AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060098

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060098.t1 MTR_6g059530 92.118 203 14 1 1 201 1 203 1.85e-123 347
MS.gene060098.t1 MTR_6g059410 89.655 203 18 2 1 201 1 202 1.42e-118 335
MS.gene060098.t1 MTR_6g059650 55.670 194 76 5 17 201 19 211 6.98e-65 199
MS.gene060098.t1 MTR_6g065460 55.340 206 77 7 1 193 1 204 2.43e-57 180
MS.gene060098.t1 MTR_6g065460 50.980 204 65 7 1 193 1 180 4.89e-48 155
MS.gene060098.t1 MTR_6g059760 48.804 209 90 11 1 196 1 205 8.88e-48 155
MS.gene060098.t1 MTR_6g044780 44.186 215 101 10 1 199 1 212 2.31e-41 140
MS.gene060098.t1 MTR_6g059680 47.525 202 87 9 16 201 18 216 2.90e-40 137
MS.gene060098.t1 MTR_3g463590 43.750 192 95 8 20 201 23 211 7.23e-40 135
MS.gene060098.t1 MTR_6g045097 43.256 215 103 10 1 199 1 212 3.52e-39 134
MS.gene060098.t1 MTR_6g044810 43.256 215 103 10 1 199 1 212 1.19e-38 132
MS.gene060098.t1 MTR_6g045403 42.523 214 104 9 1 199 1 210 4.34e-37 129
MS.gene060098.t1 MTR_6g059730 45.116 215 101 10 1 201 1 212 1.29e-36 127
MS.gene060098.t1 MTR_6g009650 41.827 208 102 9 1 194 1 203 3.52e-34 120
MS.gene060098.t1 MTR_6g066190 40.670 209 105 9 1 195 1 204 1.32e-33 119
MS.gene060098.t1 MTR_6g017225 40.187 214 106 11 6 201 7 216 1.11e-32 120
MS.gene060098.t1 MTR_6g045433 37.662 231 102 11 1 201 1 219 2.03e-32 116
MS.gene060098.t1 MTR_6g059810 39.614 207 99 9 4 190 8 208 1.16e-30 112
MS.gene060098.t1 MTR_6g009563 39.713 209 106 9 1 194 1 204 3.35e-30 110
MS.gene060098.t1 MTR_6g066210 39.151 212 114 8 1 199 1 210 4.55e-29 107
MS.gene060098.t1 MTR_1g035770 40.291 206 101 11 6 192 7 209 1.98e-26 101
MS.gene060098.t1 MTR_6g059755 49.074 108 49 4 98 199 18 125 4.58e-25 95.1
MS.gene060098.t1 MTR_6g078070 33.171 205 123 8 1 193 1 203 6.13e-20 84.0
MS.gene060098.t1 MTR_6g078100 33.654 208 120 9 1 193 1 205 6.38e-18 78.6
MS.gene060098.t1 MTR_1g057110 36.715 207 98 11 1 194 1 187 2.49e-17 76.6
MS.gene060098.t1 MTR_6g065570 55.000 60 24 1 16 72 14 73 1.11e-14 67.0
MS.gene060098.t1 MTR_0100s0150 27.861 201 127 7 5 190 1 198 3.93e-13 65.5
MS.gene060098.t1 MTR_3g106620 30.387 181 109 9 24 194 27 200 1.58e-12 64.3
MS.gene060098.t1 MTR_0302s0030 27.723 202 127 7 5 190 1 199 3.13e-12 63.2
MS.gene060098.t1 MTR_0084s0030 29.208 202 124 8 5 190 1 199 3.64e-12 63.2
MS.gene060098.t1 MTR_0211s0080 28.283 198 127 7 5 190 1 195 6.92e-12 62.0
