AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060097

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060097.t1 MTR_6g059530 93.103 203 12 1 1 201 1 203 9.80e-125 350
MS.gene060097.t1 MTR_6g059410 89.655 203 18 2 1 201 1 202 1.20e-118 335
MS.gene060097.t1 MTR_6g059650 55.670 194 76 4 17 201 19 211 7.22e-66 202
MS.gene060097.t1 MTR_6g065460 53.659 205 82 6 1 193 1 204 1.15e-55 176
MS.gene060097.t1 MTR_6g059760 46.890 209 94 10 1 196 1 205 8.30e-47 153
MS.gene060097.t1 MTR_6g065460 49.261 203 70 6 1 193 1 180 3.65e-46 150
MS.gene060097.t1 MTR_6g059680 47.525 202 87 9 16 201 18 216 1.88e-41 140
MS.gene060097.t1 MTR_6g044780 43.721 215 102 10 1 199 1 212 2.16e-41 140
MS.gene060097.t1 MTR_3g463590 44.149 188 92 7 24 201 27 211 3.05e-41 139
MS.gene060097.t1 MTR_6g045097 42.791 215 104 10 1 199 1 212 3.06e-39 134
MS.gene060097.t1 MTR_6g059730 45.116 215 101 10 1 201 1 212 4.92e-38 131
MS.gene060097.t1 MTR_6g044810 41.860 215 106 10 1 199 1 212 7.99e-38 130
MS.gene060097.t1 MTR_6g045403 40.654 214 108 9 1 199 1 210 7.56e-35 123
MS.gene060097.t1 MTR_6g009650 41.827 208 102 9 1 194 1 203 1.38e-33 119
MS.gene060097.t1 MTR_6g066190 39.713 209 107 9 1 195 1 204 1.27e-32 117
MS.gene060097.t1 MTR_6g017225 39.720 214 107 11 6 201 7 216 1.42e-32 120
MS.gene060097.t1 MTR_6g009563 41.148 209 103 9 1 194 1 204 6.84e-32 115
MS.gene060097.t1 MTR_6g045433 36.364 231 105 11 1 201 1 219 4.74e-31 113
MS.gene060097.t1 MTR_6g059810 39.130 207 100 9 4 190 8 208 1.46e-30 111
MS.gene060097.t1 MTR_6g066210 39.906 213 111 10 1 199 1 210 3.77e-30 110
MS.gene060097.t1 MTR_1g035770 39.806 206 102 11 6 192 7 209 1.55e-25 99.0
MS.gene060097.t1 MTR_6g059755 49.074 108 49 4 98 199 18 125 3.04e-25 95.5
MS.gene060097.t1 MTR_6g078070 33.659 205 122 8 1 193 1 203 7.32e-21 86.3
MS.gene060097.t1 MTR_6g078100 33.333 207 122 7 1 193 1 205 7.50e-19 80.9
MS.gene060097.t1 MTR_1g057110 35.407 209 98 12 1 194 1 187 4.96e-18 78.6
MS.gene060097.t1 MTR_6g065570 53.333 60 25 1 16 72 14 73 4.89e-15 68.2
MS.gene060097.t1 MTR_0100s0150 27.411 197 127 7 7 190 5 198 3.43e-14 68.6
MS.gene060097.t1 MTR_0302s0030 28.643 199 126 7 4 190 5 199 1.23e-12 64.3
MS.gene060097.t1 MTR_3g106620 30.387 181 109 9 24 194 27 200 2.72e-12 63.5
MS.gene060097.t1 MTR_0084s0030 28.283 198 125 8 7 190 5 199 5.75e-12 62.4
MS.gene060097.t1 MTR_0211s0080 27.320 194 128 7 7 190 5 195 1.49e-11 61.2
