AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0254730


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0254730 MtrunA17_Chr2g0315401 90.226 133 8 1 52 184 19 146 8.83e-86 249
Msa0254730 MtrunA17_Chr2g0315341 89.600 125 13 0 60 184 1 125 2.28e-79 232
Msa0254730 MtrunA17_Chr2g0315381 49.444 180 84 4 9 184 129 305 3.13e-52 169
Msa0254730 MtrunA17_Chr2g0315371 46.893 177 83 4 9 177 126 299 2.30e-44 149
Msa0254730 MtrunA17_Chr2g0315361 49.405 168 75 5 9 169 133 297 3.02e-44 148
Msa0254730 MtrunA17_Chr7g0244981 43.860 171 73 5 9 175 107 258 2.94e-35 124
Msa0254730 MtrunA17_Chr7g0244971 54.369 103 46 1 9 111 108 209 3.59e-35 125
Msa0254730 MtrunA17_Chr8g0350621 41.606 137 72 4 9 138 96 231 3.69e-30 111
Msa0254730 MtrunA17_Chr8g0334541 47.706 109 52 2 9 116 88 192 5.13e-28 105
Msa0254730 MtrunA17_Chr8g0350631 49.425 87 29 3 45 131 5 76 1.68e-20 83.2
Msa0254730 MtrunA17_Chr3g0128671 50.000 68 34 0 20 87 123 190 1.98e-19 83.6
Msa0254730 MtrunA17_Chr8g0387981 53.333 60 28 0 24 83 132 191 1.79e-18 81.6
Msa0254730 MtrunA17_Chr5g0428351 36.885 122 67 3 9 126 169 284 2.85e-18 80.5
Msa0254730 MtrunA17_Chr7g0275531 49.180 61 31 0 23 83 117 177 5.20e-17 77.0
Msa0254730 MtrunA17_Chr3g0126391 49.180 61 31 0 23 83 132 192 6.48e-17 77.0
Msa0254730 MtrunA17_Chr8g0347251 46.875 64 34 0 23 86 135 198 1.05e-15 73.6
Msa0254730 MtrunA17_Chr4g0051881 45.570 79 38 2 23 99 177 252 2.16e-15 72.8
Msa0254730 MtrunA17_Chr4g0042831 35.514 107 66 1 2 108 256 359 2.51e-15 72.8
Msa0254730 MtrunA17_Chr8g0383351 48.333 60 28 1 22 81 158 214 1.67e-14 68.9
Msa0254730 MtrunA17_Chr5g0418191 35.000 120 66 4 4 115 300 415 6.50e-14 68.9
Msa0254730 MtrunA17_Chr5g0443131 47.761 67 30 2 23 87 156 219 1.04e-13 67.8
Msa0254730 MtrunA17_Chr7g0270191 50.847 59 26 1 23 81 144 199 1.35e-13 67.4
Msa0254730 MtrunA17_Chr3g0129361 46.667 60 29 1 22 81 142 198 1.61e-13 66.2
Msa0254730 MtrunA17_Chr5g0418781 49.153 59 27 1 23 81 123 178 2.64e-13 66.2
Msa0254730 MtrunA17_Chr7g0224801 46.667 60 29 1 22 81 91 147 2.84e-13 64.7
Msa0254730 MtrunA17_Chr7g0263531 41.860 86 46 2 18 103 356 437 4.75e-13 66.2
Msa0254730 MtrunA17_Chr1g0194481 49.153 59 27 1 23 81 157 212 5.87e-13 65.9
Msa0254730 MtrunA17_Chr8g0335811 45.902 61 30 1 22 82 152 209 8.53e-13 64.3
Msa0254730 MtrunA17_Chr7g0218081 38.961 77 44 1 6 82 392 465 1.09e-12 65.5
Msa0254730 MtrunA17_Chr2g0333851 42.029 69 38 1 14 82 159 225 1.62e-12 64.3
Msa0254730 MtrunA17_Chr4g0068541 40.541 74 40 2 9 81 192 262 2.07e-12 64.7
Msa0254730 MtrunA17_Chr7g0248721 47.541 61 28 2 22 82 139 195 3.15e-12 62.8
Msa0254730 MtrunA17_Chr5g0431811 43.750 64 36 0 24 87 672 735 3.88e-12 63.9
Msa0254730 MtrunA17_Chr5g0401821 43.056 72 39 1 25 96 200 269 4.38e-12 62.8