MS.gene060098.t1 MTR_6g078290 30.732 205 112 10 11 190 10 209 1.29e-11 61.6
MS.gene060098.t1 MTR_2g073010 27.919 197 134 6 1 193 6 198 2.33e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060098.t1 AT1G73260 34.426 183 106 7 26 197 30 209 7.31e-21 86.7
MS.gene060098.t1 AT1G17860 31.492 181 107 7 21 193 24 195 1.03e-15 72.4
MS.gene060098.t1 AT1G73325 31.220 205 126 9 4 197 7 207 3.41e-12 63.5

Find 49 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATAGTTGAAGACATAAA+TGG 0.300956 6.2:+69247993 MS.gene060098:CDS
CAACTGAAAATAACCCCTTT+TGG 0.303854 6.2:+69248462 MS.gene060098:CDS
GGTAAGTAATGTTGGCTTCA+TGG 0.309270 6.2:-69247922 None:intergenic
ACTGTTATGGTAAATCTAAC+TGG 0.326794 6.2:-69248161 None:intergenic
ACTATTTCAGCAAAAGCTAA+TGG 0.332530 6.2:-69247978 None:intergenic
AAATCTTGTAGTACAGTAAC+TGG 0.343098 6.2:-69248116 None:intergenic
CCTGGCGCTTGTAGTGATAT+TGG 0.366872 6.2:+69248404 MS.gene060098:CDS
AAAATTGAGACAATTGGTTC+AGG 0.373759 6.2:+69248341 MS.gene060098:CDS
AATGGAAACCCCGTATTTCC+TGG 0.375075 6.2:+69248011 MS.gene060098:CDS
CCTACATCCTGGGTAGGTAT+TGG 0.376991 6.2:+69248287 MS.gene060098:CDS
AAATTTAAAATTGAGACAAT+TGG 0.414016 6.2:+69248335 MS.gene060098:CDS
GATAATATTGATGCATTTCA+AGG 0.419889 6.2:+69248311 MS.gene060098:CDS
TCAACGAATACAACCCAAAA+GGG 0.432534 6.2:-69248476 None:intergenic
AGAGAAAAGGTAAGTAATGT+TGG 0.440708 6.2:-69247930 None:intergenic
ATCTCTAAAGGAGGAGGTGG+TGG 0.449806 6.2:+69248059 MS.gene060098:CDS
GAAAGTAGGTAAAGGAAAAG+AGG 0.466771 6.2:-69247956 None:intergenic
CCAATACCTACCCAGGATGT+AGG 0.475428 6.2:-69248287 None:intergenic
ATCATGAGCTAGCACCCATT+TGG 0.477611 6.2:-69248258 None:intergenic
TGGAGATTTGATTCAAACTA+CGG 0.490153 6.2:-69248519 None:intergenic
ATGATGATTTCCCTACATCC+TGG 0.490169 6.2:+69248276 MS.gene060098:CDS
AGATAAGAATGGATGGCGTC+TGG 0.490689 6.2:+69248436 MS.gene060098:CDS
GGATTGAAGCTTGGTAAGAC+AGG 0.499062 6.2:+69248080 MS.gene060098:CDS
CCATTGTTCAGTGCTCCACC+TGG 0.501984 6.2:+69248386 MS.gene060098:CDS
ATCAACGAATACAACCCAAA+AGG 0.508809 6.2:-69248477 None:intergenic
GGAAAAGAGGAGGAGAGAAA+AGG 0.510811 6.2:-69247943 None:intergenic
GGAGGTGGTGGATTGAAGCT+TGG 0.515566 6.2:+69248071 MS.gene060098:CDS
CCTCCTCCTTTAGAGATAAG+TGG 0.523049 6.2:-69248053 None:intergenic
GTGTGCTGAATCTGCCAAAT+GGG 0.523391 6.2:+69248244 MS.gene060098:CDS