MS.gene060097.t1 MTR_2g073010 28.426 197 133 6 1 193 6 198 3.99e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060097.t1 AT1G73260 34.000 200 110 8 17 197 13 209 1.03e-20 86.3
MS.gene060097.t1 AT1G17860 30.882 204 121 8 1 193 1 195 1.81e-16 74.3
MS.gene060097.t1 AT1G73325 29.268 205 132 8 4 198 7 208 1.12e-11 62.0
MS.gene060097.t1 AT1G73330 29.327 208 127 11 1 199 1 197 5.30e-11 60.1

Find 50 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCCTTTAGGGTTGTATTTC+TGG 0.060444 6.2:-69028006 MS.gene060097:CDS
CAACTGAAAATGATCCCTTT+AGG 0.293355 6.2:-69028019 MS.gene060097:CDS
AACTGAAAATGATCCCTTTA+GGG 0.300397 6.2:-69028018 MS.gene060097:CDS
GGTAAGTAATGTTGGCTTCA+TGG 0.309270 6.2:+69028559 None:intergenic
GAAACAGTTGAAGACATAAA+TGG 0.316517 6.2:-69028488 MS.gene060097:CDS
ACTATTATGGTAAATCTAAC+TGG 0.325171 6.2:+69028320 None:intergenic
CCTGGTGCTTGTATTGATAT+TGG 0.335281 6.2:-69028077 MS.gene060097:CDS
TGAATCTGCCAAATGGGTTC+TGG 0.350801 6.2:-69028231 MS.gene060097:CDS
AAATCTTGTAGAACAGTAAC+TGG 0.355500 6.2:+69028365 None:intergenic
CTGGTGCTTGTATTGATATT+GGG 0.363470 6.2:-69028076 MS.gene060097:CDS
CCTACATCTTGGGTAGGTAT+TGG 0.367664 6.2:-69028194 MS.gene060097:CDS
AAAATTGAGACAATTGGTTC+AGG 0.373759 6.2:-69028140 MS.gene060097:CDS
AATGGAAACCCCGTATTTCC+TGG 0.375075 6.2:-69028470 MS.gene060097:CDS
AAATTTAAAATTGAGACAAT+TGG 0.414016 6.2:-69028146 MS.gene060097:CDS
ACTGTTTCAGTAAAAGCTAA+TGG 0.419197 6.2:+69028503 None:intergenic
GATAATATTGATGCATTTCA+AGG 0.419889 6.2:-69028170 MS.gene060097:CDS
ATCTTGAGCCAGAACCCATT+TGG 0.420888 6.2:+69028223 None:intergenic
AAGATGATTTCCCTACATCT+TGG 0.423540 6.2:-69028205 MS.gene060097:CDS
TCCAGAAATACAACCCTAAA+GGG 0.430521 6.2:+69028005 None:intergenic
AGAGAAAAGGTAAGTAATGT+TGG 0.440708 6.2:+69028551 None:intergenic
ATCTCTAAAGGAGGAGGTGG+TGG 0.449806 6.2:-69028422 MS.gene060097:CDS
CCAATACCTACCCAAGATGT+AGG 0.454772 6.2:+69028194 None:intergenic
AGATGATTTCCCTACATCTT+GGG 0.458060 6.2:-69028204 MS.gene060097:CDS
AGATGAGAATGGATGGCGTT+TGG 0.471954 6.2:-69028045 MS.gene060097:CDS
ATCCAGAAATACAACCCTAA+AGG 0.484440 6.2:+69028004 None:intergenic
AGTAAAAGCTAATGGTAAGT+AGG 0.489860 6.2:+69028511 None:intergenic
GGAAACGAGGAGGAGAGAAA+AGG 0.497156 6.2:+69028538 None:intergenic
GGAGGTGGTGGATTGAAACT+TGG 0.507705 6.2:-69028410 MS.gene060097:CDS
AGCTAATGGTAAGTAGGTAA+AGG 0.510962 6.2:+69028517 None:intergenic
