AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1462280

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1462280 MtrunA17_Chr1g0184331 99.194 124 1 0 1 124 1 124 5.26e-89 257
Msa1462280 MtrunA17_Chr5g0400571 30.769 169 102 2 38 191 80 248 7.39e-16 73.2
Msa1462280 MtrunA17_Chr1g0187231 68.000 50 14 1 22 71 4 51 1.52e-15 71.2
Msa1462280 MtrunA17_Chr1g0168181 32.203 177 96 5 16 189 4 159 2.12e-15 70.5
Msa1462280 MtrunA17_Chr4g0032111 62.745 51 18 1 28 78 11 60 1.28e-14 68.6
Msa1462280 MtrunA17_Chr7g0239441 61.364 44 17 0 35 78 34 77 1.01e-13 65.5
Msa1462280 MtrunA17_Chr2g0315591 44.928 69 32 1 18 80 24 92 7.45e-12 62.0
Msa1462280 MtrunA17_Chr1g0184381 52.727 55 13 2 26 67 10 64 3.01e-11 59.7
Msa1462280 MtrunA17_Chr5g0396031 44.615 65 32 1 3 67 15 75 5.69e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1462280 AT5G43540.1 47.059 68 33 1 40 107 35 99 1.99e-13 64.7
Msa1462280 AT4G17810.1 30.460 174 87 6 38 191 44 203 2.30e-13 66.2
Msa1462280 AT4G17810.2 31.210 157 78 5 38 191 44 173 5.87e-13 64.3
Msa1462280 AT3G23130.1 60.870 46 15 1 25 67 29 74 1.38e-12 63.9
Msa1462280 AT3G09290.1 67.568 37 12 0 31 67 26 62 1.60e-11 60.5
Msa1462280 AT3G53820.1 75.000 32 8 0 37 68 18 49 4.54e-11 58.5
Msa1462280 AT2G37740.1 40.506 79 44 1 27 102 26 104 4.99e-11 60.8