ATTGCACCACTTATCTCTAA+AGG 0.523973 6.2:+69248047 MS.gene060098:CDS
GGAAGGTATAAAGATAAGAA+TGG 0.524313 6.2:+69248425 MS.gene060098:CDS
AGTGTGCTGAATCTGCCAAA+TGG 0.527935 6.2:+69248243 MS.gene060098:CDS
TTGGCAGATTCAGCACACTT+TGG 0.530934 6.2:-69248239 None:intergenic
CAATACCTACCCAGGATGTA+GGG 0.542912 6.2:-69248286 None:intergenic
AGCAAAAGCTAATGGAAAGT+AGG 0.543819 6.2:-69247970 None:intergenic
AGCTAATGGAAAGTAGGTAA+AGG 0.547073 6.2:-69247964 None:intergenic
CCAATATCACTACAAGCGCC+AGG 0.552948 6.2:-69248404 None:intergenic
TGATGATTTCCCTACATCCT+GGG 0.571431 6.2:+69248277 MS.gene060098:CDS
CTTATCTCTAAAGGAGGAGG+TGG 0.573275 6.2:+69248056 MS.gene060098:CDS
AGTAGGTAAAGGAAAAGAGG+AGG 0.584445 6.2:-69247953 None:intergenic
GGTATAAAGATAAGAATGGA+TGG 0.584646 6.2:+69248429 MS.gene060098:CDS
CCACTTATCTCTAAAGGAGG+AGG 0.587891 6.2:+69248053 MS.gene060098:CDS
ATTATCACCAATACCTACCC+AGG 0.608189 6.2:-69248294 None:intergenic
GCGCTTGTAGTGATATTGGA+AGG 0.629705 6.2:+69248408 MS.gene060098:CDS
GATTTCCCTACATCCTGGGT+AGG 0.630370 6.2:+69248281 MS.gene060098:CDS
CCAGGTGGAGCACTGAACAA+TGG 0.632227 6.2:-69248386 None:intergenic
GCACCACTTATCTCTAAAGG+AGG 0.639013 6.2:+69248050 MS.gene060098:CDS
CAACGAATACAACCCAAAAG+GGG 0.675837 6.2:-69248475 None:intergenic
ATATCACTACAAGCGCCAGG+TGG 0.717315 6.2:-69248401 None:intergenic
TTTACCATAACAGTAAAACG+TGG 0.801296 6.2:+69248170 MS.gene060098:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTAAAATTGAGACAAT+TGG + chr6.2:69248335-69248354 MS.gene060098:CDS 15.0%
! GAAATAGTTGAAGACATAAA+TGG + chr6.2:69247993-69248012 MS.gene060098:CDS 25.0%
! GATAATATTGATGCATTTCA+AGG + chr6.2:69248311-69248330 MS.gene060098:CDS 25.0%
AAATCTTGTAGTACAGTAAC+TGG - chr6.2:69248119-69248138 None:intergenic 30.0%
ACTATTTCAGCAAAAGCTAA+TGG - chr6.2:69247981-69248000 None:intergenic 30.0%
ACTGTTATGGTAAATCTAAC+TGG - chr6.2:69248164-69248183 None:intergenic 30.0%
AGAGAAAAGGTAAGTAATGT+TGG - chr6.2:69247933-69247952 None:intergenic 30.0%
GGTATAAAGATAAGAATGGA+TGG + chr6.2:69248429-69248448 MS.gene060098:CDS 30.0%
TTTACCATAACAGTAAAACG+TGG + chr6.2:69248170-69248189 MS.gene060098:CDS 30.0%
! AAAATTGAGACAATTGGTTC+AGG + chr6.2:69248341-69248360 MS.gene060098:CDS 30.0%
! AACTGAAAATAACCCCTTTT+GGG + chr6.2:69248463-69248482 MS.gene060098:CDS 30.0%
! GCAATATAGTATTTTCTACC+AGG - chr6.2:69248032-69248051 None:intergenic 30.0%
! GGAAGGTATAAAGATAAGAA+TGG + chr6.2:69248425-69248444 MS.gene060098:CDS 30.0%
