AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78557

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
MS.gene78557.t1 AT5G22250 56.569 274 113 3 10 280 7 277 1.55e-106 311
MS.gene78557.t1 AT3G44260 55.762 269 110 5 15 280 17 279 4.65e-100 294
MS.gene78557.t1 AT2G32070 48.315 267 129 6 15 280 10 268 7.54e-81 245
MS.gene78557.t1 AT5G10960 46.182 275 139 6 7 280 1 267 2.38e-80 244
MS.gene78557.t1 AT1G80780 46.241 266 135 5 15 280 10 267 3.10e-76 233
MS.gene78557.t1 AT1G80780 46.241 266 135 5 15 280 10 267 3.10e-76 233
MS.gene78557.t1 AT1G80780 46.241 266 135 5 15 280 10 267 4.37e-76 233
MS.gene78557.t1 AT1G15920 45.324 278 142 6 9 282 8 279 2.79e-72 224
MS.gene78557.t1 AT1G15920 45.324 278 142 6 9 282 8 279 2.79e-72 224
MS.gene78557.t1 AT1G61470 38.618 246 126 8 19 259 4 229 4.86e-42 145
MS.gene78557.t1 AT1G06450 34.532 278 153 11 10 281 3 257 1.28e-38 139
MS.gene78557.t1 AT1G27820 36.220 254 135 9 13 259 2 235 8.86e-36 130
MS.gene78557.t1 AT1G27890 37.247 247 130 9 19 259 3 230 2.27e-34 126
MS.gene78557.t1 AT3G44240 35.193 233 130 8 31 260 3 217 9.25e-33 120

Find 58 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCATGGCGCTTATGATTT+TGG 0.117389 5.2:-32888256 MS.gene78557:CDS
AAATACGCTGGAGTAGTATT+TGG 0.224745 5.2:-32887959 MS.gene78557:CDS
TGAATATGGTGAATATTCTT+TGG 0.278766 5.2:-32888656 MS.gene78557:CDS
CGTGATGTTCTTCCTGAATA+TGG 0.278966 5.2:-32888670 MS.gene78557:CDS
CAAACTTCTCTGACAATGAT+TGG 0.307379 5.2:+32888727 None:intergenic
CTTGGACTCACTTTAATAGA+TGG 0.314324 5.2:-32888508 MS.gene78557:CDS
CAATCATTGTCAGAGAAGTT+TGG 0.315172 5.2:-32888726 MS.gene78557:CDS
AAGAAATCTGCCTGATAGTT+TGG 0.321613 5.2:-32888209 MS.gene78557:CDS
AACATTCTGGAAATGTTATT+CGG 0.326580 5.2:-32888175 MS.gene78557:CDS
AGGTGGCGATGGTCGAATTT+TGG 0.360542 5.2:+32888595 None:intergenic
GCTGAACTAATGTTGACTTC+TGG 0.360897 5.2:-32888313 MS.gene78557:CDS
AGTTTAAGATCATCCACATT+AGG 0.373743 5.2:+32888538 None:intergenic
AATCATTGTCAGAGAAGTTT+GGG 0.392755 5.2:-32888725 MS.gene78557:CDS
CGATTATCGGTGTCAAAATC+AGG 0.397384 5.2:+32888472 None:intergenic
ACACCGATAATCGCTACATT+TGG 0.399135 5.2:-32888462 MS.gene78557:CDS
CTCAATGTGGATCGGGTTGT+TGG 0.408633 5.2:-32888073 MS.gene78557:CDS
TTGCCAAATGTAGCGATTAT+CGG 0.410093 5.2:+32888459 None:intergenic