Find 32 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTATCTTGTCTTTATTTAA+TGG 0.196520 tig0042133:-1358 None:intergenic
CATGATCATCGTCGTTGTTT+TGG 0.273789 tig0042133:-931 None:intergenic
TGAACTAGGAGGAGCAAAAT+TGG 0.301135 tig0042133:-1089 None:intergenic
TTCACAACTGCTCAAGCTTT+AGG 0.324072 tig0042133:+1007 Msa1462280:CDS
CATGATAACTATGGAGATCT+TGG 0.334975 tig0042133:+1130 Msa1462280:CDS
CAACAATGAAGTGGGTGAAT+TGG 0.339657 tig0042133:+1384 Msa1462280:CDS
AAAGGATGTTTGAACAAGAT+TGG 0.344523 tig0042133:+1311 Msa1462280:CDS
TGAAGTGGGTGAATTGGATT+TGG 0.376048 tig0042133:+1390 Msa1462280:CDS
CATGATCATCACATGGGAAT+TGG 0.389791 tig0042133:+950 Msa1462280:CDS
GTAGTTGATCATGATAACTA+TGG 0.421306 tig0042133:+1121 Msa1462280:CDS
AGCTCTTCGAGTCTTCTTGA+AGG 0.511682 tig0042133:-877 None:intergenic
TCCAAGTCATCTTGCAAGAG+GGG 0.518624 tig0042133:+1171 Msa1462280:CDS
GATGTTTGAACAAGATTGGA+GGG 0.521646 tig0042133:+1315 Msa1462280:CDS
TTGGATTTGGAGCTTAGACT+TGG 0.521696 tig0042133:+1403 Msa1462280:CDS
ACTACTAATTTGCTTGAACT+AGG 0.523496 tig0042133:-1103 None:intergenic
GATAGAAAACAACAATGAAG+TGG 0.546696 tig0042133:+1375 Msa1462280:CDS
ACAACTGCTCAAGCTTTAGG+TGG 0.547877 tig0042133:+1010 Msa1462280:CDS
CGATGATCATGATCATCACA+TGG 0.555921 tig0042133:+943 Msa1462280:CDS
TCACTATATTGCACATGTGA+AGG 0.565536 tig0042133:-1268 None:intergenic
ATCCAAGTCATCTTGCAAGA+GGG 0.566204 tig0042133:+1170 Msa1462280:CDS
TTGAAGGTAGCTGAATTCCA+TGG 0.575818 tig0042133:-861 None:intergenic
GGATGTTTGAACAAGATTGG+AGG 0.576231 tig0042133:+1314 Msa1462280:CDS
TACCTCAGGAGTAGTTGTTG+TGG 0.580075 tig0042133:-1215 None:intergenic
TAATTAAGAGAATCTACCTC+AGG 0.590500 tig0042133:-1229 None:intergenic
TGTTGTGTGTTGAAAATCAA+AGG 0.594228 tig0042133:+1293 Msa1462280:CDS
ATAGAAAACAACAATGAAGT+GGG 0.595407 tig0042133:+1376 Msa1462280:CDS
ACTAATTTGCTTGAACTAGG+AGG 0.604445 tig0042133:-1100 None:intergenic
AATCCAAGTCATCTTGCAAG+AGG 0.624664 tig0042133:+1169 Msa1462280:CDS
ATGTTTGAACAAGATTGGAG+GGG 0.639186 tig0042133:+1316 Msa1462280:CDS
CCAAGTCATCTTGCAAGAGG+GGG 0.654928 tig0042133:+1172 Msa1462280:CDS
ATCCACAACAACTACTCCTG+AGG 0.666114 tig0042133:+1213 Msa1462280:CDS
GATGATCATGATCATCACAT+GGG 0.724317 tig0042133:+944 Msa1462280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTATCTTGTCTTTATTTAA+TGG - tig0042133:1361-1380 None:intergenic 20.0%
! ATAGAAAACAACAATGAAGT+GGG + tig0042133:1376-1395 Msa1462280:CDS 25.0%
!! ACTACTAATTTGCTTGAACT+AGG - tig0042133:1106-1125 None:intergenic 30.0%
GTAGTTGATCATGATAACTA+TGG + tig0042133:1121-1140 Msa1462280:CDS 30.0%
TAATTAAGAGAATCTACCTC+AGG - tig0042133:1232-1251 None:intergenic 30.0%
TGTTGTGTGTTGAAAATCAA+AGG + tig0042133:1293-1312 Msa1462280:CDS 30.0%
AAAGGATGTTTGAACAAGAT+TGG + tig0042133:1311-1330 Msa1462280:CDS 30.0%
GATAGAAAACAACAATGAAG+TGG + tig0042133:1375-1394 Msa1462280:CDS 30.0%
GATGATCATGATCATCACAT+GGG + tig0042133:944-963 Msa1462280:CDS 35.0%
!!! AGGAGCAAAATTGGTTTTAG+TGG - tig0042133:1083-1102 None:intergenic 35.0%
!! ACTAATTTGCTTGAACTAGG+AGG - tig0042133:1103-1122 None:intergenic 35.0%
CATGATAACTATGGAGATCT+TGG + tig0042133:1130-1149 Msa1462280:CDS 35.0%
TCACTATATTGCACATGTGA+AGG - tig0042133:1271-1290 None:intergenic 35.0%
GATGTTTGAACAAGATTGGA+GGG + tig0042133:1315-1334 Msa1462280:CDS 35.0%
ATGTTTGAACAAGATTGGAG+GGG + tig0042133:1316-1335 Msa1462280:CDS 35.0%
! CATGATCATCGTCGTTGTTT+TGG - tig0042133:934-953 None:intergenic 40.0%
CGATGATCATGATCATCACA+TGG + tig0042133:943-962 Msa1462280:CDS 40.0%
CATGATCATCACATGGGAAT+TGG + tig0042133:950-969 Msa1462280:CDS 40.0%
! GAGTGTGTGTTTTGCAAAAG+AGG + tig0042133:983-1002 Msa1462280:CDS 40.0%
TTCACAACTGCTCAAGCTTT+AGG + tig0042133:1007-1026 Msa1462280:CDS 40.0%
TGAACTAGGAGGAGCAAAAT+TGG - tig0042133:1092-1111 None:intergenic 40.0%
AATCCAAGTCATCTTGCAAG+AGG + tig0042133:1169-1188 Msa1462280:CDS 40.0%
ATCCAAGTCATCTTGCAAGA+GGG + tig0042133:1170-1189 Msa1462280:CDS 40.0%
GGATGTTTGAACAAGATTGG+AGG + tig0042133:1314-1333 Msa1462280:CDS 40.0%
CAACAATGAAGTGGGTGAAT+TGG + tig0042133:1384-1403 Msa1462280:CDS 40.0%
TGAAGTGGGTGAATTGGATT+TGG + tig0042133:1390-1409 Msa1462280:CDS 40.0%
! TTGGATTTGGAGCTTAGACT+TGG + tig0042133:1403-1422 Msa1462280:CDS 40.0%
AGCTCTTCGAGTCTTCTTGA+AGG - tig0042133:880-899 None:intergenic 45.0%
!! ACAACTGCTCAAGCTTTAGG+TGG + tig0042133:1010-1029 Msa1462280:CDS 45.0%
TCCAAGTCATCTTGCAAGAG+GGG + tig0042133:1171-1190 Msa1462280:CDS 45.0%
ATCCACAACAACTACTCCTG+AGG + tig0042133:1213-1232 Msa1462280:CDS 45.0%
TACCTCAGGAGTAGTTGTTG+TGG - tig0042133:1218-1237 None:intergenic 45.0%
CCAAGTCATCTTGCAAGAGG+GGG + tig0042133:1172-1191 Msa1462280:CDS 50.0%
CCCCCTCTTGCAAGATGACT+TGG - tig0042133:1175-1194 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0042133 gene 863 1438 863 ID=Msa1462280;Name=Msa1462280
tig0042133 mRNA 863 1438 863 ID=Msa1462280-mRNA-1;Parent=Msa1462280;Name=Msa1462280-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|191
tig0042133 exon 863 1438 863 ID=Msa1462280-mRNA-1:exon:23591;Parent=Msa1462280-mRNA-1
tig0042133 CDS 863 1438 863 ID=Msa1462280-mRNA-1:cds;Parent=Msa1462280-mRNA-1
Gene Sequence

