AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1462780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1462780 MtrunA17_Chr8g0391341 97.222 216 6 0 1 216 1 216 3.14e-158 436
Msa1462780 MtrunA17_Chr4g0067891 93.056 216 6 1 1 216 1 207 8.88e-148 409
Msa1462780 MtrunA17_Chr3g0079401 39.888 178 95 4 38 213 19 186 3.37e-38 130
Msa1462780 MtrunA17_Chr4g0056601 34.951 206 118 5 9 213 11 201 5.16e-37 128
Msa1462780 MtrunA17_Chr4g0018281 40.588 170 87 4 44 211 36 193 6.89e-37 127
Msa1462780 MtrunA17_Chr5g0398871 40.351 171 93 4 42 211 46 208 4.78e-36 126
Msa1462780 MtrunA17_Chr4g0018251 40.237 169 89 3 44 211 36 193 1.20e-35 124
Msa1462780 MtrunA17_Chr4g0018241 37.688 199 107 5 11 208 8 190 4.74e-35 123
Msa1462780 MtrunA17_Chr3g0079381 36.932 176 99 4 38 211 18 183 5.01e-34 120
Msa1462780 MtrunA17_Chr4g0011711 34.884 172 107 2 44 213 32 200 3.38e-33 119
Msa1462780 MtrunA17_Chr4g0011701 32.850 207 126 4 9 213 5 200 7.19e-33 117
Msa1462780 MtrunA17_Chr1g0195561 34.419 215 117 5 1 215 1 191 8.23e-33 117
Msa1462780 MtrunA17_Chr7g0269361 34.884 172 100 3 45 216 34 193 1.20e-32 117
Msa1462780 MtrunA17_Chr4g0011681 30.952 210 132 4 6 213 2 200 1.01e-31 115
Msa1462780 MtrunA17_Chr3g0079371 33.333 183 113 2 28 209 50 224 5.82e-31 113
Msa1462780 MtrunA17_Chr4g0011721 33.721 172 109 2 44 213 32 200 1.58e-30 112
Msa1462780 MtrunA17_Chr2g0301381 36.994 173 89 4 43 212 33 188 5.05e-28 105
Msa1462780 MtrunA17_Chr4g0018231 31.925 213 132 6 1 211 1 202 3.23e-26 100
Msa1462780 MtrunA17_Chr7g0230391 34.706 170 101 5 43 206 42 207 2.84e-25 98.6
Msa1462780 MtrunA17_Chr4g0070161 31.884 207 113 9 7 208 11 194 3.30e-25 97.8
Msa1462780 MtrunA17_Chr3g0092681 32.317 164 90 6 45 207 78 221 5.81e-17 76.6
Msa1462780 MtrunA17_Chr3g0080391 29.697 165 101 4 45 207 71 222 3.20e-16 76.6
Msa1462780 MtrunA17_Chr8g0354901 29.518 166 101 4 45 207 76 228 3.00e-15 73.9
Msa1462780 MtrunA17_Chr8g0345211 25.150 167 108 3 45 208 77 229 5.89e-14 70.1
Msa1462780 MtrunA17_Chr8g0345281 25.581 172 117 3 44 213 67 229 3.18e-13 68.2
Msa1462780 MtrunA17_Chr3g0126771 25.000 200 140 4 9 206 42 233 1.57e-12 65.9
Msa1462780 MtrunA17_Chr1g0147051 26.506 166 113 4 45 206 82 242 1.97e-12 65.9
Msa1462780 MtrunA17_Chr7g0272141 24.623 199 137 4 10 206 3 190 5.96e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1462780 AT2G01610.1 56.842 190 76 4 33 216 33 222 2.34e-70 214
Msa1462780 AT1G14890.1 54.106 207 77 5 9 214 29 218 1.23e-68 209
