AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044101


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044101.t1 MTR_1g018420 96.186 236 5 2 1 236 1 232 2.78e-170 468
MS.gene044101.t1 MTR_3g102980 60.887 248 69 10 1 234 1 234 7.52e-83 247
MS.gene044101.t1 MTR_1g106730 43.233 266 84 13 1 225 3 242 6.64e-48 158
MS.gene044101.t1 MTR_1g062780 35.417 192 93 7 43 204 81 271 2.13e-22 93.2
MS.gene044101.t1 MTR_4g027440 50.000 84 42 0 81 164 220 303 7.04e-20 87.4
MS.gene044101.t1 MTR_4g028610 29.630 243 95 6 25 203 134 364 1.87e-18 84.0
MS.gene044101.t1 MTR_0160s0030 32.524 206 81 6 38 210 164 344 3.13e-18 82.8
MS.gene044101.t1 MTR_4g109340 39.490 157 57 8 74 200 341 489 6.00e-17 79.7
MS.gene044101.t1 MTR_7g100100 36.134 119 67 2 81 199 34 143 3.32e-16 73.9
MS.gene044101.t1 MTR_5g099040 44.954 109 35 3 81 165 130 237 6.23e-16 75.5
MS.gene044101.t1 MTR_5g062300 48.352 91 40 3 80 163 118 208 9.88e-16 74.3
MS.gene044101.t1 MTR_1g090703 28.251 223 111 7 21 197 81 300 1.76e-15 74.7
MS.gene044101.t1 MTR_1g067650 32.258 124 65 3 79 195 37 148 1.32e-14 69.7
MS.gene044101.t1 MTR_1g115345 43.902 82 37 2 81 161 45 118 1.76e-14 70.1
MS.gene044101.t1 MTR_1g067640 32.258 124 65 3 79 195 36 147 1.78e-14 69.3
MS.gene044101.t1 MTR_7g023560 32.168 143 62 5 32 168 2 115 7.09e-14 68.2
MS.gene044101.t1 MTR_1g067660 37.500 96 46 2 79 172 33 116 4.22e-13 65.5
MS.gene044101.t1 MTR_4g057230 31.098 164 67 5 44 161 67 230 2.84e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044101.t1 AT1G27730 51.613 248 83 11 1 232 1 227 1.90e-61 192
MS.gene044101.t1 AT5G04340 51.092 229 97 7 1 216 1 227 2.62e-52 169
MS.gene044101.t1 AT3G19580 42.023 257 96 9 1 213 1 248 2.22e-46 155
MS.gene044101.t1 AT3G19580 42.023 257 96 9 1 213 1 248 2.22e-46 155
MS.gene044101.t1 AT5G43170 46.186 236 71 10 1 224 1 192 1.85e-44 148
MS.gene044101.t1 AT5G67450 39.669 242 96 7 1 197 1 237 4.89e-36 128
MS.gene044101.t1 AT3G49930 40.000 205 70 6 25 210 36 206 3.61e-35 125
MS.gene044101.t1 AT2G28200 36.139 202 82 8 37 200 70 262 1.53e-24 99.0
MS.gene044101.t1 AT3G60580 38.462 182 83 5 38 210 122 283 1.09e-23 96.7
MS.gene044101.t1 AT2G45120 38.554 166 85 4 38 197 146 300 1.21e-23 97.1
MS.gene044101.t1 AT1G49900 43.802 121 60 3 50 168 160 274 1.82e-21 93.2
MS.gene044101.t1 AT1G49900 48.544 103 40 3 80 180 749 840 3.25e-20 89.4
MS.gene044101.t1 AT5G03510 30.769 195 98 5 39 200 69 259 4.38e-18 81.6
MS.gene044101.t1 AT5G04390 28.879 232 112 8 39 232 96 312 1.36e-17 80.9
MS.gene044101.t1 AT1G02040 32.804 189 95 6 5 162 61 248 8.57e-17 78.2
MS.gene044101.t1 AT5G56200 42.735 117 52 3 83 186 344 458 2.71e-16 77.8
MS.gene044101.t1 AT2G37430 37.313 134 61 4 32 161 2 116 9.02e-16 73.2
MS.gene044101.t1 AT3G53600 30.769 169 92 5 32 195 2 150 1.71e-15 72.4
MS.gene044101.t1 AT4G35280 37.405 131 54 5 39 163 138 246 2.52e-15 73.9
MS.gene044101.t1 AT1G02030 45.679 81 35 1 81 161 160 231 3.83e-15 73.2
MS.gene044101.t1 AT3G46090 43.182 88 38 2 81 168 40 115 1.90e-14 69.3
MS.gene044101.t1 AT2G17180 30.723 166 74 6 39 197 121 252 7.81e-14 69.3
MS.gene044101.t1 AT2G28710 36.364 121 41 3 43 161 14 100 1.07e-13 67.0
MS.gene044101.t1 AT3G46080 44.186 86 34 2 78 161 34 107 1.10e-12 64.3
MS.gene044101.t1 AT5G61470 40.000 85 33 2 81 162 228 297 1.21e-12 66.6
MS.gene044101.t1 AT3G10470 31.111 180 67 5 39 161 104 283 1.43e-12 66.6
MS.gene044101.t1 AT3G46070 38.043 92 49 2 70 161 25 108 1.12e-11 61.6
MS.gene044101.t1 AT5G59820 37.037 108 52 3 73 179 31 123 2.12e-11 60.8