AAAGAATATTCACCATATTC+AGG 0.416250 5.2:+32888658 None:intergenic
TCGATAGACACTGAATTTCC+TGG 0.427087 5.2:-32888631 MS.gene78557:CDS
CATTGTATGGTGGTCTTGAT+CGG 0.438293 5.2:-32888108 MS.gene78557:CDS
AACTATCAGGCAGATTTCTT+CGG 0.444161 5.2:+32888212 None:intergenic
TGTCAACAAGCTGTCGGATC+CGG 0.457649 5.2:+32888036 None:intergenic
TATTCAAGAAATCAATGACT+TGG 0.469568 5.2:-32888285 MS.gene78557:CDS
CGCTACTGCAATGCATTGTA+TGG 0.477422 5.2:-32888121 MS.gene78557:CDS
ATGGCAGACGTTTCATAAGT+TGG 0.479969 5.2:-32888014 MS.gene78557:CDS
TGTAGTAATCAGAGGGTTGA+AGG 0.480186 5.2:+32888575 None:intergenic
GTTGACTTGCTTCGTCGACA+AGG 0.507118 5.2:-32888385 MS.gene78557:CDS
TTCTGGAAATGTTATTCGGA+AGG 0.512713 5.2:-32888171 MS.gene78557:CDS
ATTGTATGGTGGTCTTGATC+GGG 0.514058 5.2:-32888107 MS.gene78557:CDS
AAGTACACTCAATGTGGATC+GGG 0.524067 5.2:-32888080 MS.gene78557:CDS
TTGACTTGCTTCGTCGACAA+GGG 0.527074 5.2:-32888384 MS.gene78557:CDS
TTCAATCGTTGTGTCTCTCA+AGG 0.540052 5.2:-32888355 MS.gene78557:CDS
GTTGGAAGGTCTCATCAATC+CGG 0.540408 5.2:-32888055 MS.gene78557:CDS
ATGTGGATCGGGTTGTTGGA+AGG 0.540595 5.2:-32888069 MS.gene78557:CDS
ATTCAAGAAATCAATGACTT+GGG 0.542864 5.2:-32888284 MS.gene78557:CDS
GATCTTAAACTCATCCAACT+TGG 0.545194 5.2:-32888526 MS.gene78557:CDS
TTTGGTGTATGGATAACTCC+AGG 0.545850 5.2:+32888613 None:intergenic
CAAGTACACTCAATGTGGAT+CGG 0.548190 5.2:-32888081 MS.gene78557:CDS
CACGCTCAACGTTGAAGTCA+CGG 0.550608 5.2:+32888428 None:intergenic
CTATTAAAGTGAGTCCAAGT+TGG 0.558411 5.2:+32888512 None:intergenic
CAGAGGGTTGAAGGTGGCGA+TGG 0.559485 5.2:+32888584 None:intergenic
TCAACATTAGTTCAGCAAAA+CGG 0.564358 5.2:+32888320 None:intergenic
GAAGAACATCACGAATGAGA+TGG 0.565749 5.2:+32888680 None:intergenic
GATCCGACAGCTTGTTGACA+TGG 0.577163 5.2:-32888033 MS.gene78557:CDS
CACGTATCTGTAGTAATCAG+AGG 0.581646 5.2:+32888567 None:intergenic
CATACAATGCATTGCAGTAG+CGG 0.583860 5.2:+32888122 None:intergenic
TACTGCAATGCATTGTATGG+TGG 0.597106 5.2:-32888118 MS.gene78557:CDS
CAACGGAGTCCTTGTTGTGA+GGG 0.597538 5.2:+32888404 None:intergenic
TCAACGGAGTCCTTGTTGTG+AGG 0.600831 5.2:+32888403 None:intergenic
CTCACTTTAATAGATGGTTG+CGG 0.607202 5.2:-32888502 MS.gene78557:CDS
CTGCCATGTCAACAAGCTGT+CGG 0.613501 5.2:+32888030 None:intergenic
TTGTCGACGAAGCAAGTCAA+CGG 0.630986 5.2:+32888387 None:intergenic