Msa1462780 AT1G23205.1 53.846 182 74 3 39 215 28 204 6.31e-60 187
Msa1462780 AT1G70720.2 44.860 214 106 4 3 215 8 210 1.68e-57 181
Msa1462780 AT1G70720.1 47.959 196 90 4 21 215 14 198 1.35e-56 178
Msa1462780 AT5G62350.1 40.642 187 103 3 27 212 21 200 5.62e-40 136
Msa1462780 AT4G25260.1 37.745 204 115 5 12 213 7 200 3.69e-39 134
Msa1462780 AT3G47380.1 39.153 189 105 4 28 213 20 201 2.39e-37 129
Msa1462780 AT4G12390.1 41.520 171 93 3 44 213 39 203 5.09e-36 126
Msa1462780 AT1G62770.1 37.968 187 106 5 29 213 20 198 5.30e-35 123
Msa1462780 AT4G25250.1 32.020 203 127 5 9 210 4 196 1.22e-33 119
Msa1462780 AT5G20740.1 36.019 211 114 6 10 216 7 200 9.03e-33 117
Msa1462780 AT5G20740.2 35.096 208 120 5 10 216 41 234 3.11e-32 117
Msa1462780 AT1G62760.1 37.209 172 97 4 41 211 144 305 3.94e-31 116
Msa1462780 AT5G51520.1 31.220 205 121 5 10 207 8 199 5.10e-31 113
Msa1462780 AT5G62360.1 35.294 170 97 4 43 211 42 199 7.55e-31 112
Msa1462780 AT4G00080.1 30.542 203 122 5 9 207 9 196 9.59e-26 99.8
Msa1462780 AT2G47670.1 32.370 173 104 4 44 215 48 208 7.48e-21 87.0
Msa1462780 AT3G62820.1 26.829 205 126 5 13 215 12 194 2.42e-20 85.1
Msa1462780 AT3G14300.1 27.059 170 108 4 45 207 271 431 1.01e-15 75.9
Msa1462780 AT3G14300.1 26.437 174 118 5 42 213 456 621 1.90e-11 63.2
Msa1462780 AT5G53370.2 26.066 211 135 7 10 216 78 271 1.10e-14 72.8
Msa1462780 AT5G53370.1 26.066 211 135 7 10 216 42 235 1.26e-14 72.4
Msa1462780 AT3G49220.3 28.293 205 115 4 10 206 97 277 4.52e-14 70.9
Msa1462780 AT3G49220.1 28.293 205 115 4 10 206 52 232 4.73e-14 70.9
Msa1462780 AT3G49220.2 28.293 205 115 4 10 206 97 277 5.38e-14 70.5
Msa1462780 AT5G62340.1 27.232 224 133 10 1 213 1 205 2.57e-13 66.6
Msa1462780 AT1G53830.1 25.301 166 112 4 44 207 61 216 6.57e-11 61.6

Find 61 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGCTTTGGCACTTGTTAA+TGG 0.258713 tig0042596:-11144 Msa1462780:CDS
GTTAATGGTTACGCACAAAA+AGG 0.286538 tig0042596:-11129 Msa1462780:CDS
GCAACTTGAACGGATGAATT+CGG 0.350009 tig0042596:+11623 Msa1462780:intergenic
TCTGCTCCGGTGGCGGTTGT+TGG 0.357625 tig0042596:+11672 Msa1462780:intergenic
CGAAGAAGATGATTGATAAT+AGG 0.374294 tig0042596:+11718 Msa1462780:intergenic
CAGATTGGAGCCGTGGGAAC+TGG 0.389443 tig0042596:-11339 Msa1462780:CDS
ATCTGCTTCGCGAGTGAGAT+TGG 0.399064 tig0042596:+11461 Msa1462780:intergenic
GGCGGTTGTTGGACGGAGAT+TGG 0.404587 tig0042596:+11683 Msa1462780:intergenic
GTGGGAACTGGCGCCGGTGC+CGG 0.407860 tig0042596:-11327 Msa1462780:CDS
