AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53923

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53923.t1 MTR_8g465910 92.946 241 14 1 1 241 1 238 3.40e-170 469
MS.gene53923.t1 MTR_2g090295 54.878 246 89 7 1 235 1 235 2.27e-91 269
MS.gene53923.t1 MTR_2g090330 60.000 110 40 1 36 145 25 130 3.86e-45 149
MS.gene53923.t1 MTR_2g090330 60.000 110 40 1 36 145 22 127 5.61e-45 148
MS.gene53923.t1 MTR_2g013550 41.589 214 99 7 36 233 19 222 4.50e-41 140
MS.gene53923.t1 MTR_2g090325 51.370 146 44 5 36 168 10 141 1.46e-40 138
MS.gene53923.t1 MTR_4g088875 38.462 221 111 8 24 233 11 217 3.06e-38 133
MS.gene53923.t1 MTR_4g088870 45.536 112 55 3 24 131 11 120 9.41e-31 113
MS.gene53923.t1 MTR_1g021895 48.421 95 40 2 41 135 27 112 1.65e-27 105
MS.gene53923.t1 MTR_5g019300 48.913 92 38 2 44 135 35 117 5.13e-27 104
MS.gene53923.t1 MTR_1g054260 38.525 122 71 3 22 139 62 183 1.78e-23 94.4
MS.gene53923.t1 MTR_4g029440 46.739 92 41 2 44 135 126 209 2.80e-23 97.4
MS.gene53923.t1 MTR_4g029440 46.739 92 41 2 44 135 132 215 2.81e-23 97.4
MS.gene53923.t1 MTR_1g054465 38.835 103 61 2 33 133 43 145 2.87e-23 93.6
MS.gene53923.t1 MTR_7g093390 34.722 144 70 5 5 135 118 250 1.52e-22 95.9
MS.gene53923.t1 MTR_1g054280 40.909 110 51 3 42 151 74 169 1.86e-22 92.8
MS.gene53923.t1 MTR_1g054210 44.565 92 43 3 44 135 122 205 4.67e-22 91.3
MS.gene53923.t1 MTR_2g061230 38.889 108 55 3 28 135 94 190 1.40e-19 84.7
MS.gene53923.t1 MTR_1g015390 38.667 75 34 2 34 107 353 416 1.88e-12 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53923.t1 AT4G03510 42.387 243 126 6 1 235 1 237 5.93e-57 182
MS.gene53923.t1 AT4G03510 42.387 243 126 6 1 235 1 237 5.93e-57 182
MS.gene53923.t1 AT4G03510 42.387 243 126 6 1 235 1 237 5.93e-57 182
MS.gene53923.t1 AT4G03510 42.387 243 126 6 1 235 1 237 5.93e-57 182
MS.gene53923.t1 AT4G27470 37.555 229 109 8 18 233 22 229 7.98e-39 135
MS.gene53923.t1 AT4G28270 37.688 199 85 6 39 232 14 178 1.32e-36 128
MS.gene53923.t1 AT1G19310 51.087 92 36 2 44 135 21 103 1.82e-27 105
MS.gene53923.t1 AT1G74990 37.903 124 64 3 29 152 2 112 2.64e-27 102
MS.gene53923.t1 AT2G23780 45.098 102 46 3 35 135 16 108 2.20e-25 100
MS.gene53923.t1 AT2G23780 45.098 102 46 3 35 135 16 108 2.20e-25 100
MS.gene53923.t1 AT2G23780 45.098 102 46 3 35 135 16 108 2.20e-25 100
MS.gene53923.t1 AT3G58030 42.593 108 47 3 31 135 121 216 8.19e-23 96.3
MS.gene53923.t1 AT3G58030 42.593 108 47 3 31 135 121 216 8.19e-23 96.3
MS.gene53923.t1 AT3G58030 42.593 108 47 3 31 135 121 216 8.19e-23 96.3
MS.gene53923.t1 AT3G58030 42.593 108 47 3 31 135 121 216 8.19e-23 96.3