ACGTATCTGTAGTAATCAGA+GGG 0.642679 5.2:+32888568 None:intergenic
ATACGTGTTGAAGCCTAATG+TGG 0.647752 5.2:-32888551 MS.gene78557:CDS
GGTTGCAAGTACACTCAATG+TGG 0.665808 5.2:-32888086 MS.gene78557:CDS
TGAGCGTGACCCTCACAACA+AGG 0.670125 5.2:-32888413 MS.gene78557:CDS
TATCGGTGTCAAAATCAGGA+AGG 0.683593 5.2:+32888476 None:intergenic
AGTAATCAGAGGGTTGAAGG+TGG 0.690515 5.2:+32888578 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATATTCACCATATTC+AGG + chr5.2:32888051-32888070 None:intergenic 25.0%
! AATGAATTTGAAAAATACGC+TGG - chr5.2:32888735-32888754 MS.gene78557:CDS 25.0%
! ATTCAAGAAATCAATGACTT+GGG - chr5.2:32888422-32888441 MS.gene78557:CDS 25.0%
! TATTCAAGAAATCAATGACT+TGG - chr5.2:32888421-32888440 MS.gene78557:CDS 25.0%
! TGAATATGGTGAATATTCTT+TGG - chr5.2:32888050-32888069 MS.gene78557:CDS 25.0%
!! AACATTCTGGAAATGTTATT+CGG - chr5.2:32888531-32888550 MS.gene78557:CDS 25.0%
AAAAACTCTTCCAAACTATC+AGG + chr5.2:32888510-32888529 None:intergenic 30.0%
AATCATTGTCAGAGAAGTTT+GGG - chr5.2:32887981-32888000 MS.gene78557:CDS 30.0%
TCAACATTAGTTCAGCAAAA+CGG + chr5.2:32888389-32888408 None:intergenic 30.0%
! AGTTTAAGATCATCCACATT+AGG + chr5.2:32888171-32888190 None:intergenic 30.0%
AAATACGCTGGAGTAGTATT+TGG - chr5.2:32888747-32888766 MS.gene78557:CDS 35.0%
AACTATCAGGCAGATTTCTT+CGG + chr5.2:32888497-32888516 None:intergenic 35.0%
AAGAAATCTGCCTGATAGTT+TGG - chr5.2:32888497-32888516 MS.gene78557:CDS 35.0%
ACGTATCTGTAGTAATCAGA+GGG + chr5.2:32888141-32888160 None:intergenic 35.0%
CAAACTTCTCTGACAATGAT+TGG + chr5.2:32887982-32888001 None:intergenic 35.0%
CAATCATTGTCAGAGAAGTT+TGG - chr5.2:32887980-32887999 MS.gene78557:CDS 35.0%
CTATTAAAGTGAGTCCAAGT+TGG + chr5.2:32888197-32888216 None:intergenic 35.0%
CTCACTTTAATAGATGGTTG+CGG - chr5.2:32888204-32888223 MS.gene78557:CDS 35.0%
CTTGGACTCACTTTAATAGA+TGG - chr5.2:32888198-32888217 MS.gene78557:CDS 35.0%
GATCTTAAACTCATCCAACT+TGG - chr5.2:32888180-32888199 MS.gene78557:CDS 35.0%
TTGCCAAATGTAGCGATTAT+CGG + chr5.2:32888250-32888269 None:intergenic 35.0%
! CGCTTATGATTTTGGATACT+TGG - chr5.2:32888458-32888477 MS.gene78557:CDS 35.0%
! GGAAGAGTTTTTGAACATTC+TGG - chr5.2:32888518-32888537 MS.gene78557:CDS 35.0%
! TTCTGGAAATGTTATTCGGA+AGG - chr5.2:32888535-32888554 MS.gene78557:CDS 35.0%