Msa0254730 MtrunA17_Chr5g0445311 37.349 83 48 2 1 82 340 419 1.12e-11 62.4
Msa0254730 MtrunA17_Chr3g0129321 45.902 61 30 1 22 82 116 173 1.12e-11 60.8
Msa0254730 MtrunA17_Chr2g0294231 45.763 59 29 1 23 81 202 257 1.61e-11 62.0
Msa0254730 MtrunA17_Chr1g0150281 39.241 79 42 2 4 82 124 196 1.74e-11 61.2
Msa0254730 MtrunA17_Chr3g0101131 44.262 61 31 1 22 82 413 470 1.84e-11 62.0
Msa0254730 MtrunA17_Chr7g0238921 50.000 60 27 1 22 81 122 178 2.56e-11 61.2
Msa0254730 MtrunA17_Chr4g0071521 39.726 73 42 1 25 97 246 316 3.88e-11 60.5
Msa0254730 MtrunA17_Chr1g0147881 47.368 57 28 1 25 81 263 317 7.82e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0254730 AT5G22570.1 41.781 146 72 6 14 152 99 238 5.96e-24 95.9
Msa0254730 AT1G66560.1 52.941 68 32 0 24 91 103 170 2.83e-21 87.8
Msa0254730 AT5G01900.1 54.545 66 30 0 19 84 105 170 3.38e-21 87.8
Msa0254730 AT1G66600.1 55.556 63 28 0 23 85 102 164 8.11e-21 86.7
Msa0254730 AT1G66550.2 50.746 67 33 0 25 91 104 170 4.15e-20 84.7
Msa0254730 AT1G66550.1 50.746 67 33 0 25 91 109 175 5.16e-20 84.7
Msa0254730 AT3G56400.1 44.872 78 40 1 9 86 108 182 9.85e-20 84.7
Msa0254730 AT1G80590.1 52.459 61 29 0 25 85 86 146 5.99e-19 81.3
Msa0254730 AT5G24110.1 46.341 82 39 2 23 100 112 192 1.35e-17 79.0
Msa0254730 AT4G11070.2 36.111 108 65 2 24 127 109 216 1.05e-16 76.3
Msa0254730 AT4G11070.1 36.111 108 65 2 24 127 141 248 1.67e-16 75.9
Msa0254730 AT2G46400.1 47.541 61 32 0 23 83 103 163 1.86e-15 72.8
Msa0254730 AT2G40750.1 42.500 80 43 1 4 83 135 211 2.70e-15 72.8
Msa0254730 AT4G23810.1 43.284 67 38 0 24 90 158 224 3.30e-15 72.4
Msa0254730 AT2G40740.1 45.000 60 33 0 24 83 173 232 5.10e-15 71.6
Msa0254730 AT2G40740.3 45.000 60 33 0 24 83 182 241 6.54e-15 71.6
Msa0254730 AT1G64000.1 49.180 61 28 1 22 82 112 169 1.66e-14 68.9
Msa0254730 AT2G03340.1 42.308 78 42 1 22 99 413 487 5.37e-14 69.7
Msa0254730 AT2G37260.1 50.000 60 27 1 23 82 348 404 8.42e-14 68.9
Msa0254730 AT2G37260.3 50.000 60 27 1 23 82 268 324 9.82e-14 68.6
Msa0254730 AT2G37260.2 50.000 60 27 1 23 82 266 322 1.04e-13 68.6
Msa0254730 AT5G41570.1 47.541 61 29 1 22 82 96 153 1.64e-13 65.9
Msa0254730 AT4G18170.1 50.000 60 27 1 23 82 171 227 2.23e-13 67.4
Msa0254730 AT1G29860.1 50.000 60 27 1 23 82 135 191 3.18e-13 66.6
Msa0254730 AT1G69310.4 47.458 59 28 1 23 81 146 201 3.48e-13 66.6
Msa0254730 AT1G69310.2 47.458 59 28 1 23 81 146 201 3.48e-13 66.6
Msa0254730 AT1G69310.1 47.458 59 28 1 23 81 146 201 3.48e-13 66.6
Msa0254730 AT2G46130.1 43.939 66 34 1 17 82 23 85 3.49e-13 63.2
Msa0254730 AT2G44745.1 45.902 61 30 1 22 82 143 200 6.83e-13 64.7
Msa0254730 AT4G31800.2 43.478 69 37 1 14 82 101 167 7.60e-13 65.1
Msa0254730 AT4G39410.1 45.000 60 30 1 22 81 221 277 9.16e-13 65.5
Msa0254730 AT1G13960.1 47.541 61 29 1 22 82 407 464 1.08e-12 65.9
