AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1343040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343040 MtrunA17_Chr2g0298671 97.561 41 1 0 1 41 135 175 2.19e-22 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 135 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCGGTCCCTCTATCCCTTC+TGG 0.256600 tig0006225:-228 None:intergenic
CCGGTCCCTCTATCCCTTCT+GGG 0.338318 tig0006225:-227 None:intergenic
TTATTATGTTGAATCCTTGT+AGG 0.363095 tig0006225:+2467 Msa1343040:three_prime_UTR
TGCTGCACTGGTGATAGTTC+TGG 0.369924 tig0006225:+2370 Msa1343040:three_prime_UTR
GTGACTTCAGGGACTGTTCA+TGG 0.381999 tig0006225:+177 None:intergenic
GAAAATCCCAGAAGGGATAG+AGG 0.402816 tig0006225:+221 Msa1343040:CDS
TTACTAATAAACATTTCCTT+TGG 0.412137 tig0006225:+2601 Msa1343040:three_prime_UTR
ATTAACCTTCTCACACTACT+TGG 0.432277 tig0006225:+2394 Msa1343040:three_prime_UTR
TTGGACTTCTCGTCGAGCTT+AGG 0.433130 tig0006225:-2271 None:intergenic
TTATGGTTCATCCTCATCTT+CGG 0.453143 tig0006225:-292 None:intergenic
ACTGTTCATGGTGGGGATAG+TGG 0.455681 tig0006225:+189 Msa1343040:CDS
TACATACATTTCACCCTACA+AGG 0.462101 tig0006225:-2481 None:intergenic
CAACTGGCTGAGCTAAGTTA+TGG 0.494363 tig0006225:-309 None:intergenic
CTTCAGGGACTGTTCATGGT+GGG 0.498853 tig0006225:+181 None:intergenic
ATCAGAACCTTCACTTTCAC+CGG 0.499927 tig0006225:-246 None:intergenic
AGAAGGGCAGTGCAAGCAAA+TGG 0.501067 tig0006225:+2334 Msa1343040:three_prime_UTR
TATTATGTTGAATCCTTGTA+GGG 0.511662 tig0006225:+2468 Msa1343040:three_prime_UTR
CCCAGAAGGGATAGAGGGAC+CGG 0.527779 tig0006225:+227 Msa1343040:CDS
AAGCTGTTTGGAGTTTGAGA+AGG 0.533077 tig0006225:+2317 Msa1343040:three_prime_UTR
TTTAGCTCATTCCGAAGATG+AGG 0.577901 tig0006225:+281 Msa1343040:CDS
AGTTCGTGCAAATGCTGCAC+TGG 0.581245 tig0006225:+2358 Msa1343040:three_prime_UTR
CTTAGCTCAGCCAGTTGCTG+TGG 0.583792 tig0006225:+315 Msa1343040:three_prime_UTR
AGCTGTTTGGAGTTTGAGAA+GGG 0.585646 tig0006225:+2318 Msa1343040:three_prime_UTR
TTCAGGGACTGTTCATGGTG+GGG 0.587197 tig0006225:+182 None:intergenic
TCATGGTGGGGATAGTGGTG+TGG 0.605597 tig0006225:+194 Msa1343040:CDS
TGAGACCAAGTAGTGTGAGA+AGG 0.608817 tig0006225:-2399 None:intergenic
GCATGTGCATGCTAGTTCTG+AGG 0.612108 tig0006225:-2541 None:intergenic
ACTTCAGGGACTGTTCATGG+TGG 0.613552 tig0006225:+180 None:intergenic
AAAATCCCAGAAGGGATAGA+GGG 0.622103 tig0006225:+222 Msa1343040:CDS
CATGTGCATGCTAGTTCTGA+GGG 0.626942 tig0006225:-2540 None:intergenic
GTGGAGTTGAAAATCCCAGA+AGG 0.627086 tig0006225:+213 Msa1343040:CDS
AGAGGGACCGGTGAAAGTGA+AGG 0.629757 tig0006225:+239 Msa1343040:CDS
TCAACAGAATAAGTAACCAA+AGG 0.630082 tig0006225:-2617 None:intergenic
TGGAGTTGAAAATCCCAGAA+GGG 0.668005 tig0006225:+214 Msa1343040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGTATATATTAAACTAA+AGG + tig0006225:647-666 Msa1343040:intron 10.0%
