AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90442

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 37 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGCTTCCCAACAAGATT+TGG 0.281962 2.4:+16837392 MS.gene90442:CDS
AATACTTACCTGCCATAGTT+TGG 0.380254 2.4:-16836551 None:intergenic
TTGTCCGCCGCCTTGAGAAC+CGG 0.384299 2.4:-16837513 None:intergenic
TGGAAAGCACAATCACTTGC+AGG 0.393596 2.4:+16837464 MS.gene90442:CDS
CACAGGTACTACTCCATGTA+TGG 0.401496 2.4:+16836466 None:intergenic
ACCGGTGCTGTAGAAGATTC+CGG 0.421664 2.4:-16837495 None:intergenic
ACCTCCTCTTGCAGTGTCTC+AGG 0.421775 2.4:-16837287 None:intergenic
TCACCCTCAGAGAGTTCATT+TGG 0.426316 2.4:-16837359 None:intergenic
GCCATCATTCCAAATCTTGT+TGG 0.445283 2.4:-16837401 None:intergenic
CCATCATTCCAAATCTTGTT+GGG 0.448149 2.4:-16837400 None:intergenic
CCCAACAAGATTTGGAATGA+TGG 0.449236 2.4:+16837400 MS.gene90442:CDS
GATGAGTGGTACATCACTCT+TGG 0.471040 2.4:-16837333 None:intergenic
ACTAGCAGAAGAAATAAAGA+AGG 0.473794 2.4:+16836501 MS.gene90442:CDS
TAGATGCTACTGGTGGTTTG+TGG 0.475106 2.4:+16837444 MS.gene90442:CDS
CGTTGAGGCCAAACTATGGC+AGG 0.513992 2.4:+16836543 MS.gene90442:CDS
TTCTACAGCACCGGTTCTCA+AGG 0.516974 2.4:+16837503 MS.gene90442:CDS
TTTCTCCACATGTCCATACA+TGG 0.519645 2.4:-16836479 None:intergenic
AAGGCGTTGAGGCCAAACTA+TGG 0.520975 2.4:+16836539 MS.gene90442:CDS
AAAGAAGGGTGCTGCTTCTG+TGG 0.521591 2.4:+16836516 MS.gene90442:CDS
ATGAGTGGTACATCACTCTT+GGG 0.523427 2.4:-16837332 None:intergenic
AAGGGTGCTGCTTCTGTGGA+AGG 0.526860 2.4:+16836520 MS.gene90442:CDS
GCCGGAATCTTCTACAGCAC+CGG 0.537447 2.4:+16837494 MS.gene90442:CDS
TCACTTGCAGGCAAGCCTGC+CGG 0.547692 2.4:+16837476 MS.gene90442:CDS
AATGAACTCTCTGAGGGTGA+TGG 0.567217 2.4:+16837362 MS.gene90442:CDS
TGCTTCTGTGGAAGGCGTTG+AGG 0.576351 2.4:+16836528 MS.gene90442:CDS
CACACCAAATGAACTCTCTG+AGG 0.589409 2.4:+16837355 MS.gene90442:CDS
CTACTCCATGTATGGACATG+TGG 0.614664 2.4:+16836474 MS.gene90442:CDS
ACACTGCAAGAGGAGGTGCT+TGG 0.621981 2.4:+16837293 MS.gene90442:CDS
GGTACCTGAGACACTGCAAG+AGG 0.622484 2.4:+16837283 MS.gene90442:intron
GTGCTGTAGAAGATTCCGGC+AGG 0.623342 2.4:-16837491 None:intergenic
ACCTGAGACACTGCAAGAGG+AGG 0.632122 2.4:+16837286 MS.gene90442:CDS
CTAGCAGAAGAAATAAAGAA+GGG 0.632639 2.4:+16836502 MS.gene90442:CDS
AGCACCGGTTCTCAAGGCGG+CGG 0.639495 2.4:+16837509 MS.gene90442:CDS
ACACCAAATGAACTCTCTGA+GGG 0.643435 2.4:+16837356 MS.gene90442:CDS
AGTTCATTTGGTGTGATGAG+TGG 0.662932 2.4:-16837347 None:intergenic