AGGGAAGTGTAGCATATGTC+AGG 0.436656 tig0042596:+11585 Msa1462780:intergenic
GTGGACTTTGGAGAAGCTTA+CGG 0.443650 tig0042596:+11503 Msa1462780:intergenic
AAAGTTCACGAGTAATGCTT+TGG 0.448902 tig0042596:-11157 Msa1462780:CDS
TTTGGAGAAGCTTACGGCTA+TGG 0.464721 tig0042596:+11509 Msa1462780:intergenic
GGGATTCTGTTGAACTGCAT+TGG 0.465344 tig0042596:+11551 Msa1462780:intergenic
AGAGGCGGTTCGGTGGACTT+TGG 0.468926 tig0042596:+11491 Msa1462780:intergenic
CTTAAACAGATGCGACAGAT+TGG 0.471352 tig0042596:-11354 Msa1462780:CDS
CTCCGGTGGCGGTTGTTGGA+CGG 0.475048 tig0042596:+11676 Msa1462780:intergenic
GGCGATGCGAGCGAGTTGGC+CGG 0.484500 tig0042596:+11530 Msa1462780:intergenic
GCGTCGTCGTTGGTGGTGGT+TGG 0.487249 tig0042596:+11645 Msa1462780:intergenic
GAGGAAACTGTGAGAGTGTT+GGG 0.489323 tig0042596:+11740 Msa1462780:intergenic
TGGAGGTTCTGCTCCGGTGG+CGG 0.492157 tig0042596:+11665 Msa1462780:intergenic
GGAGGAAACTGTGAGAGTGT+TGG 0.492920 tig0042596:+11739 Msa1462780:intergenic
AAACGAATCTGCTCCGGCAC+CGG 0.499792 tig0042596:+11314 Msa1462780:intergenic
TTCTGTACATCCGCTTTCAC+AGG 0.501048 tig0042596:+11198 Msa1462780:intergenic
TCGTCGTTGGTGGTGGTTGG+AGG 0.502344 tig0042596:+11648 Msa1462780:intergenic
CTCCGTCCAACAACCGCCAC+CGG 0.510383 tig0042596:-11678 Msa1462780:CDS
TGGAGAGATAAGAGGCGGTT+CGG 0.511261 tig0042596:+11481 Msa1462780:intergenic
GGTGGTTGGAGGTTCTGCTC+CGG 0.513292 tig0042596:+11659 Msa1462780:intergenic
GATGAATTCGGCGTCGTCGT+TGG 0.515433 tig0042596:+11635 Msa1462780:intergenic
GGAGCCGTGGGAACTGGCGC+CGG 0.519876 tig0042596:-11333 Msa1462780:CDS
TTCGGCGTCGTCGTTGGTGG+TGG 0.522970 tig0042596:+11641 Msa1462780:intergenic
AGTGAGATTGGAGAGATAAG+AGG 0.523775 tig0042596:+11473 Msa1462780:intergenic
GGCACCGGCGCCAGTTCCCA+CGG 0.524682 tig0042596:+11329 Msa1462780:intergenic
CTGCATTGGCGTAGCGAGAG+AGG 0.532228 tig0042596:+11565 Msa1462780:intergenic
AGAAGATGATTGATAATAGG+AGG 0.540415 tig0042596:+11721 Msa1462780:intergenic
GAATTCGGCGTCGTCGTTGG+TGG 0.541966 tig0042596:+11638 Msa1462780:intergenic
AAACAGAAACGAATCTGCTC+CGG 0.547260 tig0042596:+11308 Msa1462780:intergenic
GGTTGGAGGTTCTGCTCCGG+TGG 0.548791 tig0042596:+11662 Msa1462780:intergenic
GCGATGCGAGCGAGTTGGCC+GGG 0.559441 tig0042596:+11531 Msa1462780:intergenic
TGCATTGGCGTAGCGAGAGA+GGG 0.576173 tig0042596:+11566 Msa1462780:intergenic
TGTACAGAATCGTGTCTCGA+AGG 0.577511 tig0042596:-11184 Msa1462780:CDS
CTATGGCGATGCGAGCGAGT+TGG 0.577700 tig0042596:+11526 Msa1462780:intergenic
TACTGATGAAGAAACGTGTA+CGG 0.583108 tig0042596:-11247 Msa1462780:CDS
