AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1465880

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATTATTTGTATCTTATT+TGG 0.120705 tig0045682:-1362 Msa1465880:three_prime_UTR
GATGTAGTTATTTGCAAGTT+TGG 0.186562 tig0045682:+1962 Msa1465880:intergenic
ATATATACCATGTTTGAAAT+TGG 0.194861 tig0045682:+1816 Msa1465880:intergenic
TTATGAATTCTTTCAAATTA+AGG 0.214260 tig0045682:-1392 Msa1465880:three_prime_UTR
AGCAACAAATGACTTCAATT+TGG 0.266219 tig0045682:+1894 Msa1465880:intergenic
CAATATTCTGCACCCTCTTA+TGG 0.271660 tig0045682:-1541 Msa1465880:CDS
GAAGTCATTTGTTGCTCTCT+TGG 0.321512 tig0045682:-1887 Msa1465880:CDS
ATTTAGTTGAGCTACACTTA+TGG 0.340627 tig0045682:-1205 Msa1465880:three_prime_UTR
TTTAGTTGAGCTACACTTAT+GGG 0.344514 tig0045682:-1204 Msa1465880:three_prime_UTR
CCCTCTTATGGTTCATTCCC+TGG 0.350929 tig0045682:-1529 Msa1465880:CDS
ATGTAGTTATTTGCAAGTTT+GGG 0.355745 tig0045682:+1963 Msa1465880:intergenic
ACTACTCATGTCATCTATCA+TGG 0.395752 tig0045682:-1854 Msa1465880:CDS
TACCATGTTTGAAATTGGAT+TGG 0.399589 tig0045682:+1821 Msa1465880:intergenic
AATATTATCACTTGAAGAAT+AGG 0.400683 tig0045682:+1991 Msa1465880:intergenic
ATTGTACTATAAGAATAAAT+TGG 0.402523 tig0045682:-1338 Msa1465880:three_prime_UTR
CAGCTGTTCTGTGACTAAAC+TGG 0.419278 tig0045682:-1443 Msa1465880:three_prime_UTR
ACCAGGGAATGAACCATAAG+AGG 0.435500 tig0045682:+1528 Msa1465880:intergenic
GGTTCATTCCCTGGTGGTGG+AGG 0.445646 tig0045682:-1520 Msa1465880:CDS
CAGTTTAGTCACAGAACAGC+TGG 0.449201 tig0045682:+1444 Msa1465880:intergenic
TATGGTTCATTCCCTGGTGG+TGG 0.455953 tig0045682:-1523 Msa1465880:CDS
ATATATTGAGTACTAATTAA+CGG 0.460298 tig0045682:+1418 Msa1465880:intergenic
ACCATGTTTGAAATTGGATT+GGG 0.461990 tig0045682:+1822 Msa1465880:intergenic
AAGAGGGTGCAGAATATTGT+TGG 0.468164 tig0045682:+1545 Msa1465880:intergenic
CACATTAATAGCCCCACGGT+GGG 0.549490 tig0045682:-1483 Msa1465880:exon
TATTTATATCCTCCACCACC+AGG 0.549536 tig0045682:+1511 Msa1465880:intergenic
CCACCGTGGGGCTATTAATG+TGG 0.550176 tig0045682:+1484 Msa1465880:intergenic
CTACTCATGTCATCTATCAT+GGG 0.563545 tig0045682:-1853 Msa1465880:CDS
AATGACTTCAATTTGGAGAG+AGG 0.591876 tig0045682:+1901 Msa1465880:intergenic
GCCCAATCCAATTTCAAACA+TGG 0.609489 tig0045682:-1823 Msa1465880:intron
AGTTTAGTCACAGAACAGCT+GGG 0.611968 tig0045682:+1445 Msa1465880:intergenic
CCGTGGGGCTATTAATGTGG+AGG 0.630515 tig0045682:+1487 Msa1465880:intergenic
TCTTATGGTTCATTCCCTGG+TGG 0.633770 tig0045682:-1526 Msa1465880:CDS
CCAGGGAATGAACCATAAGA+GGG 0.637077 tig0045682:+1529 Msa1465880:intergenic