Find 60 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.179252 1.2:+4888671 None:intergenic
CGTTTAGTCCATGGAAGATT+AGG 0.289571 1.2:+4888650 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1.2:+4888028 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1.2:+4888481 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1.2:-4888116 MS.gene044101:CDS
AACTCCGTCGGTGGCGGTGG+CGG 0.338111 1.2:-4888395 MS.gene044101:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1.2:+4888014 None:intergenic
GTTCATCGAAGGTGAATTTA+GGG 0.339272 1.2:+4888672 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1.2:+4888518 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1.2:-4888269 MS.gene044101:CDS
TCCGTCGGTGGCGGTGGCGG+TGG 0.387651 1.2:-4888392 MS.gene044101:CDS
AAATTCGGAATTTCAATCTT+GGG 0.411878 1.2:+4888029 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1.2:-4888135 MS.gene044101:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1.2:-4888270 MS.gene044101:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1.2:+4888540 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1.2:+4888074 None:intergenic
GTTGCAGCTGAGGAAGTTGT+TGG 0.467673 1.2:+4888359 None:intergenic
TTGTTGTTGTCAATGGTTGT+TGG 0.473433 1.2:+4888512 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.490444 1.2:-4888230 MS.gene044101:CDS
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1.2:+4888068 None:intergenic
TGAGCTTGTGGTTGCAGCTG+AGG 0.495728 1.2:+4888349 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1.2:+4888125 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1.2:-4888295 MS.gene044101:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1.2:+4888427 None:intergenic
ACTACGAAGGTGTTGTTGGT+GGG 0.505453 1.2:-4888229 MS.gene044101:CDS
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1.2:-4888281 MS.gene044101:CDS
TTGTTGTCAATGGTTGTTGG+TGG 0.511574 1.2:+4888515 None:intergenic
CTACGAAGGTGTTGTTGGTG+GGG 0.511916 1.2:-4888228 MS.gene044101:CDS
GAATTTAGGGGTAGTAGAAG+TGG 0.512596 1.2:+4888685 None:intergenic
GAACGTTTACGTTTAGTCCA+TGG 0.526324 1.2:+4888641 None:intergenic
TTGCAGCTGAGGAAGTTGTT+GGG 0.534746 1.2:+4888360 None:intergenic
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1.2:+4888527 None:intergenic
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1.2:-4888233 MS.gene044101:CDS
TACGAAGGTGTTGTTGGTGG+GGG 0.550558 1.2:-4888227 MS.gene044101:CDS
AATTTAGGGGTAGTAGAAGT+GGG 0.550780 1.2:+4888686 None:intergenic
TGTAACTGTCTCTGAAGGTG+TGG 0.551186 1.2:-4888189 MS.gene044101:CDS
ACAAGCTCAGCCAACACAAA+CGG 0.552600 1.2:-4888335 MS.gene044101:CDS
CCAATCTTATTAGCAAACTC+CGG 0.554584 1.2:+4888116 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1.2:+4888266 None:intergenic
AACACCGCCACCGTTTGTGT+TGG 0.560436 1.2:+4888325 None:intergenic
TCGATGAACCTAATCTTCCA+TGG 0.566526 1.2:-4888658 MS.gene044101:CDS
GTAACTGTCTCTGAAGGTGT+GGG 0.567359 1.2:-4888188 MS.gene044101:CDS
TGATTTCGATCTGAATATCC+CGG 0.576158 1.2:-4888144 MS.gene044101:CDS
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1.2:-4888266 MS.gene044101:CDS
TGAAATCATGGCGGTTGGTG+TGG 0.583151 1.2:+4888552 None:intergenic
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1.2:+4888126 None:intergenic
AGGCTTGAAATCATGGCGGT+TGG 0.583949 1.2:+4888547 None:intergenic
GTTTGTGTTGGCTGAGCTTG+TGG 0.588915 1.2:+4888337 None:intergenic
TCTGCTGTAACTGTCTCTGA+AGG 0.589059 1.2:-4888194 MS.gene044101:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1.2:-4888575 MS.gene044101:CDS
TCAGCCAACACAAACGGTGG+CGG 0.606071 1.2:-4888329 MS.gene044101:CDS