CGAGATTTGAGAAACAGTCA+TGG 0.583249 tig0042596:+11406 Msa1462780:intergenic
GATGCGACAGATTGGAGCCG+TGG 0.584501 tig0042596:-11346 Msa1462780:CDS
GATGAAGAAACGTGTACGGA+TGG 0.588482 tig0042596:-11243 Msa1462780:CDS
ACAGTCATGGAGAGCGAGTG+CGG 0.590149 tig0042596:+11419 Msa1462780:intergenic
AATGCAGTTCAACAGAATCC+CGG 0.598872 tig0042596:-11549 Msa1462780:CDS
AGATGAGTAACGTGCAGACG+TGG 0.606703 tig0042596:-11284 Msa1462780:CDS
ATGCGACAGATTGGAGCCGT+GGG 0.622402 tig0042596:-11345 Msa1462780:CDS
AGAGATAAGAGGCGGTTCGG+TGG 0.627950 tig0042596:+11484 Msa1462780:intergenic
GGGAAGTGTAGCATATGTCA+GGG 0.632502 tig0042596:+11586 Msa1462780:intergenic
GCATCTGTTTAAGCGAGCCA+CGG 0.637289 tig0042596:+11364 Msa1462780:intergenic
GTGTTGCGTTGCAACTTGAA+CGG 0.641224 tig0042596:+11613 Msa1462780:intergenic
TGGACGGAGATTGGAGAATG+TGG 0.645484 tig0042596:+11692 Msa1462780:intergenic
CGTGCAGACGTGGATGAGTG+CGG 0.674734 tig0042596:-11274 Msa1462780:CDS
GAGATTGGAGAGATAAGAGG+CGG 0.675120 tig0042596:+11476 Msa1462780:intergenic
AGAAGATTGTCCTGTGAAAG+CGG 0.686477 tig0042596:-11208 Msa1462780:CDS
ACGGAGATTGGAGAATGTGG+CGG 0.690066 tig0042596:+11695 Msa1462780:intergenic
GATGCTGTTGATGAAATCCG+TGG 0.736309 tig0042596:-11381 Msa1462780:CDS
ACTCGCGAAGCAGATTACAG+CGG 0.792244 tig0042596:-11453 Msa1462780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAGATGATTGATAATAGG+AGG + tig0042596:11148-11167 None:intergenic 30.0%
! CGAAGAAGATGATTGATAAT+AGG + tig0042596:11151-11170 None:intergenic 30.0%
TACTGATGAAGAAACGTGTA+CGG - tig0042596:11619-11638 Msa1462780:CDS 35.0%
AAAGTTCACGAGTAATGCTT+TGG - tig0042596:11709-11728 Msa1462780:CDS 35.0%
! AATGCTTTGGCACTTGTTAA+TGG - tig0042596:11722-11741 Msa1462780:CDS 35.0%
GTTAATGGTTACGCACAAAA+AGG - tig0042596:11737-11756 Msa1462780:CDS 35.0%
GCAACTTGAACGGATGAATT+CGG + tig0042596:11246-11265 Msa1462780:intergenic 40.0%
AATGCAGTTCAACAGAATCC+CGG - tig0042596:11317-11336 Msa1462780:CDS 40.0%
AGTGAGATTGGAGAGATAAG+AGG + tig0042596:11396-11415 Msa1462780:intergenic 40.0%
CGAGATTTGAGAAACAGTCA+TGG + tig0042596:11463-11482 Msa1462780:intergenic 40.0%
CTTAAACAGATGCGACAGAT+TGG - tig0042596:11512-11531 Msa1462780:CDS 40.0%
AAACAGAAACGAATCTGCTC+CGG + tig0042596:11561-11580 Msa1462780:intergenic 40.0%
AGAAGATTGTCCTGTGAAAG+CGG - tig0042596:11658-11677 Msa1462780:CDS 40.0%
!! GAGGAAACTGTGAGAGTGTT+GGG + tig0042596:11129-11148 None:intergenic 45.0%
GTGTTGCGTTGCAACTTGAA+CGG + tig0042596:11256-11275 Msa1462780:intergenic 45.0%