TACAGCACCGGTTCTCAAGG+CGG 0.675217 2.4:+16837506 MS.gene90442:CDS
AGTGGTACATCACTCTTGGG+TGG 0.680288 2.4:-16837329 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTTACAAAATCAAATAAGT+CGG - chr2.4:16837194-16837213 None:intergenic 20.0%
!! TCTTAAAGCTAAAAACTAAA+AGG - chr2.4:16837045-16837064 None:intergenic 20.0%
!!! TTATTTGATTTTGTAAGTGA+AGG + chr2.4:16837196-16837215 MS.gene90442:intron 20.0%
! AGCTAAAAACTAAAAGGATA+TGG - chr2.4:16837039-16837058 None:intergenic 25.0%
! ATAGATCACATAAATGTGTT+AGG + chr2.4:16836666-16836685 MS.gene90442:intron 25.0%
! CAAATTTAGCAAGACTATTA+TGG - chr2.4:16837161-16837180 None:intergenic 25.0%
! CTAAAAACTAAAAGGATATG+GGG - chr2.4:16837037-16837056 None:intergenic 25.0%
! GCTAAAAACTAAAAGGATAT+GGG - chr2.4:16837038-16837057 None:intergenic 25.0%
! TAAGTACTTGTGAAATTGTT+TGG - chr2.4:16836977-16836996 None:intergenic 25.0%
! TCTATATAATTGCGAAATGA+AGG + chr2.4:16837069-16837088 MS.gene90442:intron 25.0%
!! AGCTCTTCATAATAGTTTTT+CGG - chr2.4:16836922-16836941 None:intergenic 25.0%
AAGAACTATTCAGAGATCAA+AGG - chr2.4:16837106-16837125 None:intergenic 30.0%
ACTAGCAGAAGAAATAAAGA+AGG + chr2.4:16836501-16836520 MS.gene90442:CDS 30.0%
ATAGAGTTGTTTATCCAAAC+AGG - chr2.4:16836799-16836818 None:intergenic 30.0%
CTAGCAGAAGAAATAAAGAA+GGG + chr2.4:16836502-16836521 MS.gene90442:CDS 30.0%
TAGAGTTGTTTATCCAAACA+GGG - chr2.4:16836798-16836817 None:intergenic 30.0%
TGCAGAAGGAAATGTAAATT+TGG - chr2.4:16836584-16836603 None:intergenic 30.0%
!! TGGTTGGTTAAATGTTTTGT+TGG + chr2.4:16836747-16836766 MS.gene90442:intron 30.0%
AATACTTACCTGCCATAGTT+TGG - chr2.4:16836554-16836573 None:intergenic 35.0%
AGTGTAATTAGCGTTACACA+AGG - chr2.4:16836705-16836724 None:intergenic 35.0%
CAATATCAGTTCATGAGCTA+AGG + chr2.4:16836632-16836651 MS.gene90442:intron 35.0%
CCATCATTCCAAATCTTGTT+GGG - chr2.4:16837403-16837422 None:intergenic 35.0%
TATGCCATTCAACTGTTACA+TGG + chr2.4:16836727-16836746 MS.gene90442:intron 35.0%
! AAAGCTTTTCTAGATGCTAC+TGG + chr2.4:16837434-16837453 MS.gene90442:CDS 35.0%
ACACCAAATGAACTCTCTGA+GGG + chr2.4:16837356-16837375 MS.gene90442:CDS 40.0%
ATGAGTGGTACATCACTCTT+GGG - chr2.4:16837335-16837354 None:intergenic 40.0%
CCAACCATGTAACAGTTGAA+TGG - chr2.4:16836734-16836753 None:intergenic 40.0%
CCATTCAACTGTTACATGGT+TGG + chr2.4:16836731-16836750 MS.gene90442:intron 40.0%
GACTATATGACGTCATGCTA+TGG - chr2.4:16836609-16836628 None:intergenic 40.0%
GCCATCATTCCAAATCTTGT+TGG - chr2.4:16837404-16837423 None:intergenic 40.0%