ACATTAATAGCCCCACGGTG+GGG 0.640090 tig0045682:-1482 Msa1465880:exon
TTATCACTTGAAGAATAGGT+AGG 0.640251 tig0045682:+1995 Msa1465880:intergenic
CCACATTAATAGCCCCACGG+TGG 0.681173 tig0045682:-1484 Msa1465880:exon
CCTCCACATTAATAGCCCCA+CGG 0.685288 tig0045682:-1487 Msa1465880:exon
ATTTATATCCTCCACCACCA+GGG 0.692132 tig0045682:+1512 Msa1465870:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATTATTTTTATAAGCAA+TGG + tig0045682:1902-1921 Msa1465880:intergenic 10.0%
!!! ATTATTATTTTTATAAGCAA+TGG + tig0045682:1902-1921 Msa1465880:intergenic 10.0%
!!! ATAGTATATATTTTGAATCA+GGG + tig0045682:1442-1461 Msa1465880:intergenic 15.0%
!!! TATAGTATATATTTTGAATC+AGG + tig0045682:1443-1462 Msa1465880:intergenic 15.0%
!!! TCACTTATCTTTTTTATATA+TGG - tig0045682:1590-1609 Msa1465880:intron 15.0%
!! ATATATTGAGTACTAATTAA+CGG + tig0045682:1761-1780 Msa1465880:intergenic 15.0%
!! TTATGAATTCTTTCAAATTA+AGG - tig0045682:1784-1803 Msa1465880:intron 15.0%
!! CAAATTATTTGTATCTTATT+TGG - tig0045682:1814-1833 Msa1465880:intron 15.0%
!! ATTGTACTATAAGAATAAAT+TGG - tig0045682:1838-1857 Msa1465880:CDS 15.0%
!!! ATAGTATATATTTTGAATCA+GGG + tig0045682:1442-1461 Msa1465880:intergenic 15.0%
!!! TATAGTATATATTTTGAATC+AGG + tig0045682:1443-1462 Msa1465880:intergenic 15.0%
!!! TCACTTATCTTTTTTATATA+TGG - tig0045682:1590-1609 Msa1465880:intron 15.0%
!! ATATATTGAGTACTAATTAA+CGG + tig0045682:1761-1780 Msa1465880:intergenic 15.0%
!! TTATGAATTCTTTCAAATTA+AGG - tig0045682:1784-1803 Msa1465880:intron 15.0%
!! CAAATTATTTGTATCTTATT+TGG - tig0045682:1814-1833 Msa1465880:intron 15.0%
!! ATTGTACTATAAGAATAAAT+TGG - tig0045682:1838-1857 Msa1465880:CDS 15.0%
!! AATATTATCACTTGAAGAAT+AGG + tig0045682:1188-1207 Msa0081540:intergenic 20.0%
!!! ATATATACCATGTTTGAAAT+TGG + tig0045682:1363-1382 Msa1465880:intergenic 20.0%
!!! TTGTTAATCTTCTGATTTTT+AGG - tig0045682:2014-2033 Msa1465880:five_prime_UTR 20.0%
!! AATATTATCACTTGAAGAAT+AGG + tig0045682:1188-1207 Msa1465880:intergenic 20.0%
!!! ATATATACCATGTTTGAAAT+TGG + tig0045682:1363-1382 Msa1465880:intergenic 20.0%
!!! TTGTTAATCTTCTGATTTTT+AGG - tig0045682:2014-2033 Msa1465880:five_prime_UTR 20.0%
! ATGTAGTTATTTGCAAGTTT+GGG + tig0045682:1216-1235 Msa0081540:intergenic 25.0%
! ATAGTAAGAATCATATCACA+TGG - tig0045682:1410-1429 Msa1465880:three_prime_UTR 25.0%
! TATAATCATATGCTTATTCG+AGG - tig0045682:1459-1478 Msa1465880:three_prime_UTR 25.0%
! CATTTAACCAATTGGAATTT+GGG - tig0045682:1485-1504 Msa1465880:exon 25.0%
!! AATTTGGGATTGATTATTGA+TGG - tig0045682:1500-1519 Msa1465880:CDS 25.0%
! ATGTAGTTATTTGCAAGTTT+GGG + tig0045682:1216-1235 Msa1465880:intergenic 25.0%
