238 105 20 1 14 118 21 119 9.35e-55 170
Msa0627870 AT2G38880.2 69.643 112 34 0 14 125 7 118 1.25e-54 171
Msa0627870 AT2G38880.1 69.643 112 34 0 14 125 7 118 1.25e-54 171
Msa0627870 AT2G38880.5 69.643 112 34 0 14 125 7 118 1.25e-54 171
Msa0627870 AT3G53340.3 75.472 106 20 1 14 119 21 120 2.76e-54 170
Msa0627870 AT3G53340.2 75.472 106 20 1 14 119 21 120 2.76e-54 170
Msa0627870 AT2G38880.4 71.429 105 30 0 14 118 7 111 1.17e-52 164
Msa0627870 AT2G38880.7 67.544 114 37 0 14 127 7 120 1.44e-52 165
Msa0627870 AT2G38880.11 71.429 105 30 0 14 118 7 111 3.44e-52 165
Msa0627870 AT2G38880.8 71.429 105 30 0 14 118 7 111 3.44e-52 165
Msa0627870 AT2G38880.9 77.660 94 21 0 25 118 18 111 5.53e-52 164
Msa0627870 AT2G38880.10 77.660 94 21 0 25 118 18 111 5.53e-52 164
Msa0627870 AT2G38880.6 77.660 94 21 0 25 118 18 111 5.53e-52 164
Msa0627870 AT2G47810.1 71.845 103 29 0 22 124 45 147 3.85e-51 162
Msa0627870 AT5G47670.2 60.714 112 44 0 16 127 17 128 6.27e-48 155
Msa0627870 AT5G47670.1 60.714 112 44 0 16 127 46 157 1.55e-47 155
Msa0627870 AT5G47670.3 60.714 112 44 0 16 127 46 157 1.55e-47 155
Msa0627870 AT1G21970.1 62.000 100 38 0 26 125 57 156 2.57e-45 150
Msa0627870 AT1G09030.1 62.500 96 36 0 28 123 3 98 1.26e-42 140
Msa0627870 AT5G08190.2 35.897 78 50 0 28 105 11 88 1.74e-14 68.2
Msa0627870 AT5G08190.1 35.897 78 50 0 28 105 11 88 1.87e-14 68.2
Msa0627870 AT5G23090.5 33.766 77 51 0 29 105 12 88 5.10e-14 67.0
Msa0627870 AT5G23090.2 33.766 77 51 0 29 105 12 88 5.10e-14 67.0
Msa0627870 AT5G23090.1 33.766 77 51 0 29 105 12 88 5.10e-14 67.0
Msa0627870 AT5G23090.4 33.766 77 51 0 29 105 12 88 5.10e-14 67.0

Find 42 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATGGTGATGATCTTCTT+TGG 0.277181 4_3:-8303271 Msa0627870:CDS
TTAATCTCTTGGAACCTCTT+TGG 0.292077 4_3:+8303074 None:intergenic
AAGTTTATCTTAATAATTAT+AGG 0.297968 4_3:-8303205 Msa0627870:CDS
GAGTTCATAAGTTTCATTAC+TGG 0.304041 4_3:-8303335 Msa0627870:CDS
TGCCACCAAACCTACGTTAC+AGG 0.318400 4_3:-8302974 Msa0627870:CDS
GAAAAGAGGAAAACAATTAA+TGG 0.329176 4_3:-8303287 Msa0627870:CDS
AGTTTATCTTAATAATTATA+GGG 0.334719 4_3:-8303204 Msa0627870:CDS
ATTGTGGATTATAGAGTAAT+TGG 0.335947 4_3:-8303044 Msa0627870:CDS
AAGAGGTTCCAAGAGATTAA+TGG 0.350652 4_3:-8303071 Msa0627870:CDS