ACCACCGCCACCGCCACCGA+CGG 0.606095 1.2:+4888391 None:intergenic
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1.2:+4888426 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1.2:-4888440 MS.gene044101:CDS
ATCACGTTGATGACTATGTG+TGG 0.647702 1.2:+4888163 None:intergenic
AGCTCAGCCAACACAAACGG+TGG 0.659448 1.2:-4888332 MS.gene044101:CDS
TGGAAGATTAGGTTCATCGA+AGG 0.659843 1.2:+4888661 None:intergenic
TTCATCGAAGGTGAATTTAG+GGG 0.676237 1.2:+4888673 None:intergenic
CACAAACGTTGTCACTACGA+AGG 0.683725 1.2:-4888242 MS.gene044101:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.753429 1.2:+4888543 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCGGAATTTCAATCT+TGG + chr1.2:4888707-4888726 None:intergenic 25.0%
! AAATTCGGAATTTCAATCTT+GGG + chr1.2:4888706-4888725 None:intergenic 25.0%
AGAACATTTGTAACTGAGTT+TGG + chr1.2:4888254-4888273 None:intergenic 30.0%
AATTTAGGGGTAGTAGAAGT+GGG + chr1.2:4888049-4888068 None:intergenic 35.0%
CCAATCTTATTAGCAAACTC+CGG + chr1.2:4888619-4888638 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG + chr1.2:4888195-4888214 None:intergenic 35.0%
GTTCATCGAAGGTGAATTTA+GGG + chr1.2:4888063-4888082 None:intergenic 35.0%
TGATTTCGATCTGAATATCC+CGG - chr1.2:4888588-4888607 MS.gene044101:CDS 35.0%
TTCATCGAAGGTGAATTTAG+GGG + chr1.2:4888062-4888081 None:intergenic 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG - chr1.2:4888437-4888456 MS.gene044101:CDS 35.0%
! GTTGTTGTTGTTGTTGTCAA+TGG + chr1.2:4888230-4888249 None:intergenic 35.0%
! TTGTTGTTGTCAATGGTTGT+TGG + chr1.2:4888223-4888242 None:intergenic 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG - chr1.2:4888289-4888308 MS.gene044101:CDS 35.0%
CGTTTAGTCCATGGAAGATT+AGG + chr1.2:4888085-4888104 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+TGG + chr1.2:4888094-4888113 None:intergenic 40.0%
GAATTTAGGGGTAGTAGAAG+TGG + chr1.2:4888050-4888069 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG + chr1.2:4888667-4888686 None:intergenic 40.0%
GGTTCATCGAAGGTGAATTT+AGG + chr1.2:4888064-4888083 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG + chr1.2:4888192-4888211 None:intergenic 40.0%
TCGATGAACCTAATCTTCCA+TGG - chr1.2:4888074-4888093 MS.gene044101:CDS 40.0%
TGGAAGATTAGGTTCATCGA+AGG + chr1.2:4888074-4888093 None:intergenic 40.0%
TTCTTCATCATCACAGGATG+AGG + chr1.2:4888661-4888680 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG + chr1.2:4888220-4888239 None:intergenic 40.0%
!! ATCACGTTGATGACTATGTG+TGG + chr1.2:4888572-4888591 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG - chr1.2:4888616-4888635 MS.gene044101:CDS 40.0%
ACAAGCTCAGCCAACACAAA+CGG - chr1.2:4888397-4888416 MS.gene044101:CDS 45.0%
CACAAACGTTGTCACTACGA+AGG - chr1.2:4888490-4888509 MS.gene044101:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG - chr1.2:4888597-4888616 MS.gene044101:CDS 45.0%
TCTGCTGTAACTGTCTCTGA+AGG - chr1.2:4888538-4888557 MS.gene044101:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG + chr1.2:4888610-4888629 None:intergenic 45.0%
TTGCAGCTGAGGAAGTTGTT+GGG + chr1.2:4888375-4888394 None:intergenic 45.0%
TTTCCGACAGGACAAGCTTT+GGG - chr1.2:4888463-4888482 MS.gene044101:CDS 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG - chr1.2:4888678-4888697 MS.gene044101:CDS 45.0%
! GTAACTGTCTCTGAAGGTGT+GGG - chr1.2:4888544-4888563 MS.gene044101:CDS 45.0%
! TGTAACTGTCTCTGAAGGTG+TGG - chr1.2:4888543-4888562 MS.gene044101:CDS 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG + chr1.2:4888217-4888236 None:intergenic 45.0%
!! ACTACGAAGGTGTTGTTGGT+GGG - chr1.2:4888503-4888522 MS.gene044101:CDS 45.0%