! TTTCATGGCGCTTATGATTT+TGG - chr5.2:32888450-32888469 MS.gene78557:CDS 35.0%
AAGTACACTCAATGTGGATC+GGG - chr5.2:32888626-32888645 MS.gene78557:CDS 40.0%
ACACCGATAATCGCTACATT+TGG - chr5.2:32888244-32888263 MS.gene78557:CDS 40.0%
ATACGTGTTGAAGCCTAATG+TGG - chr5.2:32888155-32888174 MS.gene78557:CDS 40.0%
ATGGCAGACGTTTCATAAGT+TGG - chr5.2:32888692-32888711 MS.gene78557:CDS 40.0%
CAAGTACACTCAATGTGGAT+CGG - chr5.2:32888625-32888644 MS.gene78557:CDS 40.0%
CACGTATCTGTAGTAATCAG+AGG + chr5.2:32888142-32888161 None:intergenic 40.0%
CATACAATGCATTGCAGTAG+CGG + chr5.2:32888587-32888606 None:intergenic 40.0%
CGTGATGTTCTTCCTGAATA+TGG - chr5.2:32888036-32888055 MS.gene78557:CDS 40.0%
GAAGAACATCACGAATGAGA+TGG + chr5.2:32888029-32888048 None:intergenic 40.0%
TACTGCAATGCATTGTATGG+TGG - chr5.2:32888588-32888607 MS.gene78557:CDS 40.0%
TCGATAGACACTGAATTTCC+TGG - chr5.2:32888075-32888094 MS.gene78557:CDS 40.0%
TGTAGTAATCAGAGGGTTGA+AGG + chr5.2:32888134-32888153 None:intergenic 40.0%
TTCAATCGTTGTGTCTCTCA+AGG - chr5.2:32888351-32888370 MS.gene78557:CDS 40.0%
! ATTGTATGGTGGTCTTGATC+GGG - chr5.2:32888599-32888618 MS.gene78557:CDS 40.0%
! CATTGTATGGTGGTCTTGAT+CGG - chr5.2:32888598-32888617 MS.gene78557:CDS 40.0%
! TTTGGTGTATGGATAACTCC+AGG + chr5.2:32888096-32888115 None:intergenic 40.0%
!! ATGACTTGGGTGACTTTTCA+TGG - chr5.2:32888435-32888454 MS.gene78557:CDS 40.0%
!! CGATTATCGGTGTCAAAATC+AGG + chr5.2:32888237-32888256 None:intergenic 40.0%
!! GATGGTCGAATTTTGGTGTA+TGG + chr5.2:32888107-32888126 None:intergenic 40.0%
!! GCTGAACTAATGTTGACTTC+TGG - chr5.2:32888393-32888412 MS.gene78557:CDS 40.0%
!! TATCGGTGTCAAAATCAGGA+AGG + chr5.2:32888233-32888252 None:intergenic 40.0%
AGTAATCAGAGGGTTGAAGG+TGG + chr5.2:32888131-32888150 None:intergenic 45.0%
CGCTACTGCAATGCATTGTA+TGG - chr5.2:32888585-32888604 MS.gene78557:CDS 45.0%
GGTTGCAAGTACACTCAATG+TGG - chr5.2:32888620-32888639 MS.gene78557:CDS 45.0%
GTTGGAAGGTCTCATCAATC+CGG - chr5.2:32888651-32888670 MS.gene78557:CDS 45.0%
TTGTCGACGAAGCAAGTCAA+CGG + chr5.2:32888322-32888341 None:intergenic 45.0%
!! TTGACTTGCTTCGTCGACAA+GGG - chr5.2:32888322-32888341 MS.gene78557:CDS 45.0%
CACGCTCAACGTTGAAGTCA+CGG + chr5.2:32888281-32888300 None:intergenic 50.0%
CTGCCATGTCAACAAGCTGT+CGG + chr5.2:32888679-32888698 None:intergenic 50.0%