MS.gene53923.t1 AT2G42030 40.404 99 45 3 44 141 139 224 4.68e-21 91.3
MS.gene53923.t1 AT2G44410 32.609 138 79 3 4 135 77 206 4.30e-19 85.9
MS.gene53923.t1 AT2G26350 42.169 83 31 4 25 107 312 377 2.10e-11 63.2
MS.gene53923.t1 AT2G26350 42.169 83 31 4 25 107 241 306 2.70e-11 62.8

Find 54 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTCATCCTTGGATTAT+TGG 0.208421 4.2:+60191906 None:intergenic
CCTTGAAAACTATAAGAATT+AGG 0.300025 4.2:+60191931 None:intergenic
TCCTCGCTAGTTCCATTATA+TGG 0.310263 4.2:-60192243 MS.gene53923:CDS
ATCTTTGGTGAAATGATATA+TGG 0.327321 4.2:-60191994 MS.gene53923:CDS
GTTGTAGCATTAAATGATCT+TGG 0.349454 4.2:+60192144 None:intergenic
GTTTGGCCACGGCCATATAA+TGG 0.354971 4.2:+60192231 None:intergenic
GATAACACATACGGAATCTT+TGG 0.359665 4.2:-60192009 MS.gene53923:CDS
CTTCAGACACAGTCATGGTT+TGG 0.381200 4.2:+60192214 None:intergenic
ATGATATATGGAAGGATGTT+TGG 0.416293 4.2:-60191982 MS.gene53923:CDS
TGTTGATAACTTTGATAAGT+AGG 0.417086 4.2:+60192111 None:intergenic
TTTGTGGTCATCTTTACTGC+TGG 0.419101 4.2:-60192365 MS.gene53923:CDS
ATTAAATGTCTTCTCATCCT+TGG 0.439812 4.2:+60191898 None:intergenic
GCTGGCCTTGCATTTACAAA+TGG 0.444667 4.2:-60192347 MS.gene53923:CDS
GAAGCAGAAGCCACAATGTC+CGG 0.455529 4.2:-60192289 MS.gene53923:CDS
ATCGTCCATGTACTGATCTA+AGG 0.463858 4.2:+60192539 None:intergenic
CAAAGATGGCTTATCTTCAA+AGG 0.467141 4.2:+60192497 None:intergenic
CTTTGACTGTAACATCTGCC+TGG 0.478100 4.2:-60192415 MS.gene53923:CDS
CTTGGACCCGTAGGTCTTCG+AGG 0.488512 4.2:+60192162 None:intergenic
GTGAGTTCTGATTTGCATAC+CGG 0.493695 4.2:+60192270 None:intergenic
AGATGCATTTCTATCAGAAT+CGG 0.494969 4.2:+60192443 None:intergenic
AAGGCAAGGCTCAGCAAGTA+GGG 0.503764 4.2:-60192194 MS.gene53923:CDS
TGTCGTGCCTCGAAGACCTA+CGG 0.507710 4.2:-60192169 MS.gene53923:CDS
GTCGTGCCTCGAAGACCTAC+GGG 0.518622 4.2:-60192168 MS.gene53923:CDS
CCGGGTCTTGCACACAATCC+AGG 0.522470 4.2:+60192397 None:intergenic
GATGTTTAGTACAAGTGGTT+CGG 0.525093 4.2:-60192037 MS.gene53923:CDS
GAAGGCAAGGCTCAGCAAGT+AGG 0.536195 4.2:-60192195 MS.gene53923:CDS
TCACCGATGTTTAGTACAAG+TGG 0.543488 4.2:-60192042 MS.gene53923:CDS
ATCGGCAATCACATCGGTGG+AGG 0.550014 4.2:+60192461 None:intergenic
CATGACTGTGTCTGAAGGCA+AGG 0.550095 4.2:-60192208 MS.gene53923:CDS
ATCAACATCCTCATCATCCT+CGG 0.557432 4.2:-60192095 MS.gene53923:CDS
ATCGGTGAAGGGTAACTGCT+CGG 0.568341 4.2:+60192057 None:intergenic
TTCAAGGGACCAATAATCCA+AGG 0.572138 4.2:-60191915 MS.gene53923:CDS
CTTGCCTTCAGACACAGTCA+TGG 0.574821 4.2:+60192209 None:intergenic
AAAGGTATCAATTTGAGAGA+CGG 0.577335 4.2:+60192515 None:intergenic
CTAGTTCCATTATATGGCCG+TGG 0.589093 4.2:-60192237 MS.gene53923:CDS
