AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene011816

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene011816.t1 MTR_5g017210 56.604 265 85 12 1 253 1 247 6.25e-64 200
MS.gene011816.t1 MTR_3g101810 55.656 221 64 9 21 214 40 253 3.81e-62 196
MS.gene011816.t1 MTR_8g093500 75.824 91 22 0 108 198 87 177 4.58e-46 155
MS.gene011816.t1 MTR_2g100490 52.027 148 62 4 91 229 242 389 1.03e-29 115
MS.gene011816.t1 MTR_8g015450 59.596 99 36 1 107 201 296 394 2.66e-27 108
MS.gene011816.t1 MTR_7g069590 66.667 60 20 0 141 200 32 91 8.57e-23 91.3
MS.gene011816.t1 MTR_5g079500 54.430 79 34 1 121 197 202 280 1.05e-19 86.7
MS.gene011816.t1 MTR_1g106460 52.239 67 32 0 131 197 234 300 4.71e-17 79.3
MS.gene011816.t1 MTR_1g018090 60.714 56 22 0 142 197 281 336 5.09e-17 79.7
MS.gene011816.t1 MTR_5g005110 62.963 54 20 0 144 197 233 286 7.11e-17 79.0
MS.gene011816.t1 MTR_1g106470 60.714 56 22 0 142 197 203 258 1.86e-16 77.4
MS.gene011816.t1 MTR_3g103030 55.556 63 28 0 135 197 229 291 4.52e-16 76.6
MS.gene011816.t1 MTR_1g080890 47.059 85 37 1 128 212 186 262 3.55e-15 74.3
MS.gene011816.t1 MTR_4g131160 52.778 72 26 1 142 213 203 266 1.05e-14 73.2
MS.gene011816.t1 MTR_4g131160 52.778 72 26 1 142 213 206 269 1.08e-14 73.2
MS.gene011816.t1 MTR_1g106480 64.444 45 16 0 153 197 87 131 1.75e-13 66.6
MS.gene011816.t1 MTR_2g067000 48.000 75 32 1 131 198 146 220 5.08e-13 67.8
MS.gene011816.t1 MTR_1g060700 57.407 54 23 0 145 198 357 410 2.78e-12 66.2
MS.gene011816.t1 MTR_4g033295 57.143 56 23 1 145 199 128 183 7.36e-12 63.2
MS.gene011816.t1 MTR_4g033295 57.407 54 22 1 145 197 128 181 2.01e-11 61.6
MS.gene011816.t1 MTR_2g089070 48.148 54 28 0 145 198 146 199 6.61e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene011816.t1 AT3G50330 57.843 204 69 8 17 216 11 201 2.21e-50 165
MS.gene011816.t1 AT5G67060 56.731 208 59 8 1 199 1 186 7.54e-50 164
MS.gene011816.t1 AT5G67060 57.979 188 56 6 21 199 1 174 9.41e-48 158
MS.gene011816.t1 AT4G00120 68.750 96 27 1 110 202 87 182 4.09e-39 135
MS.gene011816.t1 AT3G21330 64.894 94 33 0 107 200 241 334 3.35e-36 132
MS.gene011816.t1 AT5G09750 76.667 90 21 0 108 197 92 181 1.79e-34 124
MS.gene011816.t1 AT5G01305 69.492 59 18 0 136 194 38 96 1.09e-21 89.0
MS.gene011816.t1 AT5G37800 36.145 166 77 5 35 197 124 263 4.74e-19 84.7
MS.gene011816.t1 AT5G43175 50.725 69 34 0 129 197 126 194 3.16e-18 81.3
MS.gene011816.t1 AT4G33880 59.677 62 25 0 136 197 267 328 3.29e-18 83.2
MS.gene011816.t1 AT1G66470 36.879 141 69 4 72 197 122 257 8.50e-18 81.3
MS.gene011816.t1 AT1G27740 52.941 68 32 0 130 197 162 229 8.57e-18 80.5
MS.gene011816.t1 AT2G14760 58.065 62 26 0 136 197 238 299 3.02e-17 80.1