! GGGAAGTGTAGCATATGTCA+GGG + tig0042596:11283-11302 Msa1462780:intergenic 45.0%
! AGGGAAGTGTAGCATATGTC+AGG + tig0042596:11284-11303 Msa1462780:intergenic 45.0%
GGGATTCTGTTGAACTGCAT+TGG + tig0042596:11318-11337 Msa1462780:intergenic 45.0%
TTTGGAGAAGCTTACGGCTA+TGG + tig0042596:11360-11379 Msa1462780:intergenic 45.0%
! GTGGACTTTGGAGAAGCTTA+CGG + tig0042596:11366-11385 Msa1462780:intergenic 45.0%
GAGATTGGAGAGATAAGAGG+CGG + tig0042596:11393-11412 Msa1462780:intergenic 45.0%
! GATGCTGTTGATGAAATCCG+TGG - tig0042596:11485-11504 Msa1462780:CDS 45.0%
GATGAAGAAACGTGTACGGA+TGG - tig0042596:11623-11642 Msa1462780:CDS 45.0%
TTCTGTACATCCGCTTTCAC+AGG + tig0042596:11671-11690 Msa1462780:intergenic 45.0%
TGTACAGAATCGTGTCTCGA+AGG - tig0042596:11682-11701 Msa1462780:CDS 45.0%
! GGAGGAAACTGTGAGAGTGT+TGG + tig0042596:11130-11149 None:intergenic 50.0%
ACGGAGATTGGAGAATGTGG+CGG + tig0042596:11174-11193 None:intergenic 50.0%
TGGACGGAGATTGGAGAATG+TGG + tig0042596:11177-11196 None:intergenic 50.0%
TGGAGAGATAAGAGGCGGTT+CGG + tig0042596:11388-11407 Msa1462780:intergenic 50.0%
ATCTGCTTCGCGAGTGAGAT+TGG + tig0042596:11408-11427 Msa1462780:intergenic 50.0%
ACTCGCGAAGCAGATTACAG+CGG - tig0042596:11413-11432 Msa1462780:CDS 50.0%
GCATCTGTTTAAGCGAGCCA+CGG + tig0042596:11505-11524 Msa1462780:intergenic 50.0%
AGATGAGTAACGTGCAGACG+TGG - tig0042596:11582-11601 Msa1462780:CDS 50.0%
GATGAATTCGGCGTCGTCGT+TGG + tig0042596:11234-11253 Msa1462780:intergenic 55.0%
! TGCATTGGCGTAGCGAGAGA+GGG + tig0042596:11303-11322 Msa1462780:intergenic 55.0%
! AGAGATAAGAGGCGGTTCGG+TGG + tig0042596:11385-11404 Msa1462780:intergenic 55.0%
ACAGTCATGGAGAGCGAGTG+CGG + tig0042596:11450-11469 Msa1462780:intergenic 55.0%
ATGCGACAGATTGGAGCCGT+GGG - tig0042596:11521-11540 Msa1462780:CDS 55.0%
AAACGAATCTGCTCCGGCAC+CGG + tig0042596:11555-11574 Msa1462780:intergenic 55.0%
GGCGGTTGTTGGACGGAGAT+TGG + tig0042596:11186-11205 None:intergenic 60.0%
GGTGGTTGGAGGTTCTGCTC+CGG + tig0042596:11210-11229 Msa1462780:intergenic 60.0%
!! TCGTCGTTGGTGGTGGTTGG+AGG + tig0042596:11221-11240 Msa1462780:intergenic 60.0%
GAATTCGGCGTCGTCGTTGG+TGG + tig0042596:11231-11250 Msa1462780:intergenic 60.0%
! CTGCATTGGCGTAGCGAGAG+AGG + tig0042596:11304-11323 Msa1462780:intergenic 60.0%
CTATGGCGATGCGAGCGAGT+TGG + tig0042596:11343-11362 Msa1462780:intergenic 60.0%
!! AGAGGCGGTTCGGTGGACTT+TGG + tig0042596:11378-11397 Msa1462780:intergenic 60.0%
GATGCGACAGATTGGAGCCG+TGG - tig0042596:11520-11539 Msa1462780:CDS 60.0%
CAGATTGGAGCCGTGGGAAC+TGG - tig0042596:11527-11546 Msa1462780:CDS 60.0%
CGTGCAGACGTGGATGAGTG+CGG - tig0042596:11592-11611 Msa1462780:CDS 60.0%
CTCCGTCCAACAACCGCCAC+CGG - tig0042596:11188-11207 Msa1462780:CDS 65.0%
! CTCCGGTGGCGGTTGTTGGA+CGG + tig0042596:11193-11212 Msa1462780:intergenic 65.0%
! TCTGCTCCGGTGGCGGTTGT+TGG + tig0042596:11197-11216 Msa1462780:intergenic 65.0%
TGGAGGTTCTGCTCCGGTGG+CGG + tig0042596:11204-11223 Msa1462780:intergenic 65.0%
GGTTGGAGGTTCTGCTCCGG+TGG + tig0042596:11207-11226 Msa1462780:intergenic 65.0%
!! GCGTCGTCGTTGGTGGTGGT+TGG + tig0042596:11224-11243 Msa1462780:intergenic 65.0%
! TTCGGCGTCGTCGTTGGTGG+TGG + tig0042596:11228-11247 Msa1462780:intergenic 65.0%
! GCGATGCGAGCGAGTTGGCC+GGG + tig0042596:11338-11357 Msa1462780:intergenic 70.0%
! GGCGATGCGAGCGAGTTGGC+CGG + tig0042596:11339-11358 Msa1462780:intergenic 70.0%
GGAGCCGTGGGAACTGGCGC+CGG - tig0042596:11533-11552 Msa1462780:CDS 75.0%
!! GGCACCGGCGCCAGTTCCCA+CGG + tig0042596:11540-11559 Msa1462780:intergenic 75.0%
!! GTGGGAACTGGCGCCGGTGC+CGG - tig0042596:11539-11558 Msa1462780:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0042596 gene 11119 11769 11119 ID=Msa1462780;Name=Msa1462780
tig0042596 mRNA 11119 11769 11119 ID=Msa1462780-mRNA-1;Parent=Msa1462780;Name=Msa1462780-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|216
tig0042596 exon 11119 11769 11119 ID=Msa1462780-mRNA-1:exon:23795;Parent=Msa1462780-mRNA-1
tig0042596 CDS 11119 11769 11119 ID=Msa1462780-mRNA-1:cds;Parent=Msa1462780-mRNA-1
Gene Sequence

>Msa1462780

ATGACAACCCAACACTCTCACAGTTTCCTCCTATTATCAATCATCTTCTTCGCCGCCACATTCTCCAATCTCCGTCCAACAACCGCCACCGGAGCAGAACCTCCAACCACCACCAACGACGACGCCGAATTCATCCGTTCAAGTTGCAACGCAACACTCTACCCTGACATATGCTACACTTCCCTCTCTCGCTACGCCAATGCAGTTCAACAGAATCCCGGCCAACTCGCTCGCATCGCCATAGCCGTAAGCTTCTCCAAAGTCCACCGAACCGCCTCTTATCTCTCCAATCTCACTCGCGAAGCAGATTACAGCGGTAGTTCACGCGCCGCACTCGCTCTCCATGACTGTTTCTCAAATCTCGACGATGCTGTTGATGAAATCCGTGGCTCGCTTAAACAGATGCGACAGATTGGAGCCGTGGGAACTGGCGCCGGTGCCGGAGCAGATTCGTTTCTGTTTCAGATGAGTAACGTGCAGACGTGGATGAGTGCGGCACTTACTGATGAAGAAACGTGTACGGATGGATTTCAAGATGTAGAAGATTGTCCTGTGAAAGCGGATGTACAGAATCGTGTCTCGAAGGTGAAAAAGTTCACGAGTAATGCTTTGGCACTTGTTAATGGTTACGCACAAAAAGGAATGCCATGA

Protein sequence

>Msa1462780

MTTQHSHSFLLLSIIFFAATFSNLRPTTATGAEPPTTTNDDAEFIRSSCNATLYPDICYTSLSRYANAVQQNPGQLARIAIAVSFSKVHRTASYLSNLTREADYSGSSRAALALHDCFSNLDDAVDEIRGSLKQMRQIGAVGTGAGAGADSFLFQMSNVQTWMSAALTDEETCTDGFQDVEDCPVKADVQNRVSKVKKFTSNALALVNGYAQKGMP*