AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001410

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001410 MtrunA17_Chr1g0162931 97.163 282 7 1 1 281 1 282 0.0 565
MsaG001410 MtrunA17_Chr1g0210911 47.619 336 113 15 2 281 3 331 8.57e-74 229
MsaG001410 MtrunA17_Chr2g0320231 69.737 76 23 0 5 80 84 159 4.80e-31 119
MsaG001410 MtrunA17_Chr8g0379121 68.000 75 24 0 6 80 99 173 3.91e-30 117
MsaG001410 MtrunA17_Chr2g0288601 73.438 64 17 0 6 69 59 122 9.15e-29 106
MsaG001410 MtrunA17_Chr7g0243081 65.278 72 25 0 3 74 56 127 2.67e-28 111
MsaG001410 MtrunA17_Chr2g0283951 61.364 88 25 2 6 84 77 164 1.93e-27 109
MsaG001410 MtrunA17_Chr3g0095611 61.765 68 26 0 10 77 11 78 8.74e-25 98.6
MsaG001410 MtrunA17_Chr6g0479431 65.517 58 20 0 17 74 201 258 1.05e-21 93.2
MsaG001410 MtrunA17_Chr8g0366281 67.241 58 19 0 17 74 172 229 1.33e-21 92.8
MsaG001410 MtrunA17_Chr5g0410741 65.517 58 20 0 17 74 218 275 7.12e-21 91.3
MsaG001410 MtrunA17_Chr3g0109981 65.517 58 20 0 17 74 273 330 1.39e-20 90.9
MsaG001410 MtrunA17_Chr1g0154261 60.000 65 24 1 10 74 120 182 1.87e-20 89.0
MsaG001410 MtrunA17_Chr1g0190301 69.643 56 17 0 19 74 176 231 2.30e-20 89.7
MsaG001410 MtrunA17_Chr7g0261911 67.857 56 18 0 19 74 263 318 6.59e-20 89.0
MsaG001410 MtrunA17_Chr7g0274471 67.857 56 18 0 19 74 219 274 1.04e-19 88.2
MsaG001410 MtrunA17_Chr5g0409731 56.716 67 29 0 5 71 12 78 1.06e-17 81.3
MsaG001410 MtrunA17_Chr5g0417521 51.316 76 34 1 19 94 16 88 1.69e-17 81.3
MsaG001410 MtrunA17_Chr6g0461641 60.000 60 21 1 19 75 43 102 6.64e-17 80.1
MsaG001410 MtrunA17_Chr2g0310011 39.062 128 58 3 19 146 36 143 3.61e-16 77.4
MsaG001410 MtrunA17_Chr2g0321461 60.377 53 21 0 19 71 46 98 5.01e-16 77.4
MsaG001410 MtrunA17_Chr2g0290991 52.055 73 29 1 19 85 40 112 5.49e-16 76.6
MsaG001410 MtrunA17_Chr7g0258551 55.738 61 27 0 14 74 208 268 7.13e-16 77.0
MsaG001410 MtrunA17_Chr8g0356501 62.264 53 20 0 19 71 38 90 2.14e-15 75.1
MsaG001410 MtrunA17_Chr1g0197171 62.264 53 20 0 19 71 45 97 2.69e-15 74.3
MsaG001410 MtrunA17_Chr2g0291021 53.425 73 33 1 20 91 51 123 2.85e-15 74.7
MsaG001410 MtrunA17_Chr1g0175091 62.069 58 21 1 14 71 255 311 4.01e-15 74.7
MsaG001410 MtrunA17_Chr7g0254981 67.308 52 17 0 20 71 52 103 4.63e-15 73.6
MsaG001410 MtrunA17_Chr4g0042451 58.491 53 22 0 19 71 18 70 1.37e-14 72.8
MsaG001410 MtrunA17_Chr1g0175071 60.377 53 21 0 20 72 179 231 6.54e-14 70.9
MsaG001410 MtrunA17_Chr1g0175081 45.070 71 39 0 1 71 5 75 1.08e-13 65.9
MsaG001410 MtrunA17_Chr4g0009901 48.529 68 33 2 5 71 154 220 4.95e-13 67.8
MsaG001410 MtrunA17_Chr4g0045361 63.265 49 18 0 23 71 279 327 6.31e-13 68.2
MsaG001410 MtrunA17_Chr4g0062921 61.224 49 19 0 23 71 240 288 3.31e-12 66.2