MS.gene011816.t1 AT2G24260 41.071 112 47 3 133 226 28 138 1.81e-16 76.6
MS.gene011816.t1 AT2G24260 41.071 112 47 3 133 226 131 241 5.95e-16 76.6
MS.gene011816.t1 AT4G30980 41.584 101 51 1 131 231 126 218 1.30e-15 75.5
MS.gene011816.t1 AT4G30980 49.398 83 34 1 131 213 174 248 2.70e-15 74.7
MS.gene011816.t1 AT5G58010 47.674 86 36 2 132 216 96 173 1.50e-14 72.0
MS.gene011816.t1 AT2G14760 48.000 75 26 1 136 197 238 312 5.88e-14 70.9

Find 58 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGAAGCAGTGTCCATTT+TGG 0.242900 8.1:+27077575 None:intergenic
AATAATGTGAATTATAATTC+TGG 0.269339 8.1:-27077417 MS.gene011816:CDS
CTTCGGCGGCCTAACGGATT+CGG 0.285239 8.1:+27077707 None:intergenic
CACATTGGTGGTGGATTCAT+TGG 0.306846 8.1:-27077465 MS.gene011816:CDS
AAAGGTTGATCAGAGAATTC+AGG 0.327420 8.1:+27078017 None:intergenic
CAGTGTTGTTGGTGATTTCT+TGG 0.347528 8.1:+27077973 None:intergenic
GTGGAGATGATAGTGCATTT+TGG 0.349652 8.1:+27077931 None:intergenic
GTGTAGCTGCTAGGCATAGA+AGG 0.352095 8.1:-27077650 MS.gene011816:CDS
AAAGGATAAGTGAGAGGATA+AGG 0.357712 8.1:-27077626 MS.gene011816:CDS
TTCGGCGGCCTAACGGATTC+GGG 0.378261 8.1:+27077708 None:intergenic
AGTACCTGGTGGAACCAAAA+TGG 0.383832 8.1:-27077589 MS.gene011816:CDS
TAACTAGCTAAGCAATTGTT+TGG 0.384797 8.1:+27077347 None:intergenic
CCTTCTCTTCGGCGGCCTAA+CGG 0.391457 8.1:+27077701 None:intergenic
ATCTTCACATTCCTTCTCTT+CGG 0.392038 8.1:+27077690 None:intergenic
TGCCTAGCAGCTACACTTTG+TGG 0.400476 8.1:+27077657 None:intergenic
TAATTCTGGTTTGATGATGA+AGG 0.423318 8.1:-27077403 MS.gene011816:CDS
TCAATATTATTCAAAGTTTG+TGG 0.430454 8.1:+27077912 None:intergenic
AAAGAATTCGACTGCGAGTA+AGG 0.432337 8.1:+27077807 None:intergenic
GATTCGGGATCGATATGTAT+AGG 0.452777 8.1:+27077723 None:intergenic
AAGGTTGATCAGAGAATTCA+GGG 0.455273 8.1:+27078018 None:intergenic
GCTAAGCAATTGTTTGGAAG+TGG 0.457304 8.1:+27077353 None:intergenic
GTTGGTGATTTCTTGGTAAG+TGG 0.468287 8.1:+27077980 None:intergenic
CCGTTAGGCCGCCGAAGAGA+AGG 0.485491 8.1:-27077701 MS.gene011816:CDS
AAATAATGGAACAGTGTTGT+TGG 0.485998 8.1:+27077962 None:intergenic
GATAGCAATGATGATGCAAA+TGG 0.487640 8.1:-27078048 MS.gene011816:CDS
GTGGAACCCACCATTTGAAA+AGG 0.490966 8.1:+27077372 None:intergenic
GTGGTGGGAGTGTTATAAAA+AGG 0.493586 8.1:+27077999 None:intergenic
ATATCGATCCCGAATCCGTT+AGG 0.506193 8.1:-27077716 MS.gene011816:CDS
GTGATTTCTTGGTAAGTGGT+GGG 0.510263 8.1:+27077984 None:intergenic
GTAAGGAAATGATGAAGAGT+TGG 0.515713 8.1:+27077824 None:intergenic
TTCACACGTTGGAACAAGTA+GGG 0.518979 8.1:-27077509 MS.gene011816:CDS
GAATTCGATGGCAGCGATGA+GGG 0.520911 8.1:-27077775 MS.gene011816:CDS
GTGTGATATTCAAGTGTTGT+TGG 0.525349 8.1:+27077862 None:intergenic
GGTGATTTCTTGGTAAGTGG+TGG 0.542766 8.1:+27077983 None:intergenic