! ATAGTAAGAATCATATCACA+TGG - tig0045682:1410-1429 Msa1465880:three_prime_UTR 25.0%
! TATAATCATATGCTTATTCG+AGG - tig0045682:1459-1478 Msa1465880:three_prime_UTR 25.0%
! CATTTAACCAATTGGAATTT+GGG - tig0045682:1485-1504 Msa1465880:exon 25.0%
!! AATTTGGGATTGATTATTGA+TGG - tig0045682:1500-1519 Msa1465880:CDS 25.0%
TTATCACTTGAAGAATAGGT+AGG + tig0045682:1184-1203 Msa0081540:intergenic 30.0%
GATGTAGTTATTTGCAAGTT+TGG + tig0045682:1217-1236 Msa0081540:intergenic 30.0%
AGCAACAAATGACTTCAATT+TGG + tig0045682:1285-1304 Msa0081540:intergenic 30.0%
! ACCATGTTTGAAATTGGATT+GGG + tig0045682:1357-1376 Msa1465880:intergenic 30.0%
! TACCATGTTTGAAATTGGAT+TGG + tig0045682:1358-1377 Msa1465880:intergenic 30.0%
CCAAATTCCAATTGGTTAAA+TGG + tig0045682:1487-1506 Msa1465880:intergenic 30.0%
CCATTTAACCAATTGGAATT+TGG - tig0045682:1484-1503 Msa1465880:exon 30.0%
AATCAATCCCAAATTCCAAT+TGG + tig0045682:1495-1514 Msa1465880:intergenic 30.0%
!!! ATCTTTTTTATATATGGCGC+AGG - tig0045682:1596-1615 Msa1465880:intron 30.0%
!!! TCTTTTTTATATATGGCGCA+GGG - tig0045682:1597-1616 Msa1465880:intron 30.0%
ATTTAGTTGAGCTACACTTA+TGG - tig0045682:1971-1990 Msa1465880:five_prime_UTR 30.0%
TTTAGTTGAGCTACACTTAT+GGG - tig0045682:1972-1991 Msa1465880:five_prime_UTR 30.0%
TTATCACTTGAAGAATAGGT+AGG + tig0045682:1184-1203 Msa1465880:intergenic 30.0%
GATGTAGTTATTTGCAAGTT+TGG + tig0045682:1217-1236 Msa1465880:intergenic 30.0%
AGCAACAAATGACTTCAATT+TGG + tig0045682:1285-1304 Msa1465880:intergenic 30.0%
! ACCATGTTTGAAATTGGATT+GGG + tig0045682:1357-1376 Msa1465880:intergenic 30.0%
! TACCATGTTTGAAATTGGAT+TGG + tig0045682:1358-1377 Msa1465880:intergenic 30.0%
CCAAATTCCAATTGGTTAAA+TGG + tig0045682:1487-1506 Msa1465880:intergenic 30.0%
CCATTTAACCAATTGGAATT+TGG - tig0045682:1484-1503 Msa1465880:exon 30.0%
AATCAATCCCAAATTCCAAT+TGG + tig0045682:1495-1514 Msa1465880:intergenic 30.0%
!!! ATCTTTTTTATATATGGCGC+AGG - tig0045682:1596-1615 Msa1465880:intron 30.0%
!!! TCTTTTTTATATATGGCGCA+GGG - tig0045682:1597-1616 Msa1465880:intron 30.0%
ATTTAGTTGAGCTACACTTA+TGG - tig0045682:1971-1990 Msa1465880:five_prime_UTR 30.0%
TTTAGTTGAGCTACACTTAT+GGG - tig0045682:1972-1991 Msa1465880:five_prime_UTR 30.0%
AATGACTTCAATTTGGAGAG+AGG + tig0045682:1278-1297 Msa0081540:intergenic 35.0%
ACTACTCATGTCATCTATCA+TGG - tig0045682:1322-1341 Msa1465880:three_prime_UTR 35.0%
CTACTCATGTCATCTATCAT+GGG - tig0045682:1323-1342 Msa1465880:three_prime_UTR 35.0%
AATGACTTCAATTTGGAGAG+AGG + tig0045682:1278-1297 Msa1465880:intergenic 35.0%