CCTCCTCCTTTAGAGATAAG+TGG 0.523049 6.2:+69028428 None:intergenic
GTGTGCTGAATCTGCCAAAT+GGG 0.523391 6.2:-69028237 MS.gene060097:CDS
ATTGCACCACTTATCTCTAA+AGG 0.523973 6.2:-69028434 MS.gene060097:CDS
CCATTGTTCAGTGCTCCACC+TGG 0.524555 6.2:-69028095 MS.gene060097:CDS
GGATTGAAACTTGGTAAGAC+AGG 0.527926 6.2:-69028401 MS.gene060097:CDS
AGTGTGCTGAATCTGCCAAA+TGG 0.527935 6.2:-69028238 MS.gene060097:CDS
TTGGCAGATTCAGCACACTT+TGG 0.530934 6.2:+69028242 None:intergenic
GGGAGGTATAAAGATGAGAA+TGG 0.551313 6.2:-69028056 MS.gene060097:CDS
CAATACCTACCCAAGATGTA+GGG 0.570789 6.2:+69028195 None:intergenic
CTTATCTCTAAAGGAGGAGG+TGG 0.573275 6.2:-69028425 MS.gene060097:CDS
GGTATAAAGATGAGAATGGA+TGG 0.586436 6.2:-69028052 MS.gene060097:CDS
CCACTTATCTCTAAAGGAGG+AGG 0.587891 6.2:-69028428 MS.gene060097:CDS
CCAATATCAATACAAGCACC+AGG 0.593116 6.2:+69028077 None:intergenic
GATTTCCCTACATCTTGGGT+AGG 0.605569 6.2:-69028200 MS.gene060097:CDS
CCAGGTGGAGCACTGAACAA+TGG 0.632227 6.2:+69028095 None:intergenic
GCACCACTTATCTCTAAAGG+AGG 0.639013 6.2:-69028431 MS.gene060097:CDS
GTGCTTGTATTGATATTGGG+AGG 0.649548 6.2:-69028073 MS.gene060097:CDS
GTAAGTAGGTAAAGGAAACG+AGG 0.653821 6.2:+69028525 None:intergenic
AGTAGGTAAAGGAAACGAGG+AGG 0.687780 6.2:+69028528 None:intergenic
ATATCAATACAAGCACCAGG+TGG 0.733791 6.2:+69028080 None:intergenic
TTTACCATAATAGTAAAACG+TGG 0.788877 6.2:-69028311 MS.gene060097:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTAAAATTGAGACAAT+TGG - chr6.2:69028385-69028404 MS.gene060097:CDS 15.0%
! ACTATTATGGTAAATCTAAC+TGG + chr6.2:69028214-69028233 None:intergenic 25.0%
! GATAATATTGATGCATTTCA+AGG - chr6.2:69028361-69028380 MS.gene060097:CDS 25.0%
! TTTACCATAATAGTAAAACG+TGG - chr6.2:69028220-69028239 MS.gene060097:CDS 25.0%
AAATCTTGTAGAACAGTAAC+TGG + chr6.2:69028169-69028188 None:intergenic 30.0%
AACTGAAAATGATCCCTTTA+GGG - chr6.2:69028513-69028532 MS.gene060097:CDS 30.0%
ACTGTTTCAGTAAAAGCTAA+TGG + chr6.2:69028031-69028050 None:intergenic 30.0%
AGAGAAAAGGTAAGTAATGT+TGG + chr6.2:69027983-69028002 None:intergenic 30.0%
AGTAAAAGCTAATGGTAAGT+AGG + chr6.2:69028023-69028042 None:intergenic 30.0%
GAAACAGTTGAAGACATAAA+TGG - chr6.2:69028043-69028062 MS.gene060097:CDS 30.0%
! AAAATTGAGACAATTGGTTC+AGG - chr6.2:69028391-69028410 MS.gene060097:CDS 30.0%
! GCAATATAGTATTTTCTACC+AGG + chr6.2:69028082-69028101 None:intergenic 30.0%
