AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41066

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41066.t1 MTR_1g057400 92.344 209 16 0 1 209 1 209 1.04e-146 406
MS.gene41066.t1 MTR_7g106000 60.952 210 75 4 2 209 22 226 1.79e-87 257
MS.gene41066.t1 MTR_7g105970 57.789 199 80 2 10 208 31 225 2.72e-79 236
MS.gene41066.t1 MTR_7g106010 57.073 205 84 3 7 209 25 227 1.24e-78 235
MS.gene41066.t1 MTR_7g106030 57.214 201 82 2 11 209 33 231 2.01e-75 227
MS.gene41066.t1 MTR_1g057290 50.000 206 102 1 5 209 12 217 1.84e-52 168
MS.gene41066.t1 MTR_1g057270 41.327 196 108 4 16 209 52 242 6.58e-43 144
MS.gene41066.t1 MTR_4g119428 39.109 202 112 5 11 206 41 237 2.44e-39 135
MS.gene41066.t1 MTR_7g105870 40.314 191 109 2 17 206 39 225 6.43e-32 115
MS.gene41066.t1 MTR_1g057300 58.929 112 41 3 1 111 1 108 3.42e-28 103
MS.gene41066.t1 MTR_2g011350 29.775 178 115 5 32 209 35 202 3.14e-20 84.7
MS.gene41066.t1 MTR_6g071410 29.730 185 115 8 15 190 2 180 2.35e-17 77.4
MS.gene41066.t1 MTR_6g070890 29.730 185 115 8 15 190 2 180 2.35e-17 77.4
MS.gene41066.t1 MTR_6g471090 29.101 189 113 9 8 190 5 178 2.47e-17 77.4
MS.gene41066.t1 MTR_6g070900 27.568 185 119 8 15 190 2 180 4.95e-15 71.2
MS.gene41066.t1 MTR_6g071400 27.568 185 119 8 15 190 2 180 4.95e-15 71.2
MS.gene41066.t1 MTR_6g471080 29.012 162 94 6 10 168 5 148 7.66e-13 65.1
MS.gene41066.t1 MTR_2g087000 25.478 157 110 3 16 172 45 194 2.59e-11 61.2
MS.gene41066.t1 MTR_1g105570 23.383 201 138 7 9 209 46 230 7.71e-11 60.1
MS.gene41066.t1 MTR_3g092790 26.027 146 102 3 44 189 49 188 8.60e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41066.t1 AT2G35980 38.424 203 117 3 10 209 30 227 2.39e-45 150
MS.gene41066.t1 AT2G35460 36.364 198 120 2 14 209 45 238 1.10e-42 144
MS.gene41066.t1 AT5G06320 39.378 193 112 3 17 209 44 231 1.98e-39 135
MS.gene41066.t1 AT3G11650 35.500 200 122 4 12 209 45 239 7.57e-36 126
MS.gene41066.t1 AT5G53730 29.213 178 116 5 34 207 40 211 7.72e-18 78.6
MS.gene41066.t1 AT1G61760 26.829 164 114 3 20 183 43 200 1.25e-15 73.2
MS.gene41066.t1 AT3G11660 26.512 215 144 6 1 208 1 208 6.18e-14 68.2
MS.gene41066.t1 AT1G32270 29.801 151 97 3 42 190 1 144 8.41e-14 69.3
MS.gene41066.t1 AT1G32270 29.801 151 97 3 42 190 1 144 1.53e-13 68.9
MS.gene41066.t1 AT4G05220 22.222 189 138 4 21 209 46 225 2.97e-13 66.6
MS.gene41066.t1 AT5G06330 26.744 172 119 5 40 208 39 206 1.22e-11 62.0

Find 42 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGTGTGATGTAAATTTCTA+AGG 0.209404 1.3:+42141606 MS.gene41066:CDS
AACATCTTCTGCCGCGGTTG+TGG 0.309180 1.3:-42141014 None:intergenic