!! TATGTATATATTAAACTAAA+GGG + tig0006225:648-667 Msa1343040:intron 10.0%
!! TGTATATGTATTAAACTAAA+TGG + tig0006225:552-571 Msa1343040:intron 15.0%
!! GTATATGTATTAAACTAAAT+GGG + tig0006225:553-572 Msa1343040:intron 15.0%
!! TTATAATTAGCAAGTTAAAA+AGG - tig0006225:610-629 None:intergenic 15.0%
!! ATGTATATATTAAACTAAAG+GGG + tig0006225:649-668 Msa1343040:intron 15.0%
!!! TACTTTTGTATTAAAGAAAT+GGG + tig0006225:1100-1119 Msa1343040:intron 15.0%
!! TATTTATTAATAATAACCCA+AGG + tig0006225:1155-1174 Msa1343040:intron 15.0%
!! ATTTATTAATAATAACCCAA+GGG + tig0006225:1156-1175 Msa1343040:intron 15.0%
!!! TATCTTTGATATTTGTTTTT+AGG - tig0006225:1235-1254 None:intergenic 15.0%
!! AGTTTCACAAATAAAATATT+AGG - tig0006225:2090-2109 None:intergenic 15.0%
!!! TAATATTTTATTTGTGAAAC+TGG + tig0006225:2089-2108 Msa1343040:intron 15.0%
!! GATTTCAAATCAAAACTAAT+GGG + tig0006225:435-454 Msa1343040:intron 20.0%
!! ATTTCAAATCAAAACTAATG+GGG + tig0006225:436-455 Msa1343040:intron 20.0%
!! ATTACATTACTAAATACAGA+GGG - tig0006225:765-784 None:intergenic 20.0%
!!! GTACTTTTGTATTAAAGAAA+TGG + tig0006225:1099-1118 Msa1343040:intron 20.0%
!! TAAATTATCATCAAGTTCTT+GGG + tig0006225:1319-1338 Msa1343040:intron 20.0%
!! GTAGTACAAATAAAATTGTA+AGG - tig0006225:1396-1415 None:intergenic 20.0%
!! TGTAAGAAATCTAAATTGTT+TGG + tig0006225:2125-2144 Msa1343040:intron 20.0%
!!! CTAATTATGTAAGATTTTCA+TGG + tig0006225:2243-2262 Msa1343040:intron 20.0%
!! TTACTAATAAACATTTCCTT+TGG + tig0006225:2601-2620 Msa1343040:three_prime_UTR 20.0%
! GGATTTCAAATCAAAACTAA+TGG + tig0006225:434-453 Msa1343040:intron 25.0%
! TTTCAAATCAAAACTAATGG+GGG + tig0006225:437-456 Msa1343040:intron 25.0%
!! GGAATTTTTCATGTTTCATA+TGG + tig0006225:465-484 Msa1343040:intron 25.0%
! AAAGATACAAGTTAGAAGAT+CGG - tig0006225:496-515 None:intergenic 25.0%
!!! TTATAATGCTTGCTTTTGAA+AGG + tig0006225:624-643 Msa1343040:intron 25.0%
! GATTGAAATTCATGAAAACA+TGG + tig0006225:680-699 Msa1343040:intron 25.0%
! CATTACATTACTAAATACAG+AGG - tig0006225:766-785 None:intergenic 25.0%
! CTCTGTATTTAGTAATGTAA+TGG + tig0006225:764-783 Msa1343040:intron 25.0%
! AAAGATAAAATCCCTAATCA+GGG + tig0006225:1248-1267 Msa1343040:intron 25.0%
! ATTAAATCTTTCCCTGATTA+GGG - tig0006225:1262-1281 None:intergenic 25.0%
! AATTAAATCTTTCCCTGATT+AGG - tig0006225:1263-1282 None:intergenic 25.0%
! CTAAATTATCATCAAGTTCT+TGG + tig0006225:1318-1337 Msa1343040:intron 25.0%
! CATAATAGATTAGATTGCTT+GGG - tig0006225:1355-1374 None:intergenic 25.0%
! ACATAATAGATTAGATTGCT+TGG - tig0006225:1356-1375 None:intergenic 25.0%
!! TACTAATGATTTTGTACTGT+AGG + tig0006225:1568-1587 Msa1343040:intron 25.0%