MsaG001410 MtrunA17_Chr2g0304841 50.909 55 26 1 17 71 212 265 2.25e-11 63.9
MsaG001410 MtrunA17_Chr4g0031961 49.231 65 32 1 7 71 120 183 3.04e-11 62.8
MsaG001410 MtrunA17_Chr4g0009981 46.377 69 35 2 5 72 102 169 4.48e-11 62.0
MsaG001410 MtrunA17_Chr7g0255711 56.364 55 23 1 17 71 90 143 7.42e-11 61.6
MsaG001410 MtrunA17_Chr7g0258531 52.830 53 25 0 20 72 215 267 8.01e-11 62.0
MsaG001410 MtrunA17_Chr4g0067981 42.857 84 43 2 17 100 214 292 8.62e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001410 AT1G14600.1 72.152 79 17 1 1 74 1 79 4.38e-32 119
MsaG001410 AT2G02060.2 82.258 62 11 0 10 71 21 82 6.57e-31 116
MsaG001410 AT2G02060.1 82.258 62 11 0 10 71 21 82 6.57e-31 116
MsaG001410 AT4G04605.1 68.493 73 23 0 9 81 5 77 3.50e-30 113
MsaG001410 AT2G40260.1 73.913 69 18 0 8 76 72 140 1.85e-28 112
MsaG001410 AT2G38300.1 69.014 71 22 0 10 80 46 116 4.47e-27 108
MsaG001410 AT2G42660.1 69.841 63 19 0 10 72 42 104 4.36e-26 103
MsaG001410 AT4G04555.1 53.333 75 35 0 6 80 2 76 2.10e-22 89.7
MsaG001410 AT1G32240.2 65.517 58 20 0 17 74 212 269 6.18e-21 91.7
MsaG001410 AT1G32240.1 65.517 58 20 0 17 74 212 269 6.83e-21 91.7
MsaG001410 AT5G16560.1 65.517 58 20 0 17 74 218 275 9.42e-21 91.3
MsaG001410 AT5G42630.2 62.069 58 22 0 17 74 104 161 1.34e-20 88.2
MsaG001410 AT4G17695.1 61.017 59 23 0 17 75 163 221 1.56e-20 89.7
MsaG001410 AT5G42630.1 62.069 58 22 0 17 74 104 161 1.79e-20 89.0
MsaG001410 AT4G04580.1 45.556 90 45 1 9 94 5 94 8.78e-20 84.3
MsaG001410 AT4G28610.1 55.263 76 33 1 20 95 227 301 1.19e-18 85.5
MsaG001410 AT5G45580.1 57.143 70 30 0 14 83 3 72 4.46e-18 82.0
MsaG001410 AT5G45580.2 57.143 70 30 0 14 83 19 88 4.78e-18 82.4
MsaG001410 AT3G04450.4 63.636 55 20 0 20 74 200 254 1.03e-17 82.8
MsaG001410 AT3G04450.2 63.636 55 20 0 20 74 200 254 1.03e-17 82.8
MsaG001410 AT3G04450.3 63.636 55 20 0 20 74 240 294 1.10e-17 81.6
MsaG001410 AT4G13640.1 37.255 153 89 4 19 170 38 184 1.24e-17 81.3
MsaG001410 AT3G04450.1 63.636 55 20 0 20 74 240 294 1.32e-17 82.8
MsaG001410 AT5G29000.1 63.636 55 20 0 20 74 190 244 1.34e-17 82.0
MsaG001410 AT5G29000.3 63.636 55 20 0 20 74 190 244 1.34e-17 82.0
MsaG001410 AT5G29000.4 63.636 55 20 0 20 74 233 287 1.78e-17 81.3
MsaG001410 AT5G29000.2 63.636 55 20 0 20 74 233 287 1.89e-17 82.0
MsaG001410 AT3G24120.1 38.400 125 74 2 19 142 42 164 1.61e-16 78.2
MsaG001410 AT4G13640.2 59.677 62 24 1 19 80 38 98 2.51e-16 77.8
MsaG001410 AT2G20400.2 63.636 55 20 0 20 74 233 287 2.68e-16 78.6
MsaG001410 AT2G20400.1 63.636 55 20 0 20 74 233 287 2.69e-16 78.6
MsaG001410 AT2G06020.1 43.478 92 46 2 13 98 81 172 3.36e-16 77.4
MsaG001410 AT3G12730.1 62.264 53 20 0 19 71 24 76 5.78e-16 75.9