GTTTCCAAATTATGCCAAAA+AGG 0.322625 1.3:-42141044 None:intergenic
ACATCTTCTGCCGCGGTTGT+GGG 0.356163 1.3:-42141013 None:intergenic
TTTAGACTTGGTGATTATAT+TGG 0.359682 1.3:+42141495 MS.gene41066:CDS
TTAATATTACCCTTAGTAGA+TGG 0.365970 1.3:-42141519 None:intergenic
GTCGTCGCTATAGTTGAATT+TGG 0.406674 1.3:-42141169 None:intergenic
TTCATTGACACTGAACTTGA+AGG 0.427389 1.3:-42141136 None:intergenic
GACTAGGTTTGCTTCAACAA+AGG 0.437058 1.3:+42141299 MS.gene41066:CDS
TTATATTGGTCCATCTACTA+AGG 0.442373 1.3:+42141509 MS.gene41066:CDS
TTAGTTCCATTAGCAACAAA+AGG 0.456789 1.3:-42141558 None:intergenic
CATCTTCTGCCGCGGTTGTG+GGG 0.481542 1.3:-42141012 None:intergenic
CCAGAGAAAACACCACTCAT+AGG 0.486502 1.3:-42141369 None:intergenic
TCGAGCTCTTAGTGTATTGT+CGG 0.489123 1.3:-42141344 None:intergenic
ACACTGAACTTGAAGGTTCG+AGG 0.490630 1.3:-42141129 None:intergenic
TTTGAACGTGATAAGAAAGA+TGG 0.497010 1.3:+42141432 MS.gene41066:CDS
TGAAATTATACTTTGAGATG+AGG 0.504513 1.3:+42141472 MS.gene41066:CDS
CAACCTCGTACTCAACTTCA+CGG 0.507914 1.3:+42141209 MS.gene41066:CDS
AGTTGAGTACGAGGTTGTAA+TGG 0.520447 1.3:-42141203 None:intergenic
TGAGTACGAGGTTGTAATGG+AGG 0.524265 1.3:-42141200 None:intergenic
CGTGTGATGTAAATTTCTAA+GGG 0.525667 1.3:+42141607 MS.gene41066:CDS
TTTCTCTGGGCAACATGTTG+TGG 0.527422 1.3:+42141383 MS.gene41066:CDS
TGAACTTGAAGGTTCGAGGT+TGG 0.527619 1.3:-42141125 None:intergenic
ATGCGTCTTACGAAGGGACT+AGG 0.531595 1.3:+42141283 MS.gene41066:CDS
GAAATTTACATCACACGTGG+TGG 0.578702 1.3:-42141601 None:intergenic
CTTCAACAAAGGTTATAACA+TGG 0.579854 1.3:+42141310 MS.gene41066:CDS
GAAGGACATGCGTCTTACGA+AGG 0.581641 1.3:+42141276 MS.gene41066:CDS
AAGGACATGCGTCTTACGAA+GGG 0.581992 1.3:+42141277 MS.gene41066:CDS
GAAGCAAAACCCCACAACCG+CGG 0.582202 1.3:+42141003 MS.gene41066:CDS
TATATTGGTCCATCTACTAA+GGG 0.590602 1.3:+42141510 MS.gene41066:CDS
CTAAGGGTAATATTAAGTGT+AGG 0.590927 1.3:+42141526 MS.gene41066:CDS
GAGTACGAGGTTGTAATGGA+GGG 0.597384 1.3:-42141199 None:intergenic
GAGGTTGTAATGGAGGGTGT+TGG 0.602071 1.3:-42141193 None:intergenic
GTAGCAATCATCGTTCTCGT+TGG 0.605038 1.3:+42141072 MS.gene41066:CDS
ATCTACTATGATGTAATCGA+AGG 0.609711 1.3:+42141258 MS.gene41066:CDS
TTTGAGATGAGGTTTAGACT+TGG 0.616430 1.3:+42141483 MS.gene41066:CDS
AAATTTACATCACACGTGGT+GGG 0.616840 1.3:-42141600 None:intergenic
AGCAACAACATCTTCTGCCG+CGG 0.641568 1.3:-42141020 None:intergenic
AAGAGCTCGAATCCTATGAG+TGG 0.682861 1.3:+42141357 MS.gene41066:CDS
GGGCCGTGAAGTTGAGTACG+AGG 0.683761 1.3:-42141212 None:intergenic
CGAGAACGATGATTGCTACG+AGG 0.746688 1.3:-42141068 None:intergenic
TTAGAAATTTACATCACACG+TGG 0.754009 1.3:-42141604 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTCTAATAATCCTTATTTTT+TGG + chr1.3:42141094-42141113 MS.gene41066:CDS 20.0%