TGTTTATCCAAACAGGGTCA+TGG - chr2.4:16836792-16836811 None:intergenic 40.0%
TTTCTCCACATGTCCATACA+TGG - chr2.4:16836482-16836501 None:intergenic 40.0%
! CCCAACAAGATTTGGAATGA+TGG + chr2.4:16837400-16837419 MS.gene90442:CDS 40.0%
! TTTGGCTTCCCAACAAGATT+TGG + chr2.4:16837392-16837411 MS.gene90442:CDS 40.0%
!! AGTTCATTTGGTGTGATGAG+TGG - chr2.4:16837350-16837369 None:intergenic 40.0%
AAAAGGATATGGGGCCTGTT+TGG - chr2.4:16837028-16837047 None:intergenic 45.0%
CACACCAAATGAACTCTCTG+AGG + chr2.4:16837355-16837374 MS.gene90442:CDS 45.0%
CAGGGTCATGGTAACAACAA+AGG - chr2.4:16836780-16836799 None:intergenic 45.0%
CTACTCCATGTATGGACATG+TGG + chr2.4:16836474-16836493 MS.gene90442:CDS 45.0%
GATGAGTGGTACATCACTCT+TGG - chr2.4:16837336-16837355 None:intergenic 45.0%
GTCATGCTATGGAATGCAGA+AGG - chr2.4:16836598-16836617 None:intergenic 45.0%
GTTGTTACCATGACCCTGTT+TGG + chr2.4:16836782-16836801 MS.gene90442:intron 45.0%
TAGATGCTACTGGTGGTTTG+TGG + chr2.4:16837444-16837463 MS.gene90442:CDS 45.0%
TCACCCTCAGAGAGTTCATT+TGG - chr2.4:16837362-16837381 None:intergenic 45.0%
TCGACTCAACCAATCCAAAC+AGG + chr2.4:16837011-16837030 MS.gene90442:intron 45.0%
! AATGAACTCTCTGAGGGTGA+TGG + chr2.4:16837362-16837381 MS.gene90442:CDS 45.0%
! GCTTTTCTAGATGCTACTGG+TGG + chr2.4:16837437-16837456 MS.gene90442:CDS 45.0%
! TGGAAAGCACAATCACTTGC+AGG + chr2.4:16837464-16837483 MS.gene90442:CDS 45.0%
!!! GAGGGTGATGGTTTTGTCTT+TGG + chr2.4:16837374-16837393 MS.gene90442:CDS 45.0%
ACTGTACTTAACCTGCGAGC+AGG + chr2.4:16837262-16837281 MS.gene90442:intron 50.0%
AGTGGTACATCACTCTTGGG+TGG - chr2.4:16837332-16837351 None:intergenic 50.0%
GATATGGGGCCTGTTTGGAT+TGG - chr2.4:16837023-16837042 None:intergenic 50.0%
!! AAAGAAGGGTGCTGCTTCTG+TGG + chr2.4:16836516-16836535 MS.gene90442:CDS 50.0%
!! AAGGCGTTGAGGCCAAACTA+TGG + chr2.4:16836539-16836558 MS.gene90442:CDS 50.0%
!! ACCGGTGCTGTAGAAGATTC+CGG - chr2.4:16837498-16837517 None:intergenic 50.0%
!! TTCTACAGCACCGGTTCTCA+AGG + chr2.4:16837503-16837522 MS.gene90442:CDS 50.0%
ACCTCCTCTTGCAGTGTCTC+AGG - chr2.4:16837290-16837309 None:intergenic 55.0%
ACCTGAGACACTGCAAGAGG+AGG + chr2.4:16837286-16837305 MS.gene90442:CDS 55.0%
CGTTGAGGCCAAACTATGGC+AGG + chr2.4:16836543-16836562 MS.gene90442:CDS 55.0%
GCCGGAATCTTCTACAGCAC+CGG + chr2.4:16837494-16837513 MS.gene90442:CDS 55.0%
GGTACCTGAGACACTGCAAG+AGG + chr2.4:16837283-16837302 MS.gene90442:intron 55.0%
GTGCTGTAGAAGATTCCGGC+AGG - chr2.4:16837494-16837513 None:intergenic 55.0%