!! GTTGTTGGTGGTGGATTCAA+AGG + chr1.2:4888208-4888227 None:intergenic 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG - chr1.2:4888499-4888518 MS.gene044101:CDS 45.0%
ACTTGCTTTGTGTCCACCGA+GGG + chr1.2:4888308-4888327 None:intergenic 50.0%
AGGCTTGAAATCATGGCGGT+TGG + chr1.2:4888188-4888207 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG - chr1.2:4888325-4888344 MS.gene044101:CDS 50.0%
GTTGCAGCTGAGGAAGTTGT+TGG + chr1.2:4888376-4888395 None:intergenic 50.0%
GTTTCCGACAGGACAAGCTT+TGG - chr1.2:4888462-4888481 MS.gene044101:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG + chr1.2:4888609-4888628 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG - chr1.2:4888292-4888311 MS.gene044101:CDS 50.0%
TGTCATAGGTCGTTTCCGAC+AGG - chr1.2:4888451-4888470 MS.gene044101:CDS 50.0%
! TGAAATCATGGCGGTTGGTG+TGG + chr1.2:4888183-4888202 None:intergenic 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG - chr1.2:4888502-4888521 MS.gene044101:CDS 50.0%
!! CTACGAAGGTGTTGTTGGTG+GGG - chr1.2:4888504-4888523 MS.gene044101:CDS 50.0%
!! GTTTGTGTTGGCTGAGCTTG+TGG + chr1.2:4888398-4888417 None:intergenic 50.0%
!! TACGAAGGTGTTGTTGGTGG+GGG - chr1.2:4888505-4888524 MS.gene044101:CDS 50.0%
AACACCGCCACCGTTTGTGT+TGG + chr1.2:4888410-4888429 None:intergenic 55.0%
AGCTCAGCCAACACAAACGG+TGG - chr1.2:4888400-4888419 MS.gene044101:CDS 55.0%
CCACCCAAAGCTTGTCCTGT+CGG + chr1.2:4888469-4888488 None:intergenic 55.0%
TCAGCCAACACAAACGGTGG+CGG - chr1.2:4888403-4888422 MS.gene044101:CDS 55.0%
TGAGCTTGTGGTTGCAGCTG+AGG + chr1.2:4888386-4888405 None:intergenic 55.0%
TGTCTCATCATGCTCGCTCG+TGG - chr1.2:4888157-4888176 MS.gene044101:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG + chr1.2:4888309-4888328 None:intergenic 55.0%
CACCGCAAAAACTCCGTCGG+TGG - chr1.2:4888328-4888347 MS.gene044101:CDS 60.0%
CGCAAAAACTCCGTCGGTGG+CGG - chr1.2:4888331-4888350 MS.gene044101:CDS 60.0%
! AAAAACTCCGTCGGTGGCGG+TGG - chr1.2:4888334-4888353 MS.gene044101:CDS 60.0%
! CGCCACCGACGGAGTTTTTG+CGG + chr1.2:4888333-4888352 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG - chr1.2:4888466-4888485 MS.gene044101:CDS 60.0%
! AACTCCGTCGGTGGCGGTGG+CGG - chr1.2:4888337-4888356 MS.gene044101:CDS 70.0%
ACCACCGCCACCGCCACCGA+CGG + chr1.2:4888344-4888363 None:intergenic 75.0%
!! TCCGTCGGTGGCGGTGGCGG+TGG - chr1.2:4888340-4888359 MS.gene044101:CDS 80.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 4888022 4888732 4888022 ID=MS.gene044101
chr1.2 mRNA 4888022 4888732 4888022 ID=MS.gene044101.t1;Parent=MS.gene044101
chr1.2 exon 4888022 4888732 4888022 ID=MS.gene044101.t1.exon1;Parent=MS.gene044101.t1
chr1.2 CDS 4888022 4888732 4888022 ID=cds.MS.gene044101.t1;Parent=MS.gene044101.t1
Gene Sequence

>MS.gene044101

ATGGCTCTTGAAGCACTTAACTCACCCACTTCTACTACCCCTAAATTCACCTTCGATGAACCTAATCTTCCATGGACTAAACGTAAACGTTCTAAACGTTCACGTTCATGCACTGAAGAAGAGTATCTTGCTCTTTGTCTCATCATGCTCGCTCGTGGCCACACCAACCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACAACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGGCGGTGGTGATGATCACCCAACAACTTCCTCAGCTGCAACCACAAGCTCAGCCAACACAAACGGTGGCGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGGGGTGCTTCTGCTTCTGCTGTAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA

Protein sequence

>MS.gene044101.t1

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTNRHDFKPLNPPPTTIDNNNNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGGGGDDHPTTSSAATTSSANTNGGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAVTVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