TGTCAACAAGCTGTCGGATC+CGG + chr5.2:32888673-32888692 None:intergenic 50.0%
! AGGTGGCGATGGTCGAATTT+TGG + chr5.2:32888114-32888133 None:intergenic 50.0%
! ATGTGGATCGGGTTGTTGGA+AGG - chr5.2:32888637-32888656 MS.gene78557:CDS 50.0%
! CAACGGAGTCCTTGTTGTGA+GGG + chr5.2:32888305-32888324 None:intergenic 50.0%
! CTCAATGTGGATCGGGTTGT+TGG - chr5.2:32888633-32888652 MS.gene78557:CDS 50.0%
! TCAACGGAGTCCTTGTTGTG+AGG + chr5.2:32888306-32888325 None:intergenic 50.0%
!! GATCCGACAGCTTGTTGACA+TGG - chr5.2:32888673-32888692 MS.gene78557:CDS 50.0%
!! GTTGACTTGCTTCGTCGACA+AGG - chr5.2:32888321-32888340 MS.gene78557:CDS 50.0%
TGAGCGTGACCCTCACAACA+AGG - chr5.2:32888293-32888312 MS.gene78557:CDS 55.0%
CAGAGGGTTGAAGGTGGCGA+TGG + chr5.2:32888125-32888144 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 32887940 32888788 32887940 ID=MS.gene78557
chr5.2 mRNA 32887940 32888788 32887940 ID=MS.gene78557.t1;Parent=MS.gene78557
chr5.2 exon 32887940 32888788 32887940 ID=MS.gene78557.t1.exon1;Parent=MS.gene78557.t1
chr5.2 CDS 32887940 32888788 32887940 ID=cds.MS.gene78557.t1;Parent=MS.gene78557.t1
Gene Sequence

>MS.gene78557

ATGACAAAAACGTGCATGCTGAGTGAAGAGTTATCAAAACCAATCATTGTCAGAGAAGTTTGGGCACACAACTTAGAGTGTGAATTCCATCTCATTCGTGATGTTCTTCCTGAATATGGTGAATATTCTTTGGTCTCGATAGACACTGAATTTCCTGGAGTTATCCATACACCAAAATTCGACCATCGCCACCTTCAACCCTCTGATTACTACAGATACGTGTTGAAGCCTAATGTGGATGATCTTAAACTCATCCAACTTGGACTCACTTTAATAGATGGTTGCGGTCACCTTCCTGATTTTGACACCGATAATCGCTACATTTGGCAATTCAACTTCCGTGACTTCAACGTTGAGCGTGACCCTCACAACAAGGACTCCGTTGACTTGCTTCGTCGACAAGGGATTGACTTCAATCGTTGTGTCTCTCAAGGTGTGAATTCATTCCGTTTTGCTGAACTAATGTTGACTTCTGGACTTCTATTCAAGAAATCAATGACTTGGGTGACTTTTCATGGCGCTTATGATTTTGGATACTTGGTGAAGATATTGATCCGAAGAAATCTGCCTGATAGTTTGGAAGAGTTTTTGAACATTCTGGAAATGTTATTCGGAAGGAATGTCTATGATTTGAAACATATGATCCGCTACTGCAATGCATTGTATGGTGGTCTTGATCGGGTTGCAAGTACACTCAATGTGGATCGGGTTGTTGGAAGGTCTCATCAATCCGGATCCGACAGCTTGTTGACATGGCAGACGTTTCATAAGTTGGTGCAAACACATTTCAGTCGCAATGAATTTGAAAAATACGCTGGAGTAGTATTTGGATTAGAAGTTTCTCGATAA
Protein sequence

>MS.gene78557.t1

MTKTCMLSEELSKPIIVREVWAHNLECEFHLIRDVLPEYGEYSLVSIDTEFPGVIHTPKFDHRHLQPSDYYRYVLKPNVDDLKLIQLGLTLIDGCGHLPDFDTDNRYIWQFNFRDFNVERDPHNKDSVDLLRRQGIDFNRCVSQGVNSFRFAELMLTSGLLFKKSMTWVTFHGAYDFGYLVKILIRRNLPDSLEEFLNILEMLFGRNVYDLKHMIRYCNALYGGLDRVASTLNVDRVVGRSHQSGSDSLLTWQTFHKLVQTHFSRNEFEKYAGVVFGLEVSR