! TTAATATTACCCTTAGTAGA+TGG - chr1.3:42141522-42141541 None:intergenic 25.0%
!!! TAGATGTTGAGTTTTTTGTT+TGG - chr1.3:42141243-42141262 None:intergenic 25.0%
!!! TGAAATTATACTTTGAGATG+AGG + chr1.3:42141472-42141491 MS.gene41066:CDS 25.0%
!!! TGAGTTTTTTGTTTGGATTA+CGG - chr1.3:42141236-42141255 None:intergenic 25.0%
!!! TTTAGACTTGGTGATTATAT+TGG + chr1.3:42141495-42141514 MS.gene41066:CDS 25.0%
ATCTACTATGATGTAATCGA+AGG + chr1.3:42141258-42141277 MS.gene41066:CDS 30.0%
CTAAGGGTAATATTAAGTGT+AGG + chr1.3:42141526-42141545 MS.gene41066:CDS 30.0%
CTTCAACAAAGGTTATAACA+TGG + chr1.3:42141310-42141329 MS.gene41066:CDS 30.0%
GTTTCCAAATTATGCCAAAA+AGG - chr1.3:42141047-42141066 None:intergenic 30.0%
TATATTGGTCCATCTACTAA+GGG + chr1.3:42141510-42141529 MS.gene41066:CDS 30.0%
TTAGAAATTTACATCACACG+TGG - chr1.3:42141607-42141626 None:intergenic 30.0%
TTAGTTCCATTAGCAACAAA+AGG - chr1.3:42141561-42141580 None:intergenic 30.0%
TTATATTGGTCCATCTACTA+AGG + chr1.3:42141509-42141528 MS.gene41066:CDS 30.0%
TTTGAACGTGATAAGAAAGA+TGG + chr1.3:42141432-42141451 MS.gene41066:CDS 30.0%
! ATTGTTCCTTTTGTTGCTAA+TGG + chr1.3:42141552-42141571 MS.gene41066:CDS 30.0%
! TTTTGTTGCTAATGGAACTA+AGG + chr1.3:42141560-42141579 MS.gene41066:CDS 30.0%
!!! GAGTTTTTTGTTTGGATTAC+GGG - chr1.3:42141235-42141254 None:intergenic 30.0%
AAATTTACATCACACGTGGT+GGG - chr1.3:42141603-42141622 None:intergenic 35.0%
GGACAATGAGCCAAAAAATA+AGG - chr1.3:42141107-42141126 None:intergenic 35.0%
TTCATTGACACTGAACTTGA+AGG - chr1.3:42141139-42141158 None:intergenic 35.0%
! TGTGGTTTTTGATCATGATC+AGG + chr1.3:42141401-42141420 MS.gene41066:CDS 35.0%
! TTTGAGATGAGGTTTAGACT+TGG + chr1.3:42141483-42141502 MS.gene41066:CDS 35.0%
AGTTGAGTACGAGGTTGTAA+TGG - chr1.3:42141206-42141225 None:intergenic 40.0%
GAAATTTACATCACACGTGG+TGG - chr1.3:42141604-42141623 None:intergenic 40.0%
GTCGTCGCTATAGTTGAATT+TGG - chr1.3:42141172-42141191 None:intergenic 40.0%
TCGAGCTCTTAGTGTATTGT+CGG - chr1.3:42141347-42141366 None:intergenic 40.0%
! AGATGTTGTTGCTGCCTTTT+TGG + chr1.3:42141030-42141049 MS.gene41066:CDS 40.0%
! CTATGAGTGGTGTTTTCTCT+GGG + chr1.3:42141370-42141389 MS.gene41066:CDS 40.0%
! GACTAGGTTTGCTTCAACAA+AGG + chr1.3:42141299-42141318 MS.gene41066:CDS 40.0%
!! GCTGCCTTTTTGGCATAATT+TGG + chr1.3:42141040-42141059 MS.gene41066:CDS 40.0%
AAGAGCTCGAATCCTATGAG+TGG + chr1.3:42141357-42141376 MS.gene41066:CDS 45.0%
AAGGACATGCGTCTTACGAA+GGG + chr1.3:42141277-42141296 MS.gene41066:CDS 45.0%
ACACTGAACTTGAAGGTTCG+AGG - chr1.3:42141132-42141151 None:intergenic 45.0%