Msa0254730 AT5G46350.1 48.333 60 28 1 23 82 182 238 1.15e-12 65.5
Msa0254730 AT4G31800.1 43.478 69 37 1 14 82 166 232 1.22e-12 65.1
Msa0254730 AT5G13080.1 47.541 61 29 1 22 82 65 122 1.24e-12 62.8
Msa0254730 AT5G49520.1 47.458 59 28 1 23 81 220 275 1.25e-12 65.5
Msa0254730 AT1G13960.2 47.541 61 29 1 22 82 254 311 3.14e-12 64.3
Msa0254730 AT2G47260.1 43.662 71 37 1 23 93 173 240 4.17e-12 63.9
Msa0254730 AT2G25000.2 44.615 65 34 1 18 82 97 159 4.58e-12 62.8
Msa0254730 AT2G25000.4 44.615 65 34 1 18 82 97 159 4.58e-12 62.8
Msa0254730 AT2G25000.3 44.615 65 34 1 18 82 119 181 5.45e-12 62.8
Msa0254730 AT2G04880.2 47.541 61 29 1 22 82 281 338 6.22e-12 63.5
Msa0254730 AT2G25000.1 44.615 65 34 1 18 82 140 202 6.60e-12 62.8
Msa0254730 AT2G04880.1 47.541 61 29 1 22 82 305 362 8.03e-12 63.2
Msa0254730 AT5G26170.1 40.984 61 33 1 22 82 111 168 8.58e-12 61.2
Msa0254730 AT5G45260.1 44.828 58 32 0 25 82 1209 1266 1.26e-11 62.8
Msa0254730 AT3G01080.2 38.961 77 44 1 6 82 326 399 3.08e-11 61.6
Msa0254730 AT3G01080.1 37.975 79 46 1 4 82 286 361 4.12e-11 61.2
Msa0254730 AT2G30590.1 50.000 58 27 1 25 82 314 369 6.23e-11 60.5
Msa0254730 AT3G01970.1 44.262 61 31 1 22 82 63 120 9.48e-11 57.8

Find 33 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATTCAGATATCACATTAT+TGG 0.160744 2_2:+48315044 Msa0254730:CDS
AACTTGAATTTGATAATTTC+AGG 0.268527 2_2:+48315259 Msa0254730:CDS
AACATAGAAGAAGTATTATT+AGG 0.316397 2_2:-48315069 None:intergenic
ATACAAGACTTACCTAATTT+AGG 0.329259 2_2:-48315339 None:intergenic
TTGATCAATTTGATTATGAT+AGG 0.331740 2_2:-48315193 None:intergenic
GGCTATGAATGGAGAAAGTA+TGG 0.339396 2_2:+48314736 Msa0254730:CDS
TTATACAGAACTATATATTA+TGG 0.345556 2_2:+48314994 Msa0254730:CDS
TAATATATAGTTCTGTATAA+TGG 0.379983 2_2:-48314991 None:intergenic
CAGGGTATTGTTCTTTGACT+TGG 0.384613 2_2:-48315113 None:intergenic
GGTAGTCTGATGATGTTAAT+TGG 0.385184 2_2:-48315218 None:intergenic
ATCATGAAATGGAACAGATT+TGG 0.391587 2_2:-48315304 None:intergenic
TAAGATCAAAAGCACTTACT+TGG 0.396882 2_2:+48314683 Msa0254730:CDS
GGTATTGTTCTTTGACTTGG+AGG 0.404519 2_2:-48315110 None:intergenic
CACTAAAATCCATCATGAAA+TGG 0.409766 2_2:-48315315 None:intergenic
TAGGGATTAATAACATCTAT+AGG 0.441096 2_2:-48315174 None:intergenic
AGTTTATAGTCACATGAGAA+AGG 0.462808 2_2:-48315240 None:intergenic
TAAATTAGGTAAGTCTTGTA+TGG 0.489366 2_2:+48315341 Msa0254730:three_prime_UTR
GATATCTGAATTCAATAAAG+AGG 0.492464 2_2:-48315034 None:intergenic
AAATCTGTTCCATTTCATGA+TGG 0.493216 2_2:+48315306 Msa0254730:CDS
AAGTCTTGTATGGTGATTTG+AGG 0.503160 2_2:+48315351 Msa0254730:three_prime_UTR
TAATTGAAGATGGCTATGAA+TGG 0.504678 2_2:+48314725 Msa0254730:CDS
TGATCAATTTGATTATGATA+GGG 0.507098 2_2:-48315192 None:intergenic
TAATCAATGCAAAATACCTC+AGG 0.531627 2_2:+48314770 Msa0254730:CDS