! AAAATAGCACACTATTATCA+GGG - tig0006225:1817-1836 None:intergenic 25.0%
! TAAAATAGCACACTATTATC+AGG - tig0006225:1818-1837 None:intergenic 25.0%
!!! TAATAGTGTGCTATTTTATC+AGG + tig0006225:1820-1839 Msa1343040:intron 25.0%
!! TATTTTATCAGGAATTTCTC+AGG + tig0006225:1831-1850 Msa1343040:intron 25.0%
!! ATTTTATCAGGAATTTCTCA+GGG + tig0006225:1832-1851 Msa1343040:intron 25.0%
! AAACAAAAAACTAAGCTGTT+TGG + tig0006225:2305-2324 Msa1343040:three_prime_UTR 25.0%
! TTATTATGTTGAATCCTTGT+AGG + tig0006225:2467-2486 Msa1343040:three_prime_UTR 25.0%
! TATTATGTTGAATCCTTGTA+GGG + tig0006225:2468-2487 Msa1343040:three_prime_UTR 25.0%
! AGAAAACTTGTTCTTTAGCT+TGG + tig0006225:340-359 Msa1343040:intron 30.0%
CATATACACAACCTTTCAAA+AGG - tig0006225:540-559 None:intergenic 30.0%
AATTAGCAAGTTAAAAAGGC+AGG - tig0006225:606-625 None:intergenic 30.0%
AAGTAAATTACTCACTTTGG+AGG - tig0006225:822-841 None:intergenic 30.0%
CCAAAGTAAATTACTCACTT+TGG - tig0006225:825-844 None:intergenic 30.0%
CCAAAGTGAGTAATTTACTT+TGG + tig0006225:822-841 Msa1343040:intron 30.0%
AAGTGAGTAATTTACTTTGG+AGG + tig0006225:825-844 Msa1343040:intron 30.0%
TAGAGGAGTCAAATTTACAT+TGG + tig0006225:1005-1024 Msa1343040:intron 30.0%
AGAGGAGTCAAATTTACATT+GGG + tig0006225:1006-1025 Msa1343040:intron 30.0%
GGCATAATTTGAATAGCATA+TGG + tig0006225:1121-1140 Msa1343040:intron 30.0%
CAAAGATAAAATCCCTAATC+AGG + tig0006225:1247-1266 Msa1343040:intron 30.0%
! GTACTACTCAAACTTTTGAA+TGG + tig0006225:1409-1428 Msa1343040:intron 30.0%
!! TGGTAATTTTATGTACTGAC+TGG + tig0006225:1429-1448 Msa1343040:intron 30.0%
TACGATTGTGTATTGTGTAT+AGG - tig0006225:1492-1511 None:intergenic 30.0%
AGAATCATTTCACAATAGCT+TGG - tig0006225:1784-1803 None:intergenic 30.0%
AGCTATTGTGAAATGATTCT+AGG + tig0006225:1784-1803 Msa1343040:intron 30.0%
CAGGGAATATATGATTGATA+AGG + tig0006225:1850-1869 Msa1343040:intron 30.0%
ACGTAACAATGTTTAGAAGA+TGG + tig0006225:2018-2037 Msa1343040:intron 30.0%
TACATAATTAGTGCTTAGCA+TGG - tig0006225:2234-2253 None:intergenic 30.0%
!! TTTTGTTTCCTCGCATTTTT+TGG - tig0006225:2293-2312 None:intergenic 30.0%
TCAACAGAATAAGTAACCAA+AGG - tig0006225:2620-2639 None:intergenic 30.0%
! TCGGAATGAGCTAAATTTTC+TGG - tig0006225:276-295 None:intergenic 35.0%
TTATGGTTCATCCTCATCTT+CGG - tig0006225:295-314 None:intergenic 35.0%
! TTTACAACCTGCCTTTTGAA+AGG + tig0006225:526-545 Msa1343040:intron 35.0%
TAAAAAGAGAACTACGCTTG+AGG + tig0006225:787-806 Msa1343040:intron 35.0%
AAAAAGAGAACTACGCTTGA+GGG + tig0006225:788-807 Msa1343040:intron 35.0%
AAAGTTACAGTTCACTCTAG+AGG + tig0006225:988-1007 Msa1343040:intron 35.0%
GTCAAATTTACATTGGGACA+AGG + tig0006225:1012-1031 Msa1343040:intron 35.0%
!!! CAAGGTGTTTTTTGGACAAA+GGG - tig0006225:1039-1058 None:intergenic 35.0%