GAAGAGTTGGTTTGAAGAGA+TGG 0.565464 8.1:+27077837 None:intergenic
TTCACATTCCTTCTCTTCGG+CGG 0.566092 8.1:+27077693 None:intergenic
ATTGGTGGTGGATTCATTGG+AGG 0.568963 8.1:-27077462 MS.gene011816:CDS
GAAGGGAAAGGATAAGTGAG+AGG 0.571416 8.1:-27077632 MS.gene011816:CDS
TTGGTGGTGGATTCATTGGA+GGG 0.580871 8.1:-27077461 MS.gene011816:CDS
TTGACATTGGAGTGTAGAAG+TGG 0.581516 8.1:+27077888 None:intergenic
AATTCTGGTTTGATGATGAA+GGG 0.584821 8.1:-27077402 MS.gene011816:CDS
AGTGAAAACTGACGGAAGCA+TGG 0.586477 8.1:-27078075 MS.gene011816:CDS
GTTCACACGTTGGAACAAGT+AGG 0.594798 8.1:-27077510 MS.gene011816:CDS
TCACAATCACACATTGGTGG+TGG 0.595725 8.1:-27077474 MS.gene011816:CDS
GAAGAAACAAGTTCACACGT+TGG 0.614768 8.1:-27077520 MS.gene011816:CDS
AGAATTCGATGGCAGCGATG+AGG 0.615506 8.1:-27077776 MS.gene011816:CDS
TGTAGCTGCTAGGCATAGAA+GGG 0.616015 8.1:-27077649 MS.gene011816:CDS
CTGCTAGGCATAGAAGGGAA+AGG 0.619057 8.1:-27077644 MS.gene011816:CDS
ATCCACAAAGTGTAGCTGCT+AGG 0.619623 8.1:-27077659 MS.gene011816:CDS
AAGGAATGTGAAGATATCAA+AGG 0.620019 8.1:-27077682 MS.gene011816:CDS
GTGTTGTTGGAAATTGACAT+TGG 0.623317 8.1:+27077875 None:intergenic
GTCGACATAGTGAAAACTGA+CGG 0.646360 8.1:-27078083 MS.gene011816:CDS
GAGTTGGTTTGAAGAGATGG+TGG 0.649591 8.1:+27077840 None:intergenic
AATAGATCACAATCACACAT+TGG 0.653131 8.1:-27077480 MS.gene011816:CDS
AGATCACAATCACACATTGG+TGG 0.659957 8.1:-27077477 MS.gene011816:CDS
TCACACGTTGGAACAAGTAG+GGG 0.679972 8.1:-27077508 MS.gene011816:CDS
ATATTACAAAGATTAGTACC+TGG 0.683168 8.1:-27077603 MS.gene011816:CDS
TTACAAAGATTAGTACCTGG+TGG 0.689802 8.1:-27077600 MS.gene011816:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATGTGAATTATAATTC+TGG - chr8.1:27078022-27078041 MS.gene011816:CDS 15.0%
!! TCAATATTATTCAAAGTTTG+TGG + chr8.1:27077530-27077549 None:intergenic 20.0%
!!! TTTTGGTTAAGGTTAAATAA+TGG + chr8.1:27077494-27077513 None:intergenic 20.0%
! ATATTACAAAGATTAGTACC+TGG - chr8.1:27077836-27077855 MS.gene011816:CDS 25.0%
!!! TTTTGAAAAGAAGAATTCGA+TGG - chr8.1:27077652-27077671 MS.gene011816:CDS 25.0%
AAGGAATGTGAAGATATCAA+AGG - chr8.1:27077757-27077776 MS.gene011816:CDS 30.0%
AATAGATCACAATCACACAT+TGG - chr8.1:27077959-27077978 MS.gene011816:CDS 30.0%
! AAATAATGGAACAGTGTTGT+TGG + chr8.1:27077480-27077499 None:intergenic 30.0%
!! AATTCTGGTTTGATGATGAA+GGG - chr8.1:27078037-27078056 MS.gene011816:CDS 30.0%
!! TAATTCTGGTTTGATGATGA+AGG - chr8.1:27078036-27078055 MS.gene011816:CDS 30.0%
!!! ATGATAGTGCATTTTGGTTA+AGG + chr8.1:27077505-27077524 None:intergenic 30.0%
AAAGGATAAGTGAGAGGATA+AGG - chr8.1:27077813-27077832 MS.gene011816:CDS 35.0%
ATCTTCACATTCCTTCTCTT+CGG + chr8.1:27077752-27077771 None:intergenic 35.0%
