AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066041

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066041.t1 MTR_1g075780 86.713 143 19 0 12 154 3 145 6.12e-92 263
MS.gene066041.t1 MTR_4g063510 35.057 174 73 5 17 154 13 182 6.15e-21 84.3
MS.gene066041.t1 MTR_1g075840 43.651 126 55 7 36 154 1 117 5.09e-17 72.4
MS.gene066041.t1 MTR_1g041455 29.747 158 91 4 14 154 13 167 6.69e-15 68.2
MS.gene066041.t1 MTR_5g056450 34.000 150 80 6 1 142 1 139 1.04e-13 65.1
MS.gene066041.t1 MTR_1g076050 49.254 67 33 1 89 154 20 86 1.56e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGACACATCAGTGAATT+TGG 0.236191 1.2:-58446920 MS.gene066041:CDS
TTATCCATCATGTTGATATA+TGG 0.253396 1.2:+58446976 None:intergenic
GTCCCTTGTTGGTGCATTGA+TGG 0.334927 1.2:+58447036 None:intergenic
CCATACCACCAGTCCCTTGT+TGG 0.378244 1.2:+58447025 None:intergenic
ATGGGAAAATTGGGTGGTAA+AGG 0.416030 1.2:+58447162 None:intergenic
TAAAGGGTTGGCCATTGATT+CGG 0.428827 1.2:+58447179 None:intergenic
TGGGAAAATTGGGTGGTAAA+GGG 0.468596 1.2:+58447163 None:intergenic
CAATCCTCAGGCCGAATCAA+TGG 0.469990 1.2:-58447190 MS.gene066041:CDS
CATTGATTCGGCCTGAGGAT+TGG 0.472364 1.2:+58447191 None:intergenic
AAGCCACCTTGAGTCTCATA+TGG 0.484456 1.2:-58447250 MS.gene066041:CDS
CCAACAAGGGACTGGTGGTA+TGG 0.486031 1.2:-58447025 MS.gene066041:CDS
CAAAATTATTGATATTGCTA+CGG 0.495293 1.2:+58447319 None:intergenic
ATTCGGCCTGAGGATTGGTA+TGG 0.511741 1.2:+58447196 None:intergenic
TTGGCCATTGATTCGGCCTG+AGG 0.541375 1.2:+58447186 None:intergenic
CCTTGTTGGTGCATTGATGG+TGG 0.554951 1.2:+58447039 None:intergenic
CTTGAGCCATATGAGACTCA+AGG 0.558137 1.2:+58447244 None:intergenic
ATTAAACCATACCAATCCTC+AGG 0.560036 1.2:-58447202 MS.gene066041:CDS
ACAACATTAGATTGTTGTTG+TGG 0.560718 1.2:+58447084 None:intergenic
ATGGAAGTCTCTCCGATCGA+TGG 0.567201 1.2:-58447006 MS.gene066041:CDS
TAAGCCATATATCAACATGA+TGG 0.571056 1.2:-58446980 MS.gene066041:CDS
TCAATGCACCAACAAGGGAC+TGG 0.598187 1.2:-58447033 MS.gene066041:CDS
TTTGGCATGGGAAAATTGGG+TGG 0.600647 1.2:+58447156 None:intergenic
CCACCATCAATGCACCAACA+AGG 0.600697 1.2:-58447039 MS.gene066041:CDS
ACAATCTAATGTTGTTGATG+TGG 0.605335 1.2:-58447076 MS.gene066041:CDS
AAAATTGGGTGGTAAAGGGT+TGG 0.611916 1.2:+58447167 None:intergenic
CACCATCAATGCACCAACAA+GGG 0.620275 1.2:-58447038 MS.gene066041:CDS
TATGGCTTAGTTCCATCGAT+CGG 0.625287 1.2:+58446994 None:intergenic
ATGCACCAACAAGGGACTGG+TGG 0.640658 1.2:-58447030 MS.gene066041:CDS
GAGCCATATGAGACTCAAGG+TGG 0.728487 1.2:+58447247 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATCAATAATTTTGTATG+TGG - chr1.2:58446942-58446961 MS.gene066041:CDS 15.0%
!! CAAAATTATTGATATTGCTA+CGG + chr1.2:58446938-58446957 None:intergenic 20.0%
!!! TTGTTTTCATGTAATGATTT+TGG + chr1.2:58447119-58447138 None:intergenic 20.0%
! TTATCCATCATGTTGATATA+TGG + chr1.2:58447281-58447300 None:intergenic 25.0%
!!! AAATAACTTGCTTTTAACGA+AGG + chr1.2:58447144-58447163 None:intergenic 25.0%
ACAATCTAATGTTGTTGATG+TGG - chr1.2:58447178-58447197 MS.gene066041:CDS 30.0%
TAAGCCATATATCAACATGA+TGG - chr1.2:58447274-58447293 MS.gene066041:CDS 30.0%
! AATGAAGACATTTTTCTCGA+TGG + chr1.2:58447306-58447325 None:intergenic 30.0%
! ACAACATTAGATTGTTGTTG+TGG + chr1.2:58447173-58447192 None:intergenic 30.0%
! ATGAAGACATTTTTCTCGAT+GGG + chr1.2:58447305-58447324 None:intergenic 30.0%
!! TCATGTAATGATTTTGGCAT+GGG + chr1.2:58447113-58447132 None:intergenic 30.0%
!! TTCATGTAATGATTTTGGCA+TGG + chr1.2:58447114-58447133 None:intergenic 30.0%
ATTAAACCATACCAATCCTC+AGG - chr1.2:58447052-58447071 MS.gene066041:CDS 35.0%
CAATGACACATCAGTGAATT+TGG - chr1.2:58447334-58447353 MS.gene066041:CDS 35.0%
!! GATTTTGGCATGGGAAAATT+GGG + chr1.2:58447104-58447123 None:intergenic 35.0%
!! TGATTTTGGCATGGGAAAAT+TGG + chr1.2:58447105-58447124 None:intergenic 35.0%
AAAATTGGGTGGTAAAGGGT+TGG + chr1.2:58447090-58447109 None:intergenic 40.0%
ATGGGAAAATTGGGTGGTAA+AGG + chr1.2:58447095-58447114 None:intergenic 40.0%
TATGGCTTAGTTCCATCGAT+CGG + chr1.2:58447263-58447282 None:intergenic 40.0%
TGGGAAAATTGGGTGGTAAA+GGG + chr1.2:58447094-58447113 None:intergenic 40.0%
!! TAAAGGGTTGGCCATTGATT+CGG + chr1.2:58447078-58447097 None:intergenic 40.0%
AAGCCACCTTGAGTCTCATA+TGG - chr1.2:58447004-58447023 MS.gene066041:CDS 45.0%
CACCATCAATGCACCAACAA+GGG - chr1.2:58447216-58447235 MS.gene066041:CDS 45.0%
CTTGAGCCATATGAGACTCA+AGG + chr1.2:58447013-58447032 None:intergenic 45.0%
TTTGGCATGGGAAAATTGGG+TGG + chr1.2:58447101-58447120 None:intergenic 45.0%
ATGGAAGTCTCTCCGATCGA+TGG - chr1.2:58447248-58447267 MS.gene066041:CDS 50.0%
CAATCCTCAGGCCGAATCAA+TGG - chr1.2:58447064-58447083 MS.gene066041:CDS 50.0%
CCACCATCAATGCACCAACA+AGG - chr1.2:58447215-58447234 MS.gene066041:CDS 50.0%
GAGCCATATGAGACTCAAGG+TGG + chr1.2:58447010-58447029 None:intergenic 50.0%
GTCCCTTGTTGGTGCATTGA+TGG + chr1.2:58447221-58447240 None:intergenic 50.0%
TCAATGCACCAACAAGGGAC+TGG - chr1.2:58447221-58447240 MS.gene066041:CDS 50.0%
! ATTCGGCCTGAGGATTGGTA+TGG + chr1.2:58447061-58447080 None:intergenic 50.0%
! CCTTGTTGGTGCATTGATGG+TGG + chr1.2:58447218-58447237 None:intergenic 50.0%
!! CATTGATTCGGCCTGAGGAT+TGG + chr1.2:58447066-58447085 None:intergenic 50.0%
ATGCACCAACAAGGGACTGG+TGG - chr1.2:58447224-58447243 MS.gene066041:CDS 55.0%
CCATACCACCAGTCCCTTGT+TGG + chr1.2:58447232-58447251 None:intergenic 55.0%
! CCAACAAGGGACTGGTGGTA+TGG - chr1.2:58447229-58447248 MS.gene066041:CDS 55.0%
!! TTGGCCATTGATTCGGCCTG+AGG + chr1.2:58447071-58447090 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 58446906 58447370 58446906 ID=MS.gene066041
chr1.2 mRNA 58446906 58447370 58446906 ID=MS.gene066041.t1;Parent=MS.gene066041
chr1.2 exon 58446906 58447370 58446906 ID=MS.gene066041.t1.exon1;Parent=MS.gene066041.t1
chr1.2 CDS 58446906 58447370 58446906 ID=cds.MS.gene066041.t1;Parent=MS.gene066041.t1
Gene Sequence