!! AAGGGTGCTGCTTCTGTGGA+AGG + chr2.4:16836520-16836539 MS.gene90442:CDS 55.0%
!! ACACTGCAAGAGGAGGTGCT+TGG + chr2.4:16837293-16837312 MS.gene90442:CDS 55.0%
!! TACAGCACCGGTTCTCAAGG+CGG + chr2.4:16837506-16837525 MS.gene90442:CDS 55.0%
!! TGCTTCTGTGGAAGGCGTTG+AGG + chr2.4:16836528-16836547 MS.gene90442:CDS 55.0%
TCACTTGCAGGCAAGCCTGC+CGG + chr2.4:16837476-16837495 MS.gene90442:CDS 60.0%
TGTCTCAGGTACCTGCTCGC+AGG - chr2.4:16837276-16837295 None:intergenic 60.0%
TTGTCCGCCGCCTTGAGAAC+CGG - chr2.4:16837516-16837535 None:intergenic 60.0%
!! AGCACCGGTTCTCAAGGCGG+CGG + chr2.4:16837509-16837528 MS.gene90442:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 16836471 16837550 16836471 ID=MS.gene90442
chr2.4 mRNA 16836471 16837550 16836471 ID=MS.gene90442.t1;Parent=MS.gene90442
chr2.4 exon 16836471 16836564 16836471 ID=MS.gene90442.t1.exon1;Parent=MS.gene90442.t1
chr2.4 CDS 16836471 16836564 16836471 ID=cds.MS.gene90442.t1;Parent=MS.gene90442.t1
chr2.4 exon 16837284 16837550 16837284 ID=MS.gene90442.t1.exon2;Parent=MS.gene90442.t1
chr2.4 CDS 16837284 16837550 16837284 ID=cds.MS.gene90442.t1;Parent=MS.gene90442.t1
Gene Sequence

>MS.gene90442

GTACTACTCCATGTATGGACATGTGGAGAAACTAGCAGAAGAAATAAAGAAGGGTGCTGCTTCTGTGGAAGGCGTTGAGGCCAAACTATGGCAGGTAAGTATTTGTATTACCAAATTTACATTTCCTTCTGCATTCCATAGCATGACGTCATATAGTCGAGCAATATCAGTTCATGAGCTAAGGCTGATTCATCTATAGATCACATAAATGTGTTAGGAAAGTAAAGAATTCCTTGTGTAACGCTAATTACACTATTATGCCATTCAACTGTTACATGGTTGGTTAAATGTTTTGTTGGCTAAGTTCCTTTGTTGTTACCATGACCCTGTTTGGATAAACAACTCTATTAAGTTCTTATAGCATAAACGCTTATCGTATAAGTGCTTATGTAACTTTTTCTATAACTAAAGATAAAATAAAGTCAGACTGTTTTCATATAAGTTGTTTCCGAAAAACTATTATGAAGAGCTTATGAGTGTGTTAGTAGTTTCTATAAGCTCTACCAAACAATTTCACAAGTACTTATGCTGTAGATAAACTCGACTCAACCAATCCAAACAGGCCCCATATCCTTTTAGTTTTTAGCTTTAAGATAGTTCTATATAATTGCGAAATGAAGGATGATCTCTTGCCTTTGATCTCTGAATAGTTCTTGTGTTTTTATTTCTAGTATACTCTCTAAAAAACCATAATAGTCTTGCTAAATTTGAAAAAGAATGCCGACTTATTTGATTTTGTAAGTGAAGGTTATGAACATTTTCATAATTTAAAAATCAGTTCTTACTTGCTAACTGTACTTAACCTGCGAGCAGGTACCTGAGACACTGCAAGAGGAGGTGCTTGGTAAAATGAGTGCACCACCCAAGAGTGATGTACCACTCATCACACCAAATGAACTCTCTGAGGGTGATGGTTTTGTCTTTGGCTTCCCAACAAGATTTGGAATGATGGCTGCTCAATTCAAAGCTTTTCTAGATGCTACTGGTGGTTTGTGGAAAGCACAATCACTTGCAGGCAAGCCTGCCGGAATCTTCTACAGCACCGGTTCTCAAGGCGGCGGACAAGAGACTACAGCGTAA
Protein sequence

>MS.gene90442.t1

VLLHVWTCGETSRRNKEGCCFCGRRUGQTMAGTUDTARGGAWUNECTTQEUCTTHHTKUTLUGUWFCLWLPNKIWNDGCSIQSFSRCYWWFVESTITCRQACRNLLQHRFSRRRTRDYSV