CTTGTACTAAACATCGGTGA+AGG 0.589508 4.2:+60192045 None:intergenic
CCTGGATTGTGTGCAAGACC+CGG 0.596839 4.2:-60192397 MS.gene53923:CDS
TCAAGCCATTTGTAAATGCA+AGG 0.597318 4.2:+60192342 None:intergenic
GATTTGCATACCGGACATTG+TGG 0.600937 4.2:+60192279 None:intergenic
GGAATTGAGTTGAATTGCCG+AGG 0.606224 4.2:+60192078 None:intergenic
TTAAATGATCTTGGACCCGT+AGG 0.606770 4.2:+60192153 None:intergenic
TTGTACTAAACATCGGTGAA+GGG 0.617159 4.2:+60192046 None:intergenic
TCTGATAGAAATGCATCTAG+TGG 0.620682 4.2:-60192438 MS.gene53923:CDS
ATCAGAATCGGCAATCACAT+CGG 0.630444 4.2:+60192455 None:intergenic
ACACAGTCATGGTTTGGCCA+CGG 0.630922 4.2:+60192220 None:intergenic
TTGAATTGCCGAGGATGATG+AGG 0.635828 4.2:+60192087 None:intergenic
AAATGGCTTGACATACAAAG+TGG 0.643704 4.2:-60192330 MS.gene53923:CDS
TTGGTGAAATGATATATGGA+AGG 0.648778 4.2:-60191990 MS.gene53923:CDS
TCGGCACTAGATAACACATA+CGG 0.649004 4.2:-60192018 MS.gene53923:CDS
AGAATCGGCAATCACATCGG+TGG 0.651949 4.2:+60192458 None:intergenic
CAAACCATGACTGTGTCTGA+AGG 0.652258 4.2:-60192213 MS.gene53923:CDS
GCCATATAATGGAACTAGCG+AGG 0.658937 4.2:+60192242 None:intergenic
AATGGCCTTAGATCAGTACA+TGG 0.660626 4.2:-60192544 MS.gene53923:CDS
GAACCACTTGTACTAAACAT+CGG 0.669442 4.2:+60192039 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACTGAATATAATCTATACA+AGG + chr4.2:60192530-60192549 None:intergenic 20.0%
!!! ATGTATAAATGTTTTCTATC+TGG + chr4.2:60192334-60192353 None:intergenic 20.0%
!!! CTAATTCTTATAGTTTTCAA+GGG - chr4.2:60192357-60192376 MS.gene53923:CDS 20.0%
! ATCTTTGGTGAAATGATATA+TGG - chr4.2:60192293-60192312 MS.gene53923:CDS 25.0%
! CCTTGAAAACTATAAGAATT+AGG + chr4.2:60192359-60192378 None:intergenic 25.0%
!! CCTAATTCTTATAGTTTTCA+AGG - chr4.2:60192356-60192375 MS.gene53923:CDS 25.0%
!!! TGTTGATAACTTTGATAAGT+AGG + chr4.2:60192179-60192198 None:intergenic 25.0%
AGATGCATTTCTATCAGAAT+CGG + chr4.2:60191847-60191866 None:intergenic 30.0%
ATGATATATGGAAGGATGTT+TGG - chr4.2:60192305-60192324 MS.gene53923:CDS 30.0%
ATTAAATGTCTTCTCATCCT+TGG + chr4.2:60192392-60192411 None:intergenic 30.0%
GTTGTAGCATTAAATGATCT+TGG + chr4.2:60192146-60192165 None:intergenic 30.0%
TTGGTGAAATGATATATGGA+AGG - chr4.2:60192297-60192316 MS.gene53923:CDS 30.0%
! ATAAGCCATCTTTGAAAAAC+TGG - chr4.2:60191799-60191818 MS.gene53923:intron 30.0%
!! AAAGGTATCAATTTGAGAGA+CGG + chr4.2:60191775-60191794 None:intergenic 30.0%
!! GTTTTCCAGTTTTTCAAAGA+TGG + chr4.2:60191807-60191826 None:intergenic 30.0%
AAATGGCTTGACATACAAAG+TGG - chr4.2:60191957-60191976 MS.gene53923:CDS 35.0%
ACAAAACTAAGCTGCAAAAG+AGG + chr4.2:60192451-60192470 None:intergenic 35.0%