ATTATTAATTTCAACATGTC+CGG 0.359734 4_3:-8303545 None:intergenic
TAATGGTGATGATCTTCTTT+GGG 0.364795 4_3:-8303270 Msa0627870:CDS
GACTTCCTACAGGACTTGTT+TGG 0.366205 4_3:+8303510 None:intergenic
TGTTTGGTTTCTCTTATTCC+CGG 0.387356 4_3:+8303526 None:intergenic
CAATCCCTCCATTAATCTCT+TGG 0.406112 4_3:+8303063 None:intergenic
GATGAAACAGAACATGCAAT+TGG 0.429214 4_3:-8303014 Msa0627870:CDS
CCTGATGTTGGACTTCCTAC+AGG 0.434628 4_3:+8303500 None:intergenic
ATACGGCTCACGTTGGCAAT+TGG 0.452960 4_3:+8303431 None:intergenic
TCTGAGATGTTTCCTGATGT+TGG 0.453105 4_3:+8303488 None:intergenic
CTTTGGGCTATGACAACACT+TGG 0.464387 4_3:-8303254 Msa0627870:CDS
AATAATTATAGGGAAATTGA+AGG 0.468083 4_3:-8303194 Msa0627870:CDS
TCAACCCTGTAACGTAGGTT+TGG 0.472415 4_3:+8302969 None:intergenic
TCAATTGATGTTAATGATGT+TGG 0.481755 4_3:-8303113 Msa0627870:CDS
CCTGTAGGAAGTCCAACATC+AGG 0.498605 4_3:-8303500 Msa0627870:CDS
ACCTACGTTACAGGGTTGAA+TGG 0.502904 4_3:-8302965 Msa0627870:CDS
TTATTAATTTCAACATGTCC+GGG 0.509564 4_3:-8303544 None:intergenic
AGAGATTAATGGAGGGATTG+TGG 0.513734 4_3:-8303060 Msa0627870:CDS
ACAGAACATGCAATTGGAAG+TGG 0.518322 4_3:-8303008 Msa0627870:CDS
CTCAAAAGAAGCAAAGGAAA+CGG 0.525390 4_3:-8303375 Msa0627870:CDS
ATTGATGTTAATGATGTTGG+TGG 0.525414 4_3:-8303110 Msa0627870:CDS
ACCCTGTAACGTAGGTTTGG+TGG 0.528618 4_3:+8302972 None:intergenic
GATGTTAATGATGTTGGTGG+TGG 0.530464 4_3:-8303107 Msa0627870:CDS
CATCATCAAAAGAACAAGAC+AGG 0.530857 4_3:-8303460 Msa0627870:CDS
ATAAGTGCCAGAGAGAAAAG+AGG 0.537335 4_3:-8303301 Msa0627870:CDS
TTATTAAGATAAACTTTCAA+AGG 0.539135 4_3:+8303212 None:intergenic
GCCACCAAACCTACGTTACA+GGG 0.557356 4_3:-8302973 Msa0627870:CDS
TAAAATCTCAAAAGAAGCAA+AGG 0.579705 4_3:-8303381 Msa0627870:CDS
AGAAACCAAACAAGTCCTGT+AGG 0.592028 4_3:-8303515 Msa0627870:CDS
GGCTCACGTTGGCAATTGGT+AGG 0.609486 4_3:+8303435 None:intergenic
ACCATTCAACCCTGTAACGT+AGG 0.617328 4_3:+8302964 None:intergenic
AGGTTCCAAGAGATTAATGG+AGG 0.632716 4_3:-8303068 Msa0627870:CDS
GGTTCCAAGAGATTAATGGA+GGG 0.665223 4_3:-8303067 Msa0627870:CDS
TTTCATTATACGGCTCACGT+TGG 0.672250 4_3:+8303424 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTTTATCTTAATAATTAT+AGG - chr4_3:8303287-8303306 Msa0627870:CDS 10.0%
!! AGTTTATCTTAATAATTATA+GGG - chr4_3:8303288-8303307 Msa0627870:CDS 10.0%