GGAGGCTGTCATTGAAGCTA+AGG 0.539380 2_2:-48315092 None:intergenic
GAAAGTGGTGATGAAAATGC+AGG 0.541358 2_2:-48315132 None:intergenic
GTTTATAGTCACATGAGAAA+GGG 0.556371 2_2:-48315239 None:intergenic
ATGAAATGGAACAGATTTGG+TGG 0.571370 2_2:-48315301 None:intergenic
AAGATCAAAAGCACTTACTT+GGG 0.571753 2_2:+48314684 Msa0254730:CDS
AAAAGCACTTACTTGGGAGA+AGG 0.572656 2_2:+48314690 Msa0254730:CDS
TATATAGTTCTGTATAATGG+AGG 0.574674 2_2:-48314988 None:intergenic
ATATAGTTCTGTATAATGGA+GGG 0.609422 2_2:-48314987 None:intergenic
ACATGTGCAGAGAATTCAAG+AGG 0.632753 2_2:+48314963 Msa0254730:CDS
AAAGTGGTGATGAAAATGCA+GGG 0.652523 2_2:-48315131 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATATATAGTTCTGTATAA+TGG - chr2_2:48314994-48315013 None:intergenic 15.0%
!! TTATACAGAACTATATATTA+TGG + chr2_2:48314994-48315013 Msa0254730:CDS 15.0%
!! TTATTCATTAAGAATTGACA+GGG - chr2_2:48314862-48314881 None:intergenic 20.0%
!! ATTATTCATTAAGAATTGAC+AGG - chr2_2:48314863-48314882 None:intergenic 20.0%
!! CAATATATGATTCATATCAT+AGG + chr2_2:48314890-48314909 Msa0254730:intron 20.0%
!!! AACATAGAAGAAGTATTATT+AGG - chr2_2:48315072-48315091 None:intergenic 20.0%
!! TGATCAATTTGATTATGATA+GGG - chr2_2:48315195-48315214 None:intergenic 20.0%
!! TTGATCAATTTGATTATGAT+AGG - chr2_2:48315196-48315215 None:intergenic 20.0%
!!! AACTTGAATTTGATAATTTC+AGG + chr2_2:48315259-48315278 Msa0254730:CDS 20.0%
!!! AGCTCAATTTTAATTGAAGA+TGG + chr2_2:48314715-48314734 Msa0254730:CDS 25.0%
! ATTGAAGATATATATACCTG+AGG - chr2_2:48314789-48314808 None:intergenic 25.0%
!! ATATAGTTCTGTATAATGGA+GGG - chr2_2:48314990-48315009 None:intergenic 25.0%
!! TATATAGTTCTGTATAATGG+AGG - chr2_2:48314991-48315010 None:intergenic 25.0%
! GATATCTGAATTCAATAAAG+AGG - chr2_2:48315037-48315056 None:intergenic 25.0%
! GAATTCAGATATCACATTAT+TGG + chr2_2:48315044-48315063 Msa0254730:CDS 25.0%
! TAGGGATTAATAACATCTAT+AGG - chr2_2:48315177-48315196 None:intergenic 25.0%
! ATACAAGACTTACCTAATTT+AGG - chr2_2:48315342-48315361 None:intergenic 25.0%
!! TAAATTAGGTAAGTCTTGTA+TGG + chr2_2:48315341-48315360 Msa0254730:three_prime_UTR 25.0%
!! TAAGATCAAAAGCACTTACT+TGG + chr2_2:48314683-48314702 Msa0254730:CDS 30.0%
!! AAGATCAAAAGCACTTACTT+GGG + chr2_2:48314684-48314703 Msa0254730:CDS 30.0%
TAATTGAAGATGGCTATGAA+TGG + chr2_2:48314725-48314744 Msa0254730:CDS 30.0%
TAATCAATGCAAAATACCTC+AGG + chr2_2:48314770-48314789 Msa0254730:CDS 30.0%
! AAGAGGTTTTGCAATTATGA+TGG - chr2_2:48315020-48315039 None:intergenic 30.0%
GTTTATAGTCACATGAGAAA+GGG - chr2_2:48315242-48315261 None:intergenic 30.0%
AGTTTATAGTCACATGAGAA+AGG - chr2_2:48315243-48315262 None:intergenic 30.0%
ATCATGAAATGGAACAGATT+TGG - chr2_2:48315307-48315326 None:intergenic 30.0%
AAATCTGTTCCATTTCATGA+TGG + chr2_2:48315306-48315325 Msa0254730:CDS 30.0%