GTAAGGAAATGATGAAGAGT+TGG + chr8.1:27077618-27077637 None:intergenic 35.0%
TTACAAAGATTAGTACCTGG+TGG - chr8.1:27077839-27077858 MS.gene011816:CDS 35.0%
! AAAGGTTGATCAGAGAATTC+AGG + chr8.1:27077425-27077444 None:intergenic 35.0%
! AAGGTTGATCAGAGAATTCA+GGG + chr8.1:27077424-27077443 None:intergenic 35.0%
! GATAGCAATGATGATGCAAA+TGG - chr8.1:27077391-27077410 MS.gene011816:CDS 35.0%
! GTGTGATATTCAAGTGTTGT+TGG + chr8.1:27077580-27077599 None:intergenic 35.0%
! GTGTTGTTGGAAATTGACAT+TGG + chr8.1:27077567-27077586 None:intergenic 35.0%
! TGTCAACCTTTTCAAATGGT+GGG - chr8.1:27078061-27078080 MS.gene011816:CDS 35.0%
! TTGTCAACCTTTTCAAATGG+TGG - chr8.1:27078060-27078079 MS.gene011816:CDS 35.0%
AAAGAATTCGACTGCGAGTA+AGG + chr8.1:27077635-27077654 None:intergenic 40.0%
AGATCACAATCACACATTGG+TGG - chr8.1:27077962-27077981 MS.gene011816:CDS 40.0%
GAAGAAACAAGTTCACACGT+TGG - chr8.1:27077919-27077938 MS.gene011816:CDS 40.0%
GATTCGGGATCGATATGTAT+AGG + chr8.1:27077719-27077738 None:intergenic 40.0%
GCTAAGCAATTGTTTGGAAG+TGG + chr8.1:27078089-27078108 None:intergenic 40.0%
GTCGACATAGTGAAAACTGA+CGG - chr8.1:27077356-27077375 MS.gene011816:CDS 40.0%
GTGATTTCTTGGTAAGTGGT+GGG + chr8.1:27077458-27077477 None:intergenic 40.0%
TTCACACGTTGGAACAAGTA+GGG - chr8.1:27077930-27077949 MS.gene011816:CDS 40.0%
TTGACATTGGAGTGTAGAAG+TGG + chr8.1:27077554-27077573 None:intergenic 40.0%
! CATTGAAGCAGTGTCCATTT+TGG + chr8.1:27077867-27077886 None:intergenic 40.0%
! GGGTTGTCAACCTTTTCAAA+TGG - chr8.1:27078057-27078076 MS.gene011816:CDS 40.0%
!! CAGTGTTGTTGGTGATTTCT+TGG + chr8.1:27077469-27077488 None:intergenic 40.0%
!! GAAGAGTTGGTTTGAAGAGA+TGG + chr8.1:27077605-27077624 None:intergenic 40.0%
!! GTGGAGATGATAGTGCATTT+TGG + chr8.1:27077511-27077530 None:intergenic 40.0%
!! GTGGTGGGAGTGTTATAAAA+AGG + chr8.1:27077443-27077462 None:intergenic 40.0%
!! GTTGGTGATTTCTTGGTAAG+TGG + chr8.1:27077462-27077481 None:intergenic 40.0%
AGTACCTGGTGGAACCAAAA+TGG - chr8.1:27077850-27077869 MS.gene011816:CDS 45.0%
AGTGAAAACTGACGGAAGCA+TGG - chr8.1:27077364-27077383 MS.gene011816:CDS 45.0%
ATATCGATCCCGAATCCGTT+AGG - chr8.1:27077723-27077742 MS.gene011816:CDS 45.0%
ATCCACAAAGTGTAGCTGCT+AGG - chr8.1:27077780-27077799 MS.gene011816:CDS 45.0%
GAAGGGAAAGGATAAGTGAG+AGG - chr8.1:27077807-27077826 MS.gene011816:CDS 45.0%
GGTGATTTCTTGGTAAGTGG+TGG + chr8.1:27077459-27077478 None:intergenic 45.0%
GTGGAACCCACCATTTGAAA+AGG + chr8.1:27078070-27078089 None:intergenic 45.0%
GTTCACACGTTGGAACAAGT+AGG - chr8.1:27077929-27077948 MS.gene011816:CDS 45.0%
TCACAATCACACATTGGTGG+TGG - chr8.1:27077965-27077984 MS.gene011816:CDS 45.0%
TCACACGTTGGAACAAGTAG+GGG - chr8.1:27077931-27077950 MS.gene011816:CDS 45.0%