ACTACTCATGTCATCTATCA+TGG - tig0045682:1322-1341 Msa1465880:three_prime_UTR 35.0%
CTACTCATGTCATCTATCAT+GGG - tig0045682:1323-1342 Msa1465880:three_prime_UTR 35.0%
! GAAGTCATTTGTTGCTCTCT+TGG - tig0045682:1289-1308 Msa1465880:three_prime_UTR 40.0%
GCCCAATCCAATTTCAAACA+TGG - tig0045682:1353-1372 Msa1465880:three_prime_UTR 40.0%
! AAGAGGGTGCAGAATATTGT+TGG + tig0045682:1634-1653 Msa1465880:intergenic 40.0%
CAATATTCTGCACCCTCTTA+TGG - tig0045682:1635-1654 Msa1465880:intron 40.0%
ATTTATATCCTCCACCACCA+GGG + tig0045682:1667-1686 Msa1465880:intergenic 40.0%
TATTTATATCCTCCACCACC+AGG + tig0045682:1668-1687 Msa1465880:intergenic 40.0%
AGTTTAGTCACAGAACAGCT+GGG + tig0045682:1734-1753 Msa1465880:intergenic 40.0%
! GAAGTCATTTGTTGCTCTCT+TGG - tig0045682:1289-1308 Msa1465880:three_prime_UTR 40.0%
GCCCAATCCAATTTCAAACA+TGG - tig0045682:1353-1372 Msa1465880:three_prime_UTR 40.0%
! AAGAGGGTGCAGAATATTGT+TGG + tig0045682:1634-1653 Msa1465880:intergenic 40.0%
CAATATTCTGCACCCTCTTA+TGG - tig0045682:1635-1654 Msa1465880:intron 40.0%
ATTTATATCCTCCACCACCA+GGG + tig0045682:1667-1686 Msa1465880:intergenic 40.0%
TATTTATATCCTCCACCACC+AGG + tig0045682:1668-1687 Msa1465880:intergenic 40.0%
AGTTTAGTCACAGAACAGCT+GGG + tig0045682:1734-1753 Msa1465880:intergenic 40.0%
CGAGGCTCCATTTAACCAAT+TGG - tig0045682:1477-1496 Msa1465880:three_prime_UTR 45.0%
CCAGGGAATGAACCATAAGA+GGG + tig0045682:1650-1669 Msa1465880:intergenic 45.0%
ACCAGGGAATGAACCATAAG+AGG + tig0045682:1651-1670 Msa1465880:intergenic 45.0%
TCTTATGGTTCATTCCCTGG+TGG - tig0045682:1650-1669 Msa1465880:intron 45.0%
! TGATTATTTTCCCCACCGTG+GGG + tig0045682:1707-1726 Msa1465880:intergenic 45.0%
! GTGATTATTTTCCCCACCGT+GGG + tig0045682:1708-1727 Msa1465880:intergenic 45.0%
! AGTGATTATTTTCCCCACCG+TGG + tig0045682:1709-1728 Msa1465880:intergenic 45.0%
CAGTTTAGTCACAGAACAGC+TGG + tig0045682:1735-1754 Msa1465880:intergenic 45.0%
CAGCTGTTCTGTGACTAAAC+TGG - tig0045682:1733-1752 Msa1465880:intron 45.0%
CGAGGCTCCATTTAACCAAT+TGG - tig0045682:1477-1496 Msa1465880:three_prime_UTR 45.0%
CCAGGGAATGAACCATAAGA+GGG + tig0045682:1650-1669 Msa1465880:intergenic 45.0%
ACCAGGGAATGAACCATAAG+AGG + tig0045682:1651-1670 Msa1465880:intergenic 45.0%
TCTTATGGTTCATTCCCTGG+TGG - tig0045682:1650-1669 Msa1465880:intron 45.0%
! TGATTATTTTCCCCACCGTG+GGG + tig0045682:1707-1726 Msa1465880:intergenic 45.0%
! GTGATTATTTTCCCCACCGT+GGG + tig0045682:1708-1727 Msa1465880:intergenic 45.0%
! AGTGATTATTTTCCCCACCG+TGG + tig0045682:1709-1728 Msa1465880:intergenic 45.0%
CAGTTTAGTCACAGAACAGC+TGG + tig0045682:1735-1754 Msa1465880:intergenic 45.0%
CAGCTGTTCTGTGACTAAAC+TGG - tig0045682:1733-1752 Msa1465880:intron 45.0%
CCCTCTTATGGTTCATTCCC+TGG - tig0045682:1647-1666 Msa1465880:intron 50.0%
TATGGTTCATTCCCTGGTGG+TGG - tig0045682:1653-1672 Msa1465880:intron 50.0%
CCTCCACATTAATAGCCCCA+CGG - tig0045682:1689-1708 Msa1465880:intron 50.0%
CACATTAATAGCCCCACGGT+GGG - tig0045682:1693-1712 Msa1465880:intron 50.0%
ACATTAATAGCCCCACGGTG+GGG - tig0045682:1694-1713 Msa1465880:intron 50.0%
CCCTCTTATGGTTCATTCCC+TGG - tig0045682:1647-1666 Msa1465880:intron 50.0%
TATGGTTCATTCCCTGGTGG+TGG - tig0045682:1653-1672 Msa1465880:intron 50.0%
CCTCCACATTAATAGCCCCA+CGG - tig0045682:1689-1708 Msa1465880:intron 50.0%
CACATTAATAGCCCCACGGT+GGG - tig0045682:1693-1712 Msa1465880:intron 50.0%
ACATTAATAGCCCCACGGTG+GGG - tig0045682:1694-1713 Msa1465880:intron 50.0%
CCGTGGGGCTATTAATGTGG+AGG + tig0045682:1692-1711 Msa1465880:intergenic 55.0%
CCACCGTGGGGCTATTAATG+TGG + tig0045682:1695-1714 Msa1465880:intergenic 55.0%
CCACATTAATAGCCCCACGG+TGG - tig0045682:1692-1711 Msa1465880:intron 55.0%
CCGTGGGGCTATTAATGTGG+AGG + tig0045682:1692-1711 Msa1465880:intergenic 55.0%
CCACCGTGGGGCTATTAATG+TGG + tig0045682:1695-1714 Msa1465880:intergenic 55.0%
CCACATTAATAGCCCCACGG+TGG - tig0045682:1692-1711 Msa1465880:intron 55.0%
!! GGTTCATTCCCTGGTGGTGG+AGG - tig0045682:1656-1675 Msa1465880:intron 60.0%
!! GGTTCATTCCCTGGTGGTGG+AGG - tig0045682:1656-1675 Msa1465880:intron 60.0%
Chromosome Type Strat End Strand Name
tig0045682 gene 1156 2042 1156 ID=Msa1465880;Name=Msa1465880
tig0045682 mRNA 1156 2042 1156 ID=Msa1465880-mRNA-1;Parent=Msa1465880;Name=Msa1465880-mRNA-1;_AED=0.01;_eAED=0.01;_QI=113|1|1|1|1|1|2|342|62
tig0045682 exon 1156 1580 1156 ID=Msa1465880-mRNA-1:exon:24918;Parent=Msa1465880-mRNA-1
tig0045682 exon 1824 2042 1824 ID=Msa1465880-mRNA-1:exon:24917;Parent=Msa1465880-mRNA-1
tig0045682 five_prime_UTR 1930 2042 1930 ID=Msa1465880-mRNA-1:five_prime_utr;Parent=Msa1465880-mRNA-1
tig0045682 CDS 1824 1929 1824 ID=Msa1465880-mRNA-1:cds;Parent=Msa1465880-mRNA-1
tig0045682 CDS 1498 1580 1498 ID=Msa1465880-mRNA-1:cds;Parent=Msa1465880-mRNA-1
tig0045682 three_prime_UTR 1156 1497 1156 ID=Msa1465880-mRNA-1:three_prime_utr;Parent=Msa1465880-mRNA-1
Gene Sequence

>Msa1465880

ATGACTCCTCTCTCCAAATTGAAGTCATTTGTTGCTCTCTTGGCAATACTTTTACTACTCATGTCATCTATCATGGGTATTGCTGCCCAATCCAATTTCAAACATGGGCGAAAACTTTTCCAACAATATTCTGCACCCTCTTATGGTTCATTCCCTGGTGGTGGAGGATATAAATATCCTCCACATTAA
Protein sequence

>Msa1465880

MTPLSKLKSFVALLAILLLLMSSIMGIAAQSNFKHGRKLFQQYSAPSYGSFPGGGGYKYPPH*