CAAAGATGGCTTATCTTCAA+AGG + chr4.2:60191793-60191812 None:intergenic 35.0%
GAACCACTTGTACTAAACAT+CGG + chr4.2:60192251-60192270 None:intergenic 35.0%
GATAACACATACGGAATCTT+TGG - chr4.2:60192278-60192297 MS.gene53923:CDS 35.0%
GATGTTTAGTACAAGTGGTT+CGG - chr4.2:60192250-60192269 MS.gene53923:CDS 35.0%
TCAAGCCATTTGTAAATGCA+AGG + chr4.2:60191948-60191967 None:intergenic 35.0%
TCTGATAGAAATGCATCTAG+TGG - chr4.2:60191849-60191868 MS.gene53923:intron 35.0%
TCTTCTCATCCTTGGATTAT+TGG + chr4.2:60192384-60192403 None:intergenic 35.0%
TTGTACTAAACATCGGTGAA+GGG + chr4.2:60192244-60192263 None:intergenic 35.0%
ATCAACATCCTCATCATCCT+CGG - chr4.2:60192192-60192211 MS.gene53923:CDS 40.0%
ATCAGAATCGGCAATCACAT+CGG + chr4.2:60191835-60191854 None:intergenic 40.0%
CTTGTACTAAACATCGGTGA+AGG + chr4.2:60192245-60192264 None:intergenic 40.0%
TCACCGATGTTTAGTACAAG+TGG - chr4.2:60192245-60192264 MS.gene53923:CDS 40.0%
TCCTCGCTAGTTCCATTATA+TGG - chr4.2:60192044-60192063 MS.gene53923:CDS 40.0%
TCGGCACTAGATAACACATA+CGG - chr4.2:60192269-60192288 MS.gene53923:CDS 40.0%
TGACCACAAAAAGTGACTAC+CGG + chr4.2:60191912-60191931 None:intergenic 40.0%
TTAAATGATCTTGGACCCGT+AGG + chr4.2:60192137-60192156 None:intergenic 40.0%
TTCAAGGGACCAATAATCCA+AGG - chr4.2:60192372-60192391 MS.gene53923:CDS 40.0%
TTTGTGGTCATCTTTACTGC+TGG - chr4.2:60191922-60191941 MS.gene53923:CDS 40.0%
! ATCGTCCATGTACTGATCTA+AGG + chr4.2:60191751-60191770 None:intergenic 40.0%
! GTGAGTTCTGATTTGCATAC+CGG + chr4.2:60192020-60192039 None:intergenic 40.0%
CAAACCATGACTGTGTCTGA+AGG - chr4.2:60192074-60192093 MS.gene53923:CDS 45.0%
CTAGTTCCATTATATGGCCG+TGG - chr4.2:60192050-60192069 MS.gene53923:CDS 45.0%
CTTCAGACACAGTCATGGTT+TGG + chr4.2:60192076-60192095 None:intergenic 45.0%
CTTTGACTGTAACATCTGCC+TGG - chr4.2:60191872-60191891 MS.gene53923:CDS 45.0%
GACCACAAAAAGTGACTACC+GGG + chr4.2:60191911-60191930 None:intergenic 45.0%
GATTTGCATACCGGACATTG+TGG + chr4.2:60192011-60192030 None:intergenic 45.0%
TTGAATTGCCGAGGATGATG+AGG + chr4.2:60192203-60192222 None:intergenic 45.0%
! GCCATATAATGGAACTAGCG+AGG + chr4.2:60192048-60192067 None:intergenic 45.0%
! TGGCTTCTGCTTCTCGTTTT+CGG + chr4.2:60191991-60192010 None:intergenic 45.0%
!! GCTGGCCTTGCATTTACAAA+TGG - chr4.2:60191940-60191959 MS.gene53923:CDS 45.0%
!! GGAATTGAGTTGAATTGCCG+AGG + chr4.2:60192212-60192231 None:intergenic 45.0%
AAGGCAAGGCTCAGCAAGTA+GGG - chr4.2:60192093-60192112 MS.gene53923:CDS 50.0%
AGAATCGGCAATCACATCGG+TGG + chr4.2:60191832-60191851 None:intergenic 50.0%
ATCGGTGAAGGGTAACTGCT+CGG + chr4.2:60192233-60192252 None:intergenic 50.0%
CATGACTGTGTCTGAAGGCA+AGG - chr4.2:60192079-60192098 MS.gene53923:CDS 50.0%