CACTAAAATCCATCATGAAA+TGG - chr2_2:48315318-48315337 None:intergenic 30.0%
!! GGATTTTAGTGACCTAAATT+AGG + chr2_2:48315327-48315346 Msa0254730:exon 30.0%
! AAAGTGGTGATGAAAATGCA+GGG - chr2_2:48315134-48315153 None:intergenic 35.0%
!! TGTTTTGTTGGTACAGAAAG+TGG - chr2_2:48315150-48315169 None:intergenic 35.0%
!!! TCTATAGGCTCTTGTTTTGT+TGG - chr2_2:48315162-48315181 None:intergenic 35.0%
! GGTAGTCTGATGATGTTAAT+TGG - chr2_2:48315221-48315240 None:intergenic 35.0%
ATGAAATGGAACAGATTTGG+TGG - chr2_2:48315304-48315323 None:intergenic 35.0%
! AAGTCTTGTATGGTGATTTG+AGG + chr2_2:48315351-48315370 Msa0254730:three_prime_UTR 35.0%
!! AAAAGCACTTACTTGGGAGA+AGG + chr2_2:48314690-48314709 Msa0254730:CDS 40.0%
GGCTATGAATGGAGAAAGTA+TGG + chr2_2:48314736-48314755 Msa0254730:CDS 40.0%
ACATGTGCAGAGAATTCAAG+AGG + chr2_2:48314963-48314982 Msa0254730:CDS 40.0%
!! GGTATTGTTCTTTGACTTGG+AGG - chr2_2:48315113-48315132 None:intergenic 40.0%
!! CAGGGTATTGTTCTTTGACT+TGG - chr2_2:48315116-48315135 None:intergenic 40.0%
! GAAAGTGGTGATGAAAATGC+AGG - chr2_2:48315135-48315154 None:intergenic 40.0%
GGAGGCTGTCATTGAAGCTA+AGG - chr2_2:48315095-48315114 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 48314661 48315385 48314661 ID=Msa0254730;Name=Msa0254730
chr2_2 mRNA 48314661 48315385 48314661 ID=Msa0254730-mRNA-1;Parent=Msa0254730;Name=Msa0254730-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|1|0.5|1|1|1|2|50|184
chr2_2 exon 48314661 48314791 48314661 ID=Msa0254730-mRNA-1:exon:14572;Parent=Msa0254730-mRNA-1
chr2_2 exon 48314912 48315385 48314912 ID=Msa0254730-mRNA-1:exon:14573;Parent=Msa0254730-mRNA-1
chr2_2 CDS 48314661 48314791 48314661 ID=Msa0254730-mRNA-1:cds;Parent=Msa0254730-mRNA-1
chr2_2 CDS 48314912 48315335 48314912 ID=Msa0254730-mRNA-1:cds;Parent=Msa0254730-mRNA-1
chr2_2 three_prime_UTR 48315336 48315385 48315336 ID=Msa0254730-mRNA-1:three_prime_utr;Parent=Msa0254730-mRNA-1
Gene Sequence

>Msa0254730

TTGGTAGACTATTTCACTTTGATAAGATCAAAAGCACTTACTTGGGAGAAGGATAGCTCAATTTTAATTGAAGATGGCTATGAATGGAGAAAGTATGGACAAAAGAAGATAATCAATGCAAAATACCTCAGGAGCTACTACAGATGCAGTTACAAAAGTGATGAAGAATGTGAAGCTATGAAACATGTGCAGAGAATTCAAGAGGACCCTCCATTATACAGAACTATATATTATGGCCATCATAATTGCAAAACCTCTTTATTGAATTCAGATATCACATTATTGGAACCTAATAATACTTCTTCTATGTTCCTTAGCTTCAATGACAGCCTCCAAGTCAAAGAACAATACCCTGCATTTTCATCACCACTTTCTGTACCAACAAAACAAGAGCCTATAGATGTTATTAATCCCTATCATAATCAAATTGATCAAGACCAATTAACATCATCAGACTACCCTTTCTCATGTGACTATAAACTTGAATTTGATAATTTCAGGCATGCTGCTATGCTATCATCCACCAAATCTGTTCCATTTCATGATGGATTTTAG

Protein sequence

>Msa0254730

LVDYFTLIRSKALTWEKDSSILIEDGYEWRKYGQKKIINAKYLRSYYRCSYKSDEECEAMKHVQRIQEDPPLYRTIYYGHHNCKTSLLNSDITLLEPNNTSSMFLSFNDSLQVKEQYPAFSSPLSVPTKQEPIDVINPYHNQIDQDQLTSSDYPFSCDYKLEFDNFRHAAMLSSTKSVPFHDGF*