!! TTATTAAGATAAACTTTCAA+AGG + chr4_3:8303283-8303302 None:intergenic 15.0%
!! AATAATTATAGGGAAATTGA+AGG - chr4_3:8303298-8303317 Msa0627870:CDS 20.0%
! TAAAATCTCAAAAGAAGCAA+AGG - chr4_3:8303111-8303130 Msa0627870:CDS 25.0%
! GAAAAGAGGAAAACAATTAA+TGG - chr4_3:8303205-8303224 Msa0627870:CDS 25.0%
! TCAATTGATGTTAATGATGT+TGG - chr4_3:8303379-8303398 Msa0627870:CDS 25.0%
!! ATTGTGGATTATAGAGTAAT+TGG - chr4_3:8303448-8303467 Msa0627870:CDS 25.0%
!! TTTGAGATTTTAGCATTTGC+TGG + chr4_3:8303103-8303122 None:intergenic 30.0%
GAGTTCATAAGTTTCATTAC+TGG - chr4_3:8303157-8303176 Msa0627870:CDS 30.0%
! TTAATGGTGATGATCTTCTT+TGG - chr4_3:8303221-8303240 Msa0627870:CDS 30.0%
! TAATGGTGATGATCTTCTTT+GGG - chr4_3:8303222-8303241 Msa0627870:CDS 30.0%
!!! CTTGGTTTTGAAAACTATGT+TGG - chr4_3:8303256-8303275 Msa0627870:CDS 30.0%
ATTGATGTTAATGATGTTGG+TGG - chr4_3:8303382-8303401 Msa0627870:CDS 30.0%
! TGTTTGGTTTCTCTTATTCC+CGG + chr4_3:8302969-8302988 None:intergenic 35.0%
CATCATCAAAAGAACAAGAC+AGG - chr4_3:8303032-8303051 Msa0627870:CDS 35.0%
! GAAGGGCTCTTTTCATTATA+CGG + chr4_3:8303081-8303100 None:intergenic 35.0%
!! GATTTTAGCATTTGCTGGAA+GGG + chr4_3:8303098-8303117 None:intergenic 35.0%
!! AGATTTTAGCATTTGCTGGA+AGG + chr4_3:8303099-8303118 None:intergenic 35.0%
CTCAAAAGAAGCAAAGGAAA+CGG - chr4_3:8303117-8303136 Msa0627870:CDS 35.0%
! TTGTTTTCCTCTTTTCTCTC+TGG + chr4_3:8303201-8303220 None:intergenic 35.0%
TTAATCTCTTGGAACCTCTT+TGG + chr4_3:8303421-8303440 None:intergenic 35.0%
AAGAGGTTCCAAGAGATTAA+TGG - chr4_3:8303421-8303440 Msa0627870:CDS 35.0%
GATGAAACAGAACATGCAAT+TGG - chr4_3:8303478-8303497 Msa0627870:CDS 35.0%
AGAAACCAAACAAGTCCTGT+AGG - chr4_3:8302977-8302996 Msa0627870:CDS 40.0%
! TCTGAGATGTTTCCTGATGT+TGG + chr4_3:8303007-8303026 None:intergenic 40.0%
TTTCATTATACGGCTCACGT+TGG + chr4_3:8303071-8303090 None:intergenic 40.0%
ATAAGTGCCAGAGAGAAAAG+AGG - chr4_3:8303191-8303210 Msa0627870:CDS 40.0%
! GATGTTAATGATGTTGGTGG+TGG - chr4_3:8303385-8303404 Msa0627870:CDS 40.0%
! GTGGATTTTATGCTCCAAAG+AGG - chr4_3:8303404-8303423 Msa0627870:CDS 40.0%
AGGTTCCAAGAGATTAATGG+AGG - chr4_3:8303424-8303443 Msa0627870:CDS 40.0%
GGTTCCAAGAGATTAATGGA+GGG - chr4_3:8303425-8303444 Msa0627870:CDS 40.0%
CAATCCCTCCATTAATCTCT+TGG + chr4_3:8303432-8303451 None:intergenic 40.0%