>Msa1462280

ATGGAATTCAGCTACCTTCAAGAAGACTCGAAGAGCTCGAGCGATGAAAACATCGATCGATCATCTGACCAAAACAACGACGATGATCATGATCATCACATGGGAATTGGTAGATCTTATGAGTGTGTGTTTTGCAAAAGAGGTTTCACAACTGCTCAAGCTTTAGGTGGACACATGAACATACATAGAAAAGATAGAGCAAATAACAACAAAAGTGCCACTAAAACCAATTTTGCTCCTCCTAGTTCAAGCAAATTAGTAGTTGATCATGATAACTATGGAGATCTTGGATTTTATTCAACAATTAATCCAAGTCATCTTGCAAGAGGGGGTTATTATTCTTCAATTTCATCCACAACAACTACTCCTGAGGTAGATTCTCTTAATTATCATCAAATATATTTTCCTTCACATGTGCAATATAGTGAGATGTTGTGTGTTGAAAATCAAAGGATGTTTGAACAAGATTGGAGGGGTTTGAGCTTGTATACAAATCCATTAAATAAAGACAAGATAGAAAACAACAATGAAGTGGGTGAATTGGATTTGGAGCTTAGACTTGGTCATTATCCATAG
Protein sequence

>Msa1462280

MEFSYLQEDSKSSSDENIDRSSDQNNDDDHDHHMGIGRSYECVFCKRGFTTAQALGGHMNIHRKDRANNNKSATKTNFAPPSSSKLVVDHDNYGDLGFYSTINPSHLARGGYYSSISSTTTTPEVDSLNYHQIYFPSHVQYSEMLCVENQRMFEQDWRGLSLYTNPLNKDKIENNNEVGELDLELRLGHYP*