! GTATTTTCTACCAGGAAATA+CGG + chr6.2:69028074-69028093 None:intergenic 30.0%
! TAAAGGGATCATTTTCAGTT+GGG + chr6.2:69028513-69028532 None:intergenic 30.0%
! TATTTTCTACCAGGAAATAC+GGG + chr6.2:69028073-69028092 None:intergenic 30.0%
! TGTTCTACAAGATTTTTCTG+AGG - chr6.2:69028174-69028193 MS.gene060097:CDS 30.0%
AAGATGATTTCCCTACATCT+TGG - chr6.2:69028326-69028345 MS.gene060097:CDS 35.0%
AGATGATTTCCCTACATCTT+GGG - chr6.2:69028327-69028346 MS.gene060097:CDS 35.0%
AGCTAATGGTAAGTAGGTAA+AGG + chr6.2:69028017-69028036 None:intergenic 35.0%
ATCCAGAAATACAACCCTAA+AGG + chr6.2:69028530-69028549 None:intergenic 35.0%
ATTGCACCACTTATCTCTAA+AGG - chr6.2:69028097-69028116 MS.gene060097:CDS 35.0%
CAACTGAAAATGATCCCTTT+AGG - chr6.2:69028512-69028531 MS.gene060097:CDS 35.0%
GGTATAAAGATGAGAATGGA+TGG - chr6.2:69028479-69028498 MS.gene060097:CDS 35.0%
TCCAGAAATACAACCCTAAA+GGG + chr6.2:69028529-69028548 None:intergenic 35.0%
! ATTTTCTACCAGGAAATACG+GGG + chr6.2:69028072-69028091 None:intergenic 35.0%
! CTAAAGGGATCATTTTCAGT+TGG + chr6.2:69028514-69028533 None:intergenic 35.0%
! CTGGTGCTTGTATTGATATT+GGG - chr6.2:69028455-69028474 MS.gene060097:CDS 35.0%
! GACACCACGTTTTACTATTA+TGG + chr6.2:69028227-69028246 None:intergenic 35.0%
!!! GATTTTTCTGAGGTTGTTAG+AGG - chr6.2:69028184-69028203 MS.gene060097:CDS 35.0%
ATATCAATACAAGCACCAGG+TGG + chr6.2:69028454-69028473 None:intergenic 40.0%
CAATACCTACCCAAGATGTA+GGG + chr6.2:69028339-69028358 None:intergenic 40.0%
CCAATATCAATACAAGCACC+AGG + chr6.2:69028457-69028476 None:intergenic 40.0%
GGATTGAAACTTGGTAAGAC+AGG - chr6.2:69028130-69028149 MS.gene060097:CDS 40.0%
GTAAGTAGGTAAAGGAAACG+AGG + chr6.2:69028009-69028028 None:intergenic 40.0%
! CCTGGTGCTTGTATTGATAT+TGG - chr6.2:69028454-69028473 MS.gene060097:CDS 40.0%
! GGGAGGTATAAAGATGAGAA+TGG - chr6.2:69028475-69028494 MS.gene060097:CDS 40.0%
! GTGCTTGTATTGATATTGGG+AGG - chr6.2:69028458-69028477 MS.gene060097:CDS 40.0%
!! TCCCTTTAGGGTTGTATTTC+TGG - chr6.2:69028525-69028544 MS.gene060097:CDS 40.0%
AATGGAAACCCCGTATTTCC+TGG - chr6.2:69028061-69028080 MS.gene060097:CDS 45.0%
AGATGAGAATGGATGGCGTT+TGG - chr6.2:69028486-69028505 MS.gene060097:CDS 45.0%
AGTAGGTAAAGGAAACGAGG+AGG + chr6.2:69028006-69028025 None:intergenic 45.0%
AGTGTGCTGAATCTGCCAAA+TGG - chr6.2:69028293-69028312 MS.gene060097:CDS 45.0%
ATCTTGAGCCAGAACCCATT+TGG + chr6.2:69028311-69028330 None:intergenic 45.0%