! GTATTTTCTACCAGGAAATA+CGG - chr6.2:69248024-69248043 None:intergenic 30.0%
! TATTTTCTACCAGGAAATAC+GGG - chr6.2:69248023-69248042 None:intergenic 30.0%
! TGTACTACAAGATTTTTCTG+AGG + chr6.2:69248124-69248143 MS.gene060098:CDS 30.0%
!! AAAAGGGGTTATTTTCAGTT+GGG - chr6.2:69248463-69248482 None:intergenic 30.0%
AGCAAAAGCTAATGGAAAGT+AGG - chr6.2:69247973-69247992 None:intergenic 35.0%
AGCTAATGGAAAGTAGGTAA+AGG - chr6.2:69247967-69247986 None:intergenic 35.0%
ATCAACGAATACAACCCAAA+AGG - chr6.2:69248480-69248499 None:intergenic 35.0%
ATTGCACCACTTATCTCTAA+AGG + chr6.2:69248047-69248066 MS.gene060098:CDS 35.0%
GAAAGTAGGTAAAGGAAAAG+AGG - chr6.2:69247959-69247978 None:intergenic 35.0%
TCAACGAATACAACCCAAAA+GGG - chr6.2:69248479-69248498 None:intergenic 35.0%
! ATTTTCTACCAGGAAATACG+GGG - chr6.2:69248022-69248041 None:intergenic 35.0%
! CAACTGAAAATAACCCCTTT+TGG + chr6.2:69248462-69248481 MS.gene060098:CDS 35.0%
!! CAAAAGGGGTTATTTTCAGT+TGG - chr6.2:69248464-69248483 None:intergenic 35.0%
!!! GATTTTTCTGAGGTTGTTAG+AGG + chr6.2:69248134-69248153 MS.gene060098:CDS 35.0%
AGTAGGTAAAGGAAAAGAGG+AGG - chr6.2:69247956-69247975 None:intergenic 40.0%
ATGATGATTTCCCTACATCC+TGG + chr6.2:69248276-69248295 MS.gene060098:CDS 40.0%
ATTATCACCAATACCTACCC+AGG - chr6.2:69248297-69248316 None:intergenic 40.0%
CAACGAATACAACCCAAAAG+GGG - chr6.2:69248478-69248497 None:intergenic 40.0%
TGATGATTTCCCTACATCCT+GGG + chr6.2:69248277-69248296 MS.gene060098:CDS 40.0%
! GACACCACGTTTTACTGTTA+TGG - chr6.2:69248177-69248196 None:intergenic 40.0%
!!! TACGGCTTTTTCAGATTCAG+TGG - chr6.2:69248504-69248523 None:intergenic 40.0%
AATGGAAACCCCGTATTTCC+TGG + chr6.2:69248011-69248030 MS.gene060098:CDS 45.0%
AGATAAGAATGGATGGCGTC+TGG + chr6.2:69248436-69248455 MS.gene060098:CDS 45.0%
AGTGTGCTGAATCTGCCAAA+TGG + chr6.2:69248243-69248262 MS.gene060098:CDS 45.0%
ATCATGAGCTAGCACCCATT+TGG - chr6.2:69248261-69248280 None:intergenic 45.0%
CAATACCTACCCAGGATGTA+GGG - chr6.2:69248289-69248308 None:intergenic 45.0%
GCGCTTGTAGTGATATTGGA+AGG + chr6.2:69248408-69248427 MS.gene060098:CDS 45.0%
GGAAAAGAGGAGGAGAGAAA+AGG - chr6.2:69247946-69247965 None:intergenic 45.0%
GGATTGAAGCTTGGTAAGAC+AGG + chr6.2:69248080-69248099 MS.gene060098:CDS 45.0%
GTGTGCTGAATCTGCCAAAT+GGG + chr6.2:69248244-69248263 MS.gene060098:CDS 45.0%