CTTGCCTTCAGACACAGTCA+TGG + chr4.2:60192081-60192100 None:intergenic 50.0%
GAAGCAGAAGCCACAATGTC+CGG - chr4.2:60191998-60192017 MS.gene53923:CDS 50.0%
GTTTGGCCACGGCCATATAA+TGG + chr4.2:60192059-60192078 None:intergenic 50.0%
! ACACAGTCATGGTTTGGCCA+CGG + chr4.2:60192070-60192089 None:intergenic 50.0%
!!! GACCCGGTAGTCACTTTTTG+TGG - chr4.2:60191906-60191925 MS.gene53923:CDS 50.0%
ATCGGCAATCACATCGGTGG+AGG + chr4.2:60191829-60191848 None:intergenic 55.0%
CCTGGATTGTGTGCAAGACC+CGG - chr4.2:60191890-60191909 MS.gene53923:CDS 55.0%
GAAGGCAAGGCTCAGCAAGT+AGG - chr4.2:60192092-60192111 MS.gene53923:CDS 55.0%
TGTCGTGCCTCGAAGACCTA+CGG - chr4.2:60192118-60192137 MS.gene53923:CDS 55.0%
CCGGGTCTTGCACACAATCC+AGG + chr4.2:60191893-60191912 None:intergenic 60.0%
CTTGGACCCGTAGGTCTTCG+AGG + chr4.2:60192128-60192147 None:intergenic 60.0%
GTCGTGCCTCGAAGACCTAC+GGG - chr4.2:60192119-60192138 MS.gene53923:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 60191744 60192565 60191744 ID=MS.gene53923
chr4.2 mRNA 60191744 60192565 60191744 ID=MS.gene53923.t1;Parent=MS.gene53923
chr4.2 exon 60191869 60192565 60191869 ID=MS.gene53923.t1.exon1;Parent=MS.gene53923.t1
chr4.2 CDS 60191869 60192565 60191869 ID=cds.MS.gene53923.t1;Parent=MS.gene53923.t1
chr4.2 exon 60191744 60191772 60191744 ID=MS.gene53923.t1.exon2;Parent=MS.gene53923.t1
chr4.2 CDS 60191744 60191772 60191744 ID=cds.MS.gene53923.t1;Parent=MS.gene53923.t1
Gene Sequence

>MS.gene53923

ATGGCCTTAGATCAGTACATGGACGATACCGTCTCTCAAATTGATACCTTTGAAGATAAGCCATCTTTGAAAAACTGGAAAACCTCCACCGATGTGATTGCCGATTCTGATAGAAATGCATCTAGTGGCTTTGACTGTAACATCTGCCTGGATTGTGTGCAAGACCCGGTAGTCACTTTTTGTGGTCATCTTTACTGCTGGCCTTGCATTTACAAATGGCTTGACATACAAAGTGGCATCTCTTCCGAAAACGAGAAGCAGAAGCCACAATGTCCGGTATGCAAATCAGAACTCACTCAATCCTCGCTAGTTCCATTATATGGCCGTGGCCAAACCATGACTGTGTCTGAAGGCAAGGCTCAGCAAGTAGGGATTGTCGTGCCTCGAAGACCTACGGGTCCAAGATCATTTAATGCTACAACTGTTTCACAACCTACTTATCAAAGTTATCAACATCCTCATCATCCTCGGCAATTCAACTCAATTCCGAGCAGTTACCCTTCACCGATGTTTAGTACAAGTGGTTCGGCACTAGATAACACATACGGAATCTTTGGTGAAATGATATATGGAAGGATGTTTGGTAACCAGATAGAAAACATTTATACATATCCTAATTCTTATAGTTTTCAAGGGACCAATAATCCAAGGATGAGAAGACATTTAATGCAAGTTGATAAATCACTCAACAGAATCAGTTTTTTCCTCTTTTGCAGCTTAGTTTTGTGTGTTCTCTTATTTTGAATAATTGTACTTCATTTTCATCAGTAACAGTATATGTATCCTTGTATAGATTATATTCAGTATTCTGATTTAGCTTGA
Protein sequence

>MS.gene53923.t1

MALDQYMDDTVSQIDTFEDKPSLKNWKTSTDVIADSDRNASSGFDCNICLDCVQDPVVTFCGHLYCWPCIYKWLDIQSGISSENEKQKPQCPVCKSELTQSSLVPLYGRGQTMTVSEGKAQQVGIVVPRRPTGPRSFNATTVSQPTYQSYQHPHHPRQFNSIPSSYPSPMFSTSGSALDNTYGIFGEMIYGRMFGNQIENIYTYPNSYSFQGTNNPRMRRHLMQVDKSLNRINYIQYSDLA