AGAGATTAATGGAGGGATTG+TGG - chr4_3:8303432-8303451 Msa0627870:CDS 40.0%
ACAGAACATGCAATTGGAAG+TGG - chr4_3:8303484-8303503 Msa0627870:CDS 40.0%
! GACTTCCTACAGGACTTGTT+TGG + chr4_3:8302985-8303004 None:intergenic 45.0%
CTTTGGGCTATGACAACACT+TGG - chr4_3:8303238-8303257 Msa0627870:CDS 45.0%
TCAACCCTGTAACGTAGGTT+TGG + chr4_3:8303526-8303545 None:intergenic 45.0%
ACCTACGTTACAGGGTTGAA+TGG - chr4_3:8303527-8303546 Msa0627870:CDS 45.0%
ACCATTCAACCCTGTAACGT+AGG + chr4_3:8303531-8303550 None:intergenic 45.0%
CCTGATGTTGGACTTCCTAC+AGG + chr4_3:8302995-8303014 None:intergenic 50.0%
CCTGTAGGAAGTCCAACATC+AGG - chr4_3:8302992-8303011 Msa0627870:CDS 50.0%
ATACGGCTCACGTTGGCAAT+TGG + chr4_3:8303064-8303083 None:intergenic 50.0%
TGCCACCAAACCTACGTTAC+AGG - chr4_3:8303518-8303537 Msa0627870:CDS 50.0%
GCCACCAAACCTACGTTACA+GGG - chr4_3:8303519-8303538 Msa0627870:CDS 50.0%
ACCCTGTAACGTAGGTTTGG+TGG + chr4_3:8303523-8303542 None:intergenic 50.0%
GGCTCACGTTGGCAATTGGT+AGG + chr4_3:8303060-8303079 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 8302962 8303552 8302962 ID=Msa0627870;Name=Msa0627870
chr4_3 mRNA 8302962 8303552 8302962 ID=Msa0627870-mRNA-1;Parent=Msa0627870;Name=Msa0627870-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|-1|0|1|-1|1|1|0|196
chr4_3 exon 8302962 8303552 8302962 ID=Msa0627870-mRNA-1:exon:2442;Parent=Msa0627870-mRNA-1
chr4_3 CDS 8302962 8303552 8302962 ID=Msa0627870-mRNA-1:cds;Parent=Msa0627870-mRNA-1
Gene Sequence

>Msa0627870

ATGTCCGGGAATAAGAGAAACCAAACAAGTCCTGTAGGAAGTCCAACATCAGGAAACATCTCAGACAGTTCATCATCAAAAGAACAAGACAGGTTCCTACCAATTGCCAACGTGAGCCGTATAATGAAAAGAGCCCTTCCAGCAAATGCTAAAATCTCAAAAGAAGCAAAGGAAACGGTTCAAGAATGTGTCTCTGAGTTCATAAGTTTCATTACTGGTGAAGCTTCTGATAAGTGCCAGAGAGAAAAGAGGAAAACAATTAATGGTGATGATCTTCTTTGGGCTATGACAACACTTGGTTTTGAAAACTATGTTGGTCCTTTGAAAGTTTATCTTAATAATTATAGGGAAATTGAAGGAGAAAAGAGTAATTCTAGTGCTACTAAACAAGATGATCAATATGATCATAATTCTTCTTCAATTGATGTTAATGATGTTGGTGGTGGATTTTATGCTCCAAAGAGGTTCCAAGAGATTAATGGAGGGATTGTGGATTATAGAGTAATTGGTAATAGTGATGAAACAGAACATGCAATTGGAAGTGGTAATAGAATCATGCCACCAAACCTACGTTACAGGGTTGAATGGTAG
Protein sequence

>Msa0627870

MSGNKRNQTSPVGSPTSGNISDSSSSKEQDRFLPIANVSRIMKRALPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVGPLKVYLNNYREIEGEKSNSSATKQDDQYDHNSSSIDVNDVGGGFYAPKRFQEINGGIVDYRVIGNSDETEHAIGSGNRIMPPNLRYRVEW*