MsaG001410 AT3G13040.3 67.308 52 17 0 20 71 243 294 5.92e-16 77.8
MsaG001410 AT3G13040.1 67.308 52 17 0 20 71 243 294 5.92e-16 77.8
MsaG001410 AT3G13040.2 67.308 52 17 0 20 71 243 294 5.92e-16 77.8
MsaG001410 AT5G18240.2 58.491 53 22 0 19 71 46 98 1.36e-15 76.6
MsaG001410 AT5G18240.3 58.491 53 22 0 19 71 46 98 1.36e-15 76.6
MsaG001410 AT5G18240.5 58.491 53 22 0 19 71 46 98 1.49e-15 76.6
MsaG001410 AT5G18240.1 58.491 53 22 0 19 71 46 98 1.54e-15 76.3
MsaG001410 AT5G18240.4 58.491 53 22 0 19 71 46 98 1.54e-15 76.3
MsaG001410 AT3G04030.1 56.604 53 23 0 19 71 46 98 1.85e-15 76.3
MsaG001410 AT3G24120.2 39.167 120 70 2 19 137 42 159 1.97e-15 75.1
MsaG001410 AT3G04030.3 56.604 53 23 0 19 71 46 98 2.11e-15 75.9
MsaG001410 AT2G01060.1 67.308 52 17 0 20 71 17 68 2.80e-15 74.7
MsaG001410 AT1G79430.2 62.264 53 20 0 19 71 35 87 3.08e-15 75.1
MsaG001410 AT1G69580.1 40.698 86 48 1 19 101 35 120 3.35e-14 72.0
MsaG001410 AT1G69580.2 40.698 86 48 1 19 101 35 120 3.61e-14 72.0
MsaG001410 AT5G06800.3 61.538 52 20 0 20 71 194 245 1.05e-13 70.1
MsaG001410 AT5G06800.1 61.538 52 20 0 20 71 194 245 1.85e-13 70.1
MsaG001410 AT5G06800.2 61.538 52 20 0 20 71 194 245 1.94e-13 70.1
MsaG001410 AT3G04030.2 52.830 53 24 1 19 71 46 97 1.10e-12 67.8
MsaG001410 AT4G37180.1 55.932 59 26 0 13 71 205 263 1.88e-12 67.0
MsaG001410 AT4G37180.2 55.932 59 26 0 13 71 212 270 2.33e-12 67.0
MsaG001410 AT2G03500.1 61.224 49 19 0 23 71 238 286 3.03e-12 66.6
MsaG001410 AT5G44190.1 56.897 58 24 1 17 74 146 202 4.92e-12 65.9
MsaG001410 AT5G44190.2 56.897 58 24 1 17 74 146 202 6.06e-12 65.5
MsaG001410 AT3G62670.1 46.269 67 32 1 16 78 209 275 6.76e-12 65.9
MsaG001410 AT1G25550.1 59.184 49 20 0 23 71 214 262 7.98e-12 65.1
MsaG001410 AT5G59570.2 55.357 56 24 1 16 71 139 193 8.72e-12 64.7
MsaG001410 AT5G59570.1 55.357 56 24 1 16 71 139 193 8.72e-12 64.7
MsaG001410 AT4G37180.3 54.386 57 26 0 13 69 205 261 4.23e-11 62.4
MsaG001410 AT5G05090.1 56.364 55 23 1 17 71 80 133 4.29e-11 62.4

Find 56 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGGATTTAGCAACTATT+TGG 0.117369 1:-19707523 MsaT001410.1:CDS
CGTCCAAAACATAACTAATT+TGG 0.198867 1:-19707490 MsaT001410.1:CDS
CTTCAGTTGATGGATGTTAA+AGG 0.259007 1:-19711232 MsaT001410.1:CDS
AACTAATTTGGACCTATCTT+TGG 0.259886 1:-19707478 MsaT001410.1:CDS
GGTCCAAATTAGTTATGTTT+TGG 0.275086 1:+19707487 None:intergenic
ACTTCTCTGAGGGGAAATAT+TGG 0.286018 1:+19707575 None:intergenic
TAAGCTTGTTCTTCAGTTGA+TGG 0.287799 1:-19711242 MsaT001410.1:CDS
AGCAAATCAGTTTCTTGTTT+TGG 0.290865 1:+19709663 None:intergenic
CAGAAGATGAAGAAGATATA+AGG 0.297613 1:-19707629 MsaT001410.1:CDS
CTTCTCTGAGGGGAAATATT+GGG 0.366143 1:+19707576 None:intergenic
ACAGAAATTTCTCCCCAAAA+AGG 0.367281 1:-19710484 MsaT001410.1:intron
TCTGGATTTAGCAACTATTT+GGG 0.371762 1:-19707522 MsaT001410.1:CDS
ACATGTTAAGAGCCATTTGC+AGG 0.373744 1:-19711197 MsaT001410.1:intron
GTTTATGCCATTGAAACTCT+TGG 0.378805 1:-19711407 MsaT001410.1:CDS
ATATTCTTTCTCTGCATTCA+AGG 0.392029 1:+19709835 None:intergenic
GCAACAGCAGAAGGGAATAA+AGG 0.396273 1:-19709754 MsaT001410.1:CDS
TTTGTTGTGTTGGTTCAATA+TGG 0.396998 1:-19709728 MsaT001410.1:CDS
TTCAGTTGATGGATGTTAAA+GGG 0.399431 1:-19711231 MsaT001410.1:CDS
ACAAAGCAACGATGAAGTTC+AGG 0.401903 1:+19711428 None:intergenic
TCCAGAGTTTCTCATATCAT+TGG 0.405178 1:+19707539 None:intergenic
TTTAGAGATCATGAATCTCT+TGG 0.412921 1:-19710533 MsaT001410.1:CDS
TTTGTTTAAACCAGATGTAT+AGG 0.415716 1:-19711094 MsaT001410.1:intron
AGAAGATGAAGAAGATATAA+GGG 0.421154 1:-19707628 MsaT001410.1:CDS
CAAAGGTTCCTCGTTTAAGA+TGG 0.432536 1:-19711454 MsaT001410.1:CDS
ATGACCACCAAGAGTTTCAA+TGG 0.434104 1:+19711400 None:intergenic
GAGAAGAGAAATTCCCTCTC+AGG 0.479292 1:-19709861 MsaT001410.1:CDS
GCCAATGATATGAGAAACTC+TGG 0.480081 1:-19707540 MsaT001410.1:CDS
TTCTGGAGCATGATGATGAT+GGG 0.488907 1:-19710556 MsaT001410.1:CDS
ACGTTCAAATGGCCAAAGAT+AGG 0.495295 1:+19707466 None:intergenic
TATCAAAATCAACCTGCAAA+TGG 0.495949 1:+19711185 None:intergenic
ATATAGTTATAACGTTCAAA+TGG 0.503676 1:+19707455 None:intergenic
ATAAAGGAGATTTGTTGTGT+TGG 0.503985 1:-19709738 MsaT001410.1:CDS
ATCAACTGAAGAACAAGCTT+AGG 0.508937 1:+19711244 None:intergenic
TTTCTGGAGCATGATGATGA+TGG 0.516346 1:-19710557 MsaT001410.1:CDS
ATGAGTAGTTGTGGAAGGGA+AGG 0.528216 1:-19711500 MsaT001410.1:CDS
CATGGTTCAGCAACAGCAGA+AGG 0.534523 1:-19709763 MsaT001410.1:CDS
AAAGAATGAGTAGTTGTGGA+AGG 0.546541 1:-19711505 None:intergenic
TTATGATTATGTGCAGGACA+TGG 0.561583 1:-19709781 MsaT001410.1:CDS
TTTGAAAGAATGAGTAGTTG+TGG 0.567741 1:-19711509 None:intergenic
AGATCATGAATCTCTTGGAA+TGG 0.569091 1:-19710528 MsaT001410.1:CDS
ATTGTGAAATATTGTGGTTG+AGG 0.574028 1:+19709699 None:intergenic
AAGAAGCATTACTTCTCTGA+GGG 0.576698 1:+19707565 None:intergenic
GCATTCAAGGATTCCTGAGA+GGG 0.578921 1:+19709848 None:intergenic
GGAAAGATTGTGAAATATTG+TGG 0.579250 1:+19709693 None:intergenic
ACAAGAAACTGATTTGCTCC+AGG 0.584537 1:-19709658 MsaT001410.1:intron
AAGAATGAGTAGTTGTGGAA+GGG 0.598417 1:-19711504 None:intergenic
GAAGATGAAGAAGATATAAG+GGG 0.601789 1:-19707627 MsaT001410.1:CDS
GAGACAATATGTAAGATCAA+AGG 0.602756 1:-19711471 MsaT001410.1:CDS
AGAGGTGACTCATGCAAACA+AGG 0.619444 1:-19711065 MsaT001410.1:intron
TATGCCATTGAAACTCTTGG+TGG 0.619663 1:-19711404 MsaT001410.1:CDS
CAGATGTATAGGAGTATGAG+AGG 0.628713 1:-19711083 MsaT001410.1:CDS