CCAATACCTACCCAAGATGT+AGG + chr6.2:69028340-69028359 None:intergenic 45.0%
CCTACATCTTGGGTAGGTAT+TGG - chr6.2:69028337-69028356 MS.gene060097:CDS 45.0%
GATTTCCCTACATCTTGGGT+AGG - chr6.2:69028331-69028350 MS.gene060097:CDS 45.0%
GTGTGCTGAATCTGCCAAAT+GGG - chr6.2:69028294-69028313 MS.gene060097:CDS 45.0%
TTGGCAGATTCAGCACACTT+TGG + chr6.2:69028292-69028311 None:intergenic 45.0%
! CCACTTATCTCTAAAGGAGG+AGG - chr6.2:69028103-69028122 MS.gene060097:CDS 45.0%
! CCTCCTCCTTTAGAGATAAG+TGG + chr6.2:69028106-69028125 None:intergenic 45.0%
! CTTATCTCTAAAGGAGGAGG+TGG - chr6.2:69028106-69028125 MS.gene060097:CDS 45.0%
! GCACCACTTATCTCTAAAGG+AGG - chr6.2:69028100-69028119 MS.gene060097:CDS 45.0%
! TGAATCTGCCAAATGGGTTC+TGG - chr6.2:69028300-69028319 MS.gene060097:CDS 45.0%
GGAAACGAGGAGGAGAGAAA+AGG + chr6.2:69027996-69028015 None:intergenic 50.0%
! ATCTCTAAAGGAGGAGGTGG+TGG - chr6.2:69028109-69028128 MS.gene060097:CDS 50.0%
!! GGAGGTGGTGGATTGAAACT+TGG - chr6.2:69028121-69028140 MS.gene060097:CDS 50.0%
CCATTGTTCAGTGCTCCACC+TGG - chr6.2:69028436-69028455 MS.gene060097:CDS 55.0%
!! CCAGGTGGAGCACTGAACAA+TGG + chr6.2:69028439-69028458 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 69027974 69028579 69027974 ID=MS.gene060097
chr6.2 mRNA 69027974 69028579 69027974 ID=MS.gene060097.t1;Parent=MS.gene060097
chr6.2 exon 69027974 69028579 69027974 ID=MS.gene060097.t1.exon1;Parent=MS.gene060097.t1
chr6.2 CDS 69027974 69028579 69027974 ID=cds.MS.gene060097.t1;Parent=MS.gene060097.t1
Gene Sequence

>MS.gene060097

ATGAAGCCAACATTACTTACCTTTTCTCTCCTCCTCGTTTCCTTTACCTACTTACCATTAGCTTTTACTGAAACAGTTGAAGACATAAATGGAAACCCCGTATTTCCTGGTAGAAAATACTATATTGCACCACTTATCTCTAAAGGAGGAGGTGGTGGATTGAAACTTGGTAAGACAGGAAACTCAGAATGTCCAGTTACTGTTCTACAAGATTTTTCTGAGGTTGTTAGAGGCTTGCCAGTTAGATTTACCATAATAGTAAAACGTGGTGTCATCTTTACAACTGACAAAGTAGATATTGAATTTGTTAAGAAACCAAAGTGTGCTGAATCTGCCAAATGGGTTCTGGCTCAAGATGATTTCCCTACATCTTGGGTAGGTATTGGTGATAATATTGATGCATTTCAAGGTAAATTTAAAATTGAGACAATTGGTTCAGGAGCATACAAGCTTGTGTATTGTCCATTGTTCAGTGCTCCACCTGGTGCTTGTATTGATATTGGGAGGTATAAAGATGAGAATGGATGGCGTTTGGTCCCAACTGAAAATGATCCCTTTAGGGTTGTATTTCTGGATGCTACTGAATCTGAAAAAGCTGTAGTTTGA
Protein sequence

>MS.gene060097.t1

MKPTLLTFSLLLVSFTYLPLAFTETVEDINGNPVFPGRKYYIAPLISKGGGGGLKLGKTGNSECPVTVLQDFSEVVRGLPVRFTIIVKRGVIFTTDKVDIEFVKKPKCAESAKWVLAQDDFPTSWVGIGDNIDAFQGKFKIETIGSGAYKLVYCPLFSAPPGACIDIGRYKDENGWRLVPTENDPFRVVFLDATESEKAVV