!!! TCAAGGTGTTTTTTGGACAA+AGG - tig0006225:1040-1059 None:intergenic 35.0%
! TATCGATGTTTGTTACCCTT+GGG - tig0006225:1174-1193 None:intergenic 35.0%
! TTATCGATGTTTGTTACCCT+TGG - tig0006225:1175-1194 None:intergenic 35.0%
GCTAAATCTTATCTTGTGAC+AGG + tig0006225:1461-1480 Msa1343040:intron 35.0%
TCTTCCTATTTCCACAATAC+TGG + tig0006225:1520-1539 Msa1343040:intron 35.0%
TACACCAGTATTGTGGAAAT+AGG - tig0006225:1527-1546 None:intergenic 35.0%
! CACATTTTACACCAGTATTG+TGG - tig0006225:1534-1553 None:intergenic 35.0%
CACAATACTGGTGTAAAATG+TGG + tig0006225:1532-1551 Msa1343040:intron 35.0%
AATCTTAGTATGCGTGTCTT+TGG + tig0006225:1612-1631 Msa1343040:intron 35.0%
AATCTTAGTATGCGTGTCTT+TGG + tig0006225:1612-1631 Msa1343040:intron 35.0%
!!! GTGTTGTTTGTTTTTCCTGT+TGG + tig0006225:1734-1753 Msa1343040:intron 35.0%
!! GTTTGTTTTTCCTGTTGGTT+TGG + tig0006225:1739-1758 Msa1343040:intron 35.0%
ATTAACCTTCTCACACTACT+TGG + tig0006225:2394-2413 Msa1343040:three_prime_UTR 35.0%
TACATACATTTCACCCTACA+AGG - tig0006225:2484-2503 None:intergenic 35.0%
TGGAGTTGAAAATCCCAGAA+GGG + tig0006225:214-233 Msa1343040:CDS 40.0%
AAAATCCCAGAAGGGATAGA+GGG + tig0006225:222-241 Msa1343040:CDS 40.0%
ATCAGAACCTTCACTTTCAC+CGG - tig0006225:249-268 None:intergenic 40.0%
! TTTAGCTCATTCCGAAGATG+AGG + tig0006225:281-300 Msa1343040:CDS 40.0%
CAGAAACCATTCTTGCTGAT+GGG + tig0006225:392-411 Msa1343040:intron 40.0%
GGCAACATAGGAAGTGATAA+CGG + tig0006225:413-432 Msa1343040:intron 40.0%
ATCAAAACTAATGGGGGATG+AGG + tig0006225:443-462 Msa1343040:intron 40.0%
TCAAAACTAATGGGGGATGA+GGG + tig0006225:444-463 Msa1343040:intron 40.0%
TACACAACCTTTCAAAAGGC+AGG - tig0006225:536-555 None:intergenic 40.0%
TTAAACTAAAGGGGAGTGAC+AGG + tig0006225:658-677 Msa1343040:intron 40.0%
!! ACCACTGACTTTCTCATCAA+CGG + tig0006225:938-957 Msa1343040:intron 40.0%
!!! TAAGCGCTCAAGGTGTTTTT+TGG - tig0006225:1047-1066 None:intergenic 40.0%
GTATATTCCCAAACGTTAGC+AGG + tig0006225:1707-1726 Msa1343040:intron 40.0%
TAACAACTGCATCTTGTGTG+CGG + tig0006225:1905-1924 Msa1343040:intron 40.0%
ATTAAGAGAACGTTCTGCAG+TGG - tig0006225:1984-2003 None:intergenic 40.0%
! AAGCTGTTTGGAGTTTGAGA+AGG + tig0006225:2317-2336 Msa1343040:three_prime_UTR 40.0%
! AGCTGTTTGGAGTTTGAGAA+GGG + tig0006225:2318-2337 Msa1343040:three_prime_UTR 40.0%
GTGGAGTTGAAAATCCCAGA+AGG + tig0006225:213-232 Msa1343040:CDS 45.0%
GAAAATCCCAGAAGGGATAG+AGG + tig0006225:221-240 Msa1343040:CDS 45.0%
CAACTGGCTGAGCTAAGTTA+TGG - tig0006225:312-331 None:intergenic 45.0%
! AGTTTTCTCACCACAGCAAC+TGG - tig0006225:328-347 None:intergenic 45.0%
GCAGAAACCATTCTTGCTGA+TGG + tig0006225:391-410 Msa1343040:intron 45.0%
ATGTTGCCCATCAGCAAGAA+TGG - tig0006225:401-420 None:intergenic 45.0%
! TTCTTGCTGATGGGCAACAT+AGG + tig0006225:401-420 Msa1343040:intron 45.0%