CAACCTCGTACTCAACTTCA+CGG + chr1.3:42141209-42141228 MS.gene41066:CDS 45.0%
CCAGAGAAAACACCACTCAT+AGG - chr1.3:42141372-42141391 None:intergenic 45.0%
GTAGCAATCATCGTTCTCGT+TGG + chr1.3:42141072-42141091 MS.gene41066:CDS 45.0%
TGAACTTGAAGGTTCGAGGT+TGG - chr1.3:42141128-42141147 None:intergenic 45.0%
TGAGTACGAGGTTGTAATGG+AGG - chr1.3:42141203-42141222 None:intergenic 45.0%
TTTCTCTGGGCAACATGTTG+TGG + chr1.3:42141383-42141402 MS.gene41066:CDS 45.0%
! CCTATGAGTGGTGTTTTCTC+TGG + chr1.3:42141369-42141388 MS.gene41066:CDS 45.0%
! GAGTACGAGGTTGTAATGGA+GGG - chr1.3:42141202-42141221 None:intergenic 45.0%
AGCAACAACATCTTCTGCCG+CGG - chr1.3:42141023-42141042 None:intergenic 50.0%
ATGCGTCTTACGAAGGGACT+AGG + chr1.3:42141283-42141302 MS.gene41066:CDS 50.0%
CGAGAACGATGATTGCTACG+AGG - chr1.3:42141071-42141090 None:intergenic 50.0%
GAAGGACATGCGTCTTACGA+AGG + chr1.3:42141276-42141295 MS.gene41066:CDS 50.0%
! GAGGTTGTAATGGAGGGTGT+TGG - chr1.3:42141196-42141215 None:intergenic 50.0%
AACATCTTCTGCCGCGGTTG+TGG - chr1.3:42141017-42141036 None:intergenic 55.0%
ACATCTTCTGCCGCGGTTGT+GGG - chr1.3:42141016-42141035 None:intergenic 55.0%
GAAGCAAAACCCCACAACCG+CGG + chr1.3:42141003-42141022 MS.gene41066:CDS 55.0%
CATCTTCTGCCGCGGTTGTG+GGG - chr1.3:42141015-42141034 None:intergenic 60.0%
GGGCCGTGAAGTTGAGTACG+AGG - chr1.3:42141215-42141234 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 42140997 42141626 42140997 ID=MS.gene41066
chr1.3 mRNA 42140997 42141626 42140997 ID=MS.gene41066.t1;Parent=MS.gene41066
chr1.3 exon 42140997 42141626 42140997 ID=MS.gene41066.t1.exon1;Parent=MS.gene41066.t1
chr1.3 CDS 42140997 42141626 42140997 ID=cds.MS.gene41066.t1;Parent=MS.gene41066.t1
Gene Sequence

>MS.gene41066

ATGGCAGAAGCAAAACCCCACAACCGCGGCAGAAGATGTTGTTGCTGCCTTTTTGGCATAATTTGGAAACTCCTCGTAGCAATCATCGTTCTCGTTGGTCTAATAATCCTTATTTTTTGGCTCATTGTCCAACCTCGAACCTTCAAGTTCAGTGTCAATGAAGCAAAACTCACCAAATTCAACTATAGCGACGACACCAACACCCTCCATTACAACCTCGTACTCAACTTCACGGCCCGTAATCCAAACAAAAAACTCAACATCTACTATGATGTAATCGAAGGACATGCGTCTTACGAAGGGACTAGGTTTGCTTCAACAAAGGTTATAACATGGTTAAATTCATTCCGACAATACACTAAGAGCTCGAATCCTATGAGTGGTGTTTTCTCTGGGCAACATGTTGTGGTTTTTGATCATGATCAGGTTTCTGACTTTGAACGTGATAAGAAAGATGGAGTTTTTCATATTGATATGAAATTATACTTTGAGATGAGGTTTAGACTTGGTGATTATATTGGTCCATCTACTAAGGGTAATATTAAGTGTAGGCTTATTGTTCCTTTTGTTGCTAATGGAACTAAGGTCATGAAAGCATTTGAACCCACCACGTGTGATGTAAATTTCTAA
Protein sequence

>MS.gene41066.t1

MAEAKPHNRGRRCCCCLFGIIWKLLVAIIVLVGLIILIFWLIVQPRTFKFSVNEAKLTKFNYSDDTNTLHYNLVLNFTARNPNKKLNIYYDVIEGHASYEGTRFASTKVITWLNSFRQYTKSSNPMSGVFSGQHVVVFDHDQVSDFERDKKDGVFHIDMKLYFEMRFRLGDYIGPSTKGNIKCRLIVPFVANGTKVMKAFEPTTCDVNF