TTGGCAGATTCAGCACACTT+TGG - chr6.2:69248242-69248261 None:intergenic 45.0%
! CCACTTATCTCTAAAGGAGG+AGG + chr6.2:69248053-69248072 MS.gene060098:CDS 45.0%
! CCTCCTCCTTTAGAGATAAG+TGG - chr6.2:69248056-69248075 None:intergenic 45.0%
! CTTATCTCTAAAGGAGGAGG+TGG + chr6.2:69248056-69248075 MS.gene060098:CDS 45.0%
! GCACCACTTATCTCTAAAGG+AGG + chr6.2:69248050-69248069 MS.gene060098:CDS 45.0%
ATATCACTACAAGCGCCAGG+TGG - chr6.2:69248404-69248423 None:intergenic 50.0%
CCAATACCTACCCAGGATGT+AGG - chr6.2:69248290-69248309 None:intergenic 50.0%
CCAATATCACTACAAGCGCC+AGG - chr6.2:69248407-69248426 None:intergenic 50.0%
CCTACATCCTGGGTAGGTAT+TGG + chr6.2:69248287-69248306 MS.gene060098:CDS 50.0%
CCTGGCGCTTGTAGTGATAT+TGG + chr6.2:69248404-69248423 MS.gene060098:CDS 50.0%
GATTTCCCTACATCCTGGGT+AGG + chr6.2:69248281-69248300 MS.gene060098:CDS 50.0%
! ATCTCTAAAGGAGGAGGTGG+TGG + chr6.2:69248059-69248078 MS.gene060098:CDS 50.0%
CCATTGTTCAGTGCTCCACC+TGG + chr6.2:69248386-69248405 MS.gene060098:CDS 55.0%
!! CCAGGTGGAGCACTGAACAA+TGG - chr6.2:69248389-69248408 None:intergenic 55.0%
!! GGAGGTGGTGGATTGAAGCT+TGG + chr6.2:69248071-69248090 MS.gene060098:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 69247924 69248529 69247924 ID=MS.gene060098
chr6.2 mRNA 69247924 69248529 69247924 ID=MS.gene060098.t1;Parent=MS.gene060098
chr6.2 exon 69247924 69248529 69247924 ID=MS.gene060098.t1.exon1;Parent=MS.gene060098.t1
chr6.2 CDS 69247924 69248529 69247924 ID=cds.MS.gene060098.t1;Parent=MS.gene060098.t1
Gene Sequence

>MS.gene060098

ATGAAGCCAACATTACTTACCTTTTCTCTCCTCCTCTTTTCCTTTACCTACTTTCCATTAGCTTTTGCTGAAATAGTTGAAGACATAAATGGAAACCCCGTATTTCCTGGTAGAAAATACTATATTGCACCACTTATCTCTAAAGGAGGAGGTGGTGGATTGAAGCTTGGTAAGACAGGAAACTCAGACTGTCCAGTTACTGTACTACAAGATTTTTCTGAGGTTGTTAGAGGCTTGCCAGTTAGATTTACCATAACAGTAAAACGTGGTGTCATCTTTACAACTGACGAAGTAGATATTGAATTTGTTAAGAAACCAAAGTGTGCTGAATCTGCCAAATGGGTGCTAGCTCATGATGATTTCCCTACATCCTGGGTAGGTATTGGTGATAATATTGATGCATTTCAAGGTAAATTTAAAATTGAGACAATTGGTTCAGGAGCATACAAGCTTGTGTACTGTCCATTGTTCAGTGCTCCACCTGGCGCTTGTAGTGATATTGGAAGGTATAAAGATAAGAATGGATGGCGTCTGGTCCCAACTGAAAATAACCCCTTTTGGGTTGTATTCGTTGATGCCACTGAATCTGAAAAAGCCGTAGTTTGA
Protein sequence

>MS.gene060098.t1

MKPTLLTFSLLLFSFTYFPLAFAEIVEDINGNPVFPGRKYYIAPLISKGGGGGLKLGKTGNSDCPVTVLQDFSEVVRGLPVRFTITVKRGVIFTTDEVDIEFVKKPKCAESAKWVLAHDDFPTSWVGIGDNIDAFQGKFKIETIGSGAYKLVYCPLFSAPPGACSDIGRYKDKNGWRLVPTENNPFWVVFVDATESEKAVV