GAAGAAGCATTACTTCTCTG+AGG 0.630731 1:+19707564 None:intergenic
TGCATTCAAGGATTCCTGAG+AGG 0.645375 1:+19709847 None:intergenic
ATGGTTCAGCAACAGCAGAA+GGG 0.660060 1:-19709762 MsaT001410.1:CDS
AGAAGCATTACTTCTCTGAG+GGG 0.734541 1:+19707566 None:intergenic
TCAGGTGTCCATCTTAAACG+AGG 0.752182 1:+19711446 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 19707470 19711522 19707470 ID=MsaG001410
Chr1 mRNA 19707470 19711522 19707470 ID=MsaT001410.1;Parent=MsaG001410
Chr1 exon 19707470 19707712 19707470 ID=MsaT001410.1.exon6;Parent=MsaT001410.1
Chr1 CDS 19707470 19707712 19707470 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Chr1 exon 19709659 19709893 19709659 ID=MsaT001410.1.exon5;Parent=MsaT001410.1
Chr1 CDS 19709659 19709893 19709659 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Chr1 exon 19710485 19710611 19710485 ID=MsaT001410.1.exon4;Parent=MsaT001410.1
Chr1 CDS 19710485 19710611 19710485 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Chr1 exon 19711066 19711102 19711066 ID=MsaT001410.1.exon3;Parent=MsaT001410.1
Chr1 CDS 19711066 19711102 19711066 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Chr1 exon 19711198 19711274 19711198 ID=MsaT001410.1.exon2;Parent=MsaT001410.1
Chr1 CDS 19711198 19711274 19711198 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Chr1 exon 19711396 19711522 19711396 ID=MsaT001410.1.exon1;Parent=MsaT001410.1
Chr1 CDS 19711396 19711522 19711396 ID=cds.MsaT001410.1;Parent=MsaT001410.1
Gene Sequence

>MsaT001410.1

ATGAGTAGTTGTGGAAGGGAAGGTGTTGTGAGACAATATGTAAGATCAAAGGTTCCTCGTTTAAGATGGACACCTGAACTTCATCGTTGCTTTGTTTATGCCATTGAAACTCTTGGTGGTCATCAAAAGGCTACTCCTAAGCTTGTTCTTCAGTTGATGGATGTTAAAGGGTTAACAATTTCACATGTTAAGAGCCATTTGCAGATGTATAGGAGTATGAGAGGTGACTCATGCAAACAAGATAGGACTACTTCCGTACATAAAAAACAATCTTTTCTGGAGCATGATGATGATGGGTTTAGAGATCATGAATCTCTTGGAATGGAATCTGATTCTCTCTTTAGCTACAGAAATTTCTCCCCAAAAAGAGCTAGAATCGAGAAGAGAAATTCCCTCTCAGGAATCCTTGAATGCAGAGAAAGAATATGTGAAGAAGTTCCAAATCCATACACTACTTTTTATGATTATGTGCAGGACATGGTTCAGCAACAGCAGAAGGGAATAAAGGAGATTTGTTGTGTTGGTTCAATATGGCATACTCCTCAACCACAATATTTCACAATCTTTCCAGTGCTACCAAAACAAGAAACTGATTTGCTCCAGGTCACCAAGTTAAATGAAAAAAAGCATGTGAATGAAATTGGCAAGACTAAGAGTGTACGTGCAGAAGATGAAGAAGATATAAGGGGTTGTGAGTTGTCATTATCAATTTCATTGCCCAATATTTCCCCTCAGAGAAGTAATGCTTCTTCAGCCAATGATATGAGAAACTCTGGATTTAGCAACTATTTGGGTTGTTCCACCGTCCAAAACATAACTAATTTGGACCTATCTTTGGCCATTTGA
Protein sequence

>MsaT001410.1

MSSCGREGVVRQYVRSKVPRLRWTPELHRCFVYAIETLGGHQKATPKLVLQLMDVKGLTISHVKSHLQMYRSMRGDSCKQDRTTSVHKKQSFLEHDDDGFRDHESLGMESDSLFSYRNFSPKRARIEKRNSLSGILECRERICEEVPNPYTTFYDYVQDMVQQQQKGIKEICCVGSIWHTPQPQYFTIFPVLPKQETDLLQVTKLNEKKHVNEIGKTKSVRAEDEEDIRGCELSLSISLPNISPQRSNASSANDMRNSGFSNYLGCSTVQNITNLDLSLAI*