TGTAGCTGCTAGGCATAGAA+GGG - chr8.1:27077790-27077809 MS.gene011816:CDS 45.0%
TTCACATTCCTTCTCTTCGG+CGG + chr8.1:27077749-27077768 None:intergenic 45.0%
!! ATTGGTGGTGGATTCATTGG+AGG - chr8.1:27077977-27077996 MS.gene011816:CDS 45.0%
!! CACATTGGTGGTGGATTCAT+TGG - chr8.1:27077974-27077993 MS.gene011816:CDS 45.0%
!! GAGTTGGTTTGAAGAGATGG+TGG + chr8.1:27077602-27077621 None:intergenic 45.0%
!! TTGGTGGTGGATTCATTGGA+GGG - chr8.1:27077978-27077997 MS.gene011816:CDS 45.0%
AGAATTCGATGGCAGCGATG+AGG - chr8.1:27077663-27077682 MS.gene011816:CDS 50.0%
CTGCTAGGCATAGAAGGGAA+AGG - chr8.1:27077795-27077814 MS.gene011816:CDS 50.0%
GAATTCGATGGCAGCGATGA+GGG - chr8.1:27077664-27077683 MS.gene011816:CDS 50.0%
GTGTAGCTGCTAGGCATAGA+AGG - chr8.1:27077789-27077808 MS.gene011816:CDS 50.0%
TGCCTAGCAGCTACACTTTG+TGG + chr8.1:27077785-27077804 None:intergenic 50.0%
!!! GTGTCCATTTTGGTTCCACC+AGG + chr8.1:27077857-27077876 None:intergenic 50.0%
CCTTCTCTTCGGCGGCCTAA+CGG + chr8.1:27077741-27077760 None:intergenic 60.0%
!! CTTCGGCGGCCTAACGGATT+CGG + chr8.1:27077735-27077754 None:intergenic 60.0%
!! TTCGGCGGCCTAACGGATTC+GGG + chr8.1:27077734-27077753 None:intergenic 60.0%
CCGTTAGGCCGCCGAAGAGA+AGG - chr8.1:27077738-27077757 MS.gene011816:CDS 65.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 27077350 27078111 27077350 ID=MS.gene011816
chr8.1 mRNA 27077350 27078111 27077350 ID=MS.gene011816.t1;Parent=MS.gene011816
chr8.1 exon 27077350 27078111 27077350 ID=MS.gene011816.t1.exon1;Parent=MS.gene011816.t1
chr8.1 CDS 27077350 27078111 27077350 ID=cds.MS.gene011816.t1;Parent=MS.gene011816.t1
Gene Sequence

>MS.gene011816

ATGGATGTCGACATAGTGAAAACTGACGGAAGCATGGACATGATAGCAATGATGATGCAAATGGAAAAGTTCCCTGAATTCTCTGATCAACCTTTTTATAACACTCCCACCACTTACCAAGAAATCACCAACAACACTGTTCCATTATTTAACCTTAACCAAAATGCACTATCATCTCCACAAACTTTGAATAATATTGATCCACTTCTACACTCCAATGTCAATTTCCAACAACACTTGAATATCACACCACCATCTCTTCAAACCAACTCTTCATCATTTCCTTACTCGCAGTCGAATTCTTTTGAAAAGAAGAATTCGATGGCAGCGATGAGGGAAATGATATTTAGAATAGCAGTGATGCAACCTATACATATCGATCCCGAATCCGTTAGGCCGCCGAAGAGAAGGAATGTGAAGATATCAAAGGATCCACAAAGTGTAGCTGCTAGGCATAGAAGGGAAAGGATAAGTGAGAGGATAAGGATATTACAAAGATTAGTACCTGGTGGAACCAAAATGGACACTGCTTCAATGTTAGATGAAGCTATACATTATGTGAAGTTTTTGAAGAAACAAGTTCACACGTTGGAACAAGTAGGGGCTAATAATAGATCACAATCACACATTGGTGGTGGATTCATTGGAGGGAATAATATGATGAACAATTTTAATAATGTGAATTATAATTCTGGTTTGATGATGAAGGGTTGTCAACCTTTTCAAATGGTGGGTTCCACTTCCAAACAATTGCTTAGCTAG
Protein sequence

>MS.gene011816.t1

MDVDIVKTDGSMDMIAMMMQMEKFPEFSDQPFYNTPTTYQEITNNTVPLFNLNQNALSSPQTLNNIDPLLHSNVNFQQHLNITPPSLQTNSSSFPYSQSNSFEKKNSMAAMREMIFRIAVMQPIHIDPESVRPPKRRNVKISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQVHTLEQVGANNRSQSHIGGGFIGGNNMMNNFNNVNYNSGLMMKGCQPFQMVGSTSKQLLS