! ACCGTTGATGAGAAAGTCAG+TGG - tig0006225:942-961 None:intergenic 45.0%
CTGTCTCAAATAAGCGCTCA+AGG - tig0006225:1057-1076 None:intergenic 45.0%
! TGCTCATCTGTCACGGTTTT+AGG + tig0006225:1077-1096 Msa1343040:intron 45.0%
TTCCCAAACGTTAGCAGGAA+AGG + tig0006225:1712-1731 Msa1343040:intron 45.0%
CACCTTTCCTGCTAACGTTT+GGG - tig0006225:1717-1736 None:intergenic 45.0%
ACACCTTTCCTGCTAACGTT+TGG - tig0006225:1718-1737 None:intergenic 45.0%
CGAGAAGTCCAAAAAATGCG+AGG + tig0006225:2282-2301 Msa1343040:three_prime_UTR 45.0%
TGAGACCAAGTAGTGTGAGA+AGG - tig0006225:2402-2421 None:intergenic 45.0%
!! CATGTGCATGCTAGTTCTGA+GGG - tig0006225:2543-2562 None:intergenic 45.0%
! ACTGTTCATGGTGGGGATAG+TGG + tig0006225:189-208 Msa1343040:CDS 50.0%
GAGACAGTGCTCATCTGTCA+CGG + tig0006225:1070-1089 Msa1343040:intron 50.0%
CGAACTGACACCAAACCAAC+AGG - tig0006225:1752-1771 None:intergenic 50.0%
AGAGAACGTTCTGCAGTGGT+TGG - tig0006225:1980-1999 None:intergenic 50.0%
TTGGACTTCTCGTCGAGCTT+AGG - tig0006225:2274-2293 None:intergenic 50.0%
AGAAGGGCAGTGCAAGCAAA+TGG + tig0006225:2334-2353 Msa1343040:three_prime_UTR 50.0%
AGTTCGTGCAAATGCTGCAC+TGG + tig0006225:2358-2377 Msa1343040:three_prime_UTR 50.0%
! TGCTGCACTGGTGATAGTTC+TGG + tig0006225:2370-2389 Msa1343040:three_prime_UTR 50.0%
!! GCATGTGCATGCTAGTTCTG+AGG - tig0006225:2544-2563 None:intergenic 50.0%
! TCATGGTGGGGATAGTGGTG+TGG + tig0006225:194-213 Msa1343040:CDS 55.0%
AGAGGGACCGGTGAAAGTGA+AGG + tig0006225:239-258 Msa1343040:CDS 55.0%
CTTAGCTCAGCCAGTTGCTG+TGG + tig0006225:315-334 Msa1343040:three_prime_UTR 55.0%
CCGGTCCCTCTATCCCTTCT+GGG - tig0006225:230-249 None:intergenic 60.0%
CCCAGAAGGGATAGAGGGAC+CGG + tig0006225:227-246 Msa1343040:CDS 60.0%
ACCGGTCCCTCTATCCCTTC+TGG - tig0006225:231-250 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0006225 gene 189 2645 189 ID=Msa1343040;Name=Msa1343040
tig0006225 mRNA 189 2645 189 ID=Msa1343040-mRNA-1;Parent=Msa1343040;Name=Msa1343040-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|0|0|2|397|41
tig0006225 exon 189 336 189 ID=Msa1343040-mRNA-1:exon:3920;Parent=Msa1343040-mRNA-1
tig0006225 exon 2271 2645 2271 ID=Msa1343040-mRNA-1:exon:3921;Parent=Msa1343040-mRNA-1
tig0006225 CDS 189 314 189 ID=Msa1343040-mRNA-1:cds;Parent=Msa1343040-mRNA-1
tig0006225 three_prime_UTR 315 336 315 ID=Msa1343040-mRNA-1:three_prime_utr;Parent=Msa1343040-mRNA-1
tig0006225 three_prime_UTR 2271 2645 2271 ID=Msa1343040-mRNA-1:three_prime_utr;Parent=Msa1343040-mRNA-1
Gene Sequence

>Msa1343040

ACTGTTCATGGTGGGGATAGTGGTGTGGAGTTGAAAATCCCAGAAGGGATAGAGGGACCGGTGAAAGTGAAGGTTCTGATGTTTCCAGAAAATTTAGCTCATTCCGAAGATGAGGATGAACCATAA
Protein sequence

>Msa1343040

TVHGGDSGVELKIPEGIEGPVKVKVLMFPENLAHSEDEDEP*