>MS.gene066041

ATGGGTGACGATTTCACTCAAGAGAACAACCGTAGCAATATCAATAATTTTGTATGTGGATTGTGCAATCATGATTGTACAAACTTCGAATCACTCATAAGCCACCTTGAGTCTCATATGGCTCAAGAAAATCTTGCTATTGCAAGATTAAACCATACCAATCCTCAGGCCGAATCAATGGCCAACCCTTTACCACCCAATTTTCCCATGCCAAAATCATTACATGAAAACAAAACCTTCGTTAAAAGCAAGTTATTTCAGCAACCACAACAACAATCTAATGTTGTTGATGTGGCTTCATTTTCAGCTCCACCATCAATGCACCAACAAGGGACTGGTGGTATGGAAGTCTCTCCGATCGATGGAACTAAGCCATATATCAACATGATGGATAAACCCATCGAGAAAAATGTCTTCATTAACATCATCAATGACACATCAGTGAATTTGGAGTTAAAGCTCTAG
Protein sequence

>MS.gene066041.t1

MGDDFTQENNRSNINNFVCGLCNHDCTNFESLISHLESHMAQENLAIARLNHTNPQAESMANPLPPNFPMPKSLHENKTFVKSKLFQQPQQQSNVVDVASFSAPPSMHQQGTGGMEVSPIDGTKPYINMMDKPIEKNVFINIINDTSVNLELKL