AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043346

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043346.t1 MTR_2g089670 84.962 266 37 1 1 266 21 283 1.71e-157 447
MS.gene043346.t1 MTR_2g089765 79.245 265 50 4 2 266 16 275 4.65e-146 418
MS.gene043346.t1 MTR_2g089665 72.556 266 34 1 1 266 1 227 1.35e-132 379
MS.gene043346.t1 MTR_8g012750 65.428 269 82 7 2 267 3 263 7.50e-114 336
MS.gene043346.t1 MTR_7g015860 47.761 268 122 7 2 266 5 257 9.86e-70 222
MS.gene043346.t1 MTR_3g028210 48.925 186 89 4 1 185 7 187 1.18e-46 162
MS.gene043346.t1 MTR_7g014330 46.512 215 97 8 1 213 1 199 2.74e-44 155
MS.gene043346.t1 MTR_2g089650 37.868 272 141 9 2 266 9 259 3.96e-43 153
MS.gene043346.t1 MTR_3g435300 37.050 278 138 12 3 266 4 258 3.21e-42 145
MS.gene043346.t1 MTR_6g015850 45.699 186 89 4 2 184 8 184 4.01e-41 147
MS.gene043346.t1 MTR_7g014230 44.737 190 94 5 3 190 5 185 3.11e-40 145
MS.gene043346.t1 MTR_6g015815 44.681 188 92 4 3 187 9 187 5.67e-40 144
MS.gene043346.t1 MTR_7g014250 42.326 215 106 8 1 213 1 199 1.57e-37 137
MS.gene043346.t1 MTR_6g015830 43.147 197 99 5 2 194 8 195 2.79e-37 137
MS.gene043346.t1 MTR_3g087640 42.424 198 95 7 3 189 10 199 5.81e-37 136
MS.gene043346.t1 MTR_2g089755 36.626 243 118 10 39 266 50 271 2.00e-36 135
MS.gene043346.t1 MTR_7g014200 38.197 233 122 9 2 229 9 224 3.40e-36 134
MS.gene043346.t1 MTR_2g089735 46.753 154 75 4 39 188 39 189 4.28e-34 128
MS.gene043346.t1 MTR_7g014160 37.727 220 122 6 2 217 9 217 2.16e-33 127
MS.gene043346.t1 MTR_6g015320 40.426 188 102 4 7 193 11 189 3.19e-33 126
MS.gene043346.t1 MTR_7g014630 37.736 212 116 7 2 208 9 209 1.36e-31 120
MS.gene043346.t1 MTR_7g014610 39.896 193 101 6 2 190 8 189 8.33e-29 114
MS.gene043346.t1 MTR_7g014180 37.989 179 96 6 2 176 7 174 9.14e-28 105
MS.gene043346.t1 MTR_7g014620 37.629 194 107 6 21 209 11 195 5.43e-27 108
MS.gene043346.t1 MTR_6g015315 37.566 189 98 5 25 212 26 195 1.29e-23 99.8
MS.gene043346.t1 MTR_7g013850 35.500 200 104 9 26 215 30 214 3.04e-23 98.6
MS.gene043346.t1 MTR_7g014360 36.885 122 68 3 72 192 22 135 8.92e-18 82.4
MS.gene043346.t1 MTR_7g014340 59.155 71 27 2 1 70 1 70 4.65e-15 69.7
MS.gene043346.t1 MTR_6g015310 33.813 139 74 3 74 212 23 143 1.08e-14 73.2
MS.gene043346.t1 MTR_7g014220 59.375 64 25 1 17 80 10 72 1.23e-13 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.gene043346.t1 AT1G03940 40.741 270 135 9 3 266 9 259 2.23e-50 172
MS.gene043346.t1 AT1G03495 40.149 269 136 9 4 266 10 259 1.03e-49 167
MS.gene043346.t1 AT3G29670 34.799 273 150 11 2 266 3 255 6.29e-29 114
MS.gene043346.t1 AT5G39080 31.884 276 157 10 2 266 5 260 4.51e-27 109
MS.gene043346.t1 AT5G39090 37.566 189 107 5 2 188 5 184 6.31e-26 106
MS.gene043346.t1 AT3G29680 38.624 189 104 6 2 188 3 181 2.41e-24 101
MS.gene043346.t1 AT3G29590 37.433 187 97 8 2 184 8 178 2.72e-24 101
MS.gene043346.t1 AT5G61160 35.079 191 110 7 2 188 3 183 1.76e-23 99.4
MS.gene043346.t1 AT3G29635 35.052 194 109 7 2 188 3 186 8.35e-21 91.7
MS.gene043346.t1 AT5G39050 36.702 188 110 5 2 188 10 189 4.79e-20 89.7

Find 67 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATCATTTCATGAAATTT+TGG 0.059044 2.2:-10244041 MS.gene043346:CDS
GGAGGGGTGTTATGGGAATT+TGG 0.229278 2.2:+10244318 None:intergenic
TCACTTTCTTCGACATTTCA+TGG 0.242024 2.2:-10244494 MS.gene043346:CDS
ATTCACAAGATGCTCTAAAT+TGG 0.287826 2.2:-10244215 MS.gene043346:CDS
ATGATGAGGTTGGAGGAAAA+AGG 0.329263 2.2:+10244345 None:intergenic
TAAGCACTCCATCTCTTTCA+TGG 0.346789 2.2:+10243935 None:intergenic
GTATATAAGGAGGGGTGTTA+TGG 0.354673 2.2:+10244310 None:intergenic
TCTTGTAAGTTGGTGAGTTT+AGG 0.362354 2.2:+10243898 None:intergenic
CAGATAGAGAAGCCAGAGTT+TGG 0.386262 2.2:+10244102 None:intergenic
GAAGAAGTGTTGGAGGGTTA+AGG 0.387404 2.2:+10244368 None:intergenic
GTATGAGGTGAAGGCAAGTT+AGG 0.400483 2.2:+10244180 None:intergenic
GGTTGGTGATGGAAGTGAAT+TGG 0.400909 2.2:+10244527 None:intergenic
GTTGGTGATGGAAGTGAATT+GGG 0.408787 2.2:+10244528 None:intergenic
TATATAAGGAGGGGTGTTAT+GGG 0.421407 2.2:+10244311 None:intergenic
ATTTGGAGGGATGATGAGGT+TGG 0.424629 2.2:+10244335 None:intergenic
GGAAAGTGAGTGTTTGAGAA+TGG 0.424878 2.2:+10244389 None:intergenic
ATCTTGTATTTCTTGTAAGT+TGG 0.431916 2.2:+10243888 None:intergenic
GAATGGGAAGTGTTGTTTGT+AGG 0.432621 2.2:+10244406 None:intergenic
GAAGCCAGAGTTTGGTAGAA+TGG 0.432626 2.2:+10244110 None:intergenic
TCATCAAGGTAACGTATATA+AGG 0.436544 2.2:+10244297 None:intergenic
GTTGAAGTCTGCTGAAGATT+CGG 0.441740 2.2:+10244251 None:intergenic
GATGAGTTGGATGAGGAAAA+TGG 0.445046 2.2:+10244433 None:intergenic
AAAGTGAGAGGGAGAGTGGT+TGG 0.459506 2.2:+10244510 None:intergenic
GAAAGTGAGTGTTTGAGAAT+GGG 0.469129 2.2:+10244390 None:intergenic
TTGGTGAGTTTAGGAGCCGT+TGG 0.469411 2.2:+10243907 None:intergenic
GAAGAAAGTGAGAGGGAGAG+TGG 0.476197 2.2:+10244506 None:intergenic
AGAGGGAGAGTGGTTGGTGA+TGG 0.482203 2.2:+10244516 None:intergenic
CAACAACACAGTTATGTTGA+AGG 0.488066 2.2:-10244580 None:intergenic
GGGAATTTGGAGGGATGATG+AGG 0.494796 2.2:+10244331 None:intergenic
GATGGAAGTGAATTGGGTGG+TGG 0.495893 2.2:+10244534 None:intergenic
TGGAGGGATGATGAGGTTGG+AGG 0.507278 2.2:+10244338 None:intergenic
TACATGTATCGTTCCTCTCA+TGG 0.508285 2.2:-10244145 MS.gene043346:CDS
GTTTGTAGGAAGTGATGAGT+TGG 0.516421 2.2:+10244420 None:intergenic
TGGTAGAATGGTGATTTGAA+TGG 0.518937 2.2:+10244122 None:intergenic
GGGGTGTTATGGGAATTTGG+AGG 0.522455 2.2:+10244321 None:intergenic
TGGTGAGTTTAGGAGCCGTT+GGG 0.523739 2.2:+10243908 None:intergenic
AAGCACTCCATCTCTTTCAT+GGG 0.531994 2.2:+10243936 None:intergenic
TACAACCATGTCGCTGCAGA+CGG 0.546173 2.2:-10244072 MS.gene043346:CDS
TGAAGATTCGGCAACGGTGA+AGG 0.551527 2.2:+10244263 None:intergenic
CTTCCTTCCCATGAAAGAGA+TGG 0.561446 2.2:-10243943 MS.gene043346:CDS
ATCACCATTCTACCAAACTC+TGG 0.574194 2.2:-10244114 MS.gene043346:CDS
CAAGGTAACGTATATAAGGA+GGG 0.577627 2.2:+10244301 None:intergenic
ACTCCATCTCTTTCATGGGA+AGG 0.579240 2.2:+10243940 None:intergenic
AATTGGGTGGTGGTGCAACT+TGG 0.579309 2.2:+10244544 None:intergenic
TGTTGTACGCGGATGACTGA+AGG 0.582588 2.2:-10243771 None:intergenic
AGGAAGTGATGAGTTGGATG+AGG 0.585446 2.2:+10244426 None:intergenic
GGGTGTTATGGGAATTTGGA+GGG 0.588819 2.2:+10244322 None:intergenic
TCAAGGTAACGTATATAAGG+AGG 0.593641 2.2:+10244300 None:intergenic
TGCATCTCGAACGAGACTTG+TGG 0.601182 2.2:+10243843 None:intergenic
TCACCTCATACAGAACAAAA+CGG 0.603095 2.2:-10244168 MS.gene043346:CDS
GTCTGCTGAAGATTCGGCAA+CGG 0.604958 2.2:+10244257 None:intergenic
CAGCGACATGGTTGTAAGTG+AGG 0.605491 2.2:+10244079 None:intergenic
AAAAGGGAAGAAGTGTTGGA+GGG 0.615109 2.2:+10244362 None:intergenic
GGTGATGGAAGTGAATTGGG+TGG 0.622854 2.2:+10244531 None:intergenic
AGATGCAGCTTACGCTAACA+AGG 0.622869 2.2:-10243827 MS.gene043346:CDS
TCATGGGAAGGAAGATCAAG+AGG 0.626174 2.2:+10243952 None:intergenic
AAATGTCGAAGAAAGTGAGA+GGG 0.639421 2.2:+10244499 None:intergenic
GAAATGTCGAAGAAAGTGAG+AGG 0.646541 2.2:+10244498 None:intergenic
AAGGCAAGTTAGGAACAAGA+TGG 0.656225 2.2:+10244190 None:intergenic
AGGAGATAGAGTCTTCATCA+AGG 0.656629 2.2:+10244283 None:intergenic
GTGATTTGAATGGCCATGAG+AGG 0.670330 2.2:+10244132 None:intergenic
TGGAGTGCTTAAACACCCAA+CGG 0.672231 2.2:-10243923 MS.gene043346:CDS
TGGGAAGGAAGATCAAGAGG+CGG 0.672634 2.2:+10243955 None:intergenic
AAGGTAACGTATATAAGGAG+GGG 0.677863 2.2:+10244302 None:intergenic
CATCTTGTGAATCAGATACG+AGG 0.681815 2.2:+10244226 None:intergenic
GAAGAAGATACGTTTAACAG+CGG 0.689203 2.2:+10244458 None:intergenic
TCGTGAAGAAGTGTTGTACG+CGG 0.803377 2.2:-10243782 MS.gene043346:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGAAATACAAGATTTTGTTT+TGG - chr2.2:10244463-10244482 MS.gene043346:CDS 20.0%
!!! TCATCATTTCATGAAATTTT+GGG - chr2.2:10244301-10244320 MS.gene043346:CDS 20.0%
!!! TTCATCATTTCATGAAATTT+TGG - chr2.2:10244300-10244319 MS.gene043346:CDS 20.0%
! ATCTTGTATTTCTTGTAAGT+TGG + chr2.2:10244456-10244475 None:intergenic 25.0%
!!! GTTGTTATTGTTTTTTGCTA+TGG + chr2.2:10244342-10244361 None:intergenic 25.0%
TCATCAAGGTAACGTATATA+AGG + chr2.2:10244047-10244066 None:intergenic 30.0%
! ATTCACAAGATGCTCTAAAT+TGG - chr2.2:10244126-10244145 MS.gene043346:CDS 30.0%
!!! AGATTTTGTTTTGGAAGTCA+TGG - chr2.2:10244472-10244491 MS.gene043346:CDS 30.0%
AAATGTCGAAGAAAGTGAGA+GGG + chr2.2:10243845-10243864 None:intergenic 35.0%
AAGGTAACGTATATAAGGAG+GGG + chr2.2:10244042-10244061 None:intergenic 35.0%
CAAGGTAACGTATATAAGGA+GGG + chr2.2:10244043-10244062 None:intergenic 35.0%
GAAAGTGAGTGTTTGAGAAT+GGG + chr2.2:10243954-10243973 None:intergenic 35.0%
GAAGAAGATACGTTTAACAG+CGG + chr2.2:10243886-10243905 None:intergenic 35.0%
TCAAGGTAACGTATATAAGG+AGG + chr2.2:10244044-10244063 None:intergenic 35.0%
TCACCTCATACAGAACAAAA+CGG - chr2.2:10244173-10244192 MS.gene043346:CDS 35.0%
TCACTTTCTTCGACATTTCA+TGG - chr2.2:10243847-10243866 MS.gene043346:CDS 35.0%
TGGTAGAATGGTGATTTGAA+TGG + chr2.2:10244222-10244241 None:intergenic 35.0%
! TTTTGTTCTGTATGAGGTGA+AGG + chr2.2:10244173-10244192 None:intergenic 35.0%
!! TATATAAGGAGGGGTGTTAT+GGG + chr2.2:10244033-10244052 None:intergenic 35.0%
!! TCTTGTAAGTTGGTGAGTTT+AGG + chr2.2:10244446-10244465 None:intergenic 35.0%
AAGCACTCCATCTCTTTCAT+GGG + chr2.2:10244408-10244427 None:intergenic 40.0%
AAGGCAAGTTAGGAACAAGA+TGG + chr2.2:10244154-10244173 None:intergenic 40.0%
AGGAGATAGAGTCTTCATCA+AGG + chr2.2:10244061-10244080 None:intergenic 40.0%
ATCACCATTCTACCAAACTC+TGG - chr2.2:10244227-10244246 MS.gene043346:CDS 40.0%
ATGATGAGGTTGGAGGAAAA+AGG + chr2.2:10243999-10244018 None:intergenic 40.0%
CATCTTGTGAATCAGATACG+AGG + chr2.2:10244118-10244137 None:intergenic 40.0%
GAAATGTCGAAGAAAGTGAG+AGG + chr2.2:10243846-10243865 None:intergenic 40.0%
GGAAAGTGAGTGTTTGAGAA+TGG + chr2.2:10243955-10243974 None:intergenic 40.0%
GTTGAAGTCTGCTGAAGATT+CGG + chr2.2:10244093-10244112 None:intergenic 40.0%
GTTTGTAGGAAGTGATGAGT+TGG + chr2.2:10243924-10243943 None:intergenic 40.0%
TAAGCACTCCATCTCTTTCA+TGG + chr2.2:10244409-10244428 None:intergenic 40.0%
TACATGTATCGTTCCTCTCA+TGG - chr2.2:10244196-10244215 MS.gene043346:CDS 40.0%
TGATGAGGTTGGAGGAAAAA+GGG + chr2.2:10243998-10244017 None:intergenic 40.0%
! AGGAAAAAGGGAAGAAGTGT+TGG + chr2.2:10243986-10244005 None:intergenic 40.0%
! GATGAGTTGGATGAGGAAAA+TGG + chr2.2:10243911-10243930 None:intergenic 40.0%
!! AAAAAGGGAAGAAGTGTTGG+AGG + chr2.2:10243983-10244002 None:intergenic 40.0%
!! AAAAGGGAAGAAGTGTTGGA+GGG + chr2.2:10243982-10244001 None:intergenic 40.0%
!! GAATGGGAAGTGTTGTTTGT+AGG + chr2.2:10243938-10243957 None:intergenic 40.0%
!! GTACCGTTTTGTTCTGTATG+AGG + chr2.2:10244179-10244198 None:intergenic 40.0%
!! GTATATAAGGAGGGGTGTTA+TGG + chr2.2:10244034-10244053 None:intergenic 40.0%
!! GTTGGTGATGGAAGTGAATT+GGG + chr2.2:10243816-10243835 None:intergenic 40.0%
!! TGCTATGGCTTTTGAAAGAG+AGG + chr2.2:10244327-10244346 None:intergenic 40.0%
ACTCCATCTCTTTCATGGGA+AGG + chr2.2:10244404-10244423 None:intergenic 45.0%
AGATGCAGCTTACGCTAACA+AGG - chr2.2:10244514-10244533 MS.gene043346:CDS 45.0%
ATTTGGAGGGATGATGAGGT+TGG + chr2.2:10244009-10244028 None:intergenic 45.0%
CAGATAGAGAAGCCAGAGTT+TGG + chr2.2:10244242-10244261 None:intergenic 45.0%
CTTCCTTCCCATGAAAGAGA+TGG - chr2.2:10244398-10244417 MS.gene043346:CDS 45.0%
GAAGCCAGAGTTTGGTAGAA+TGG + chr2.2:10244234-10244253 None:intergenic 45.0%
GTATGAGGTGAAGGCAAGTT+AGG + chr2.2:10244164-10244183 None:intergenic 45.0%
GTGATTTGAATGGCCATGAG+AGG + chr2.2:10244212-10244231 None:intergenic 45.0%
TCATGGGAAGGAAGATCAAG+AGG + chr2.2:10244392-10244411 None:intergenic 45.0%
! AGGAAGTGATGAGTTGGATG+AGG + chr2.2:10243918-10243937 None:intergenic 45.0%
! GGGTGTTATGGGAATTTGGA+GGG + chr2.2:10244022-10244041 None:intergenic 45.0%
! TGGAGTGCTTAAACACCCAA+CGG - chr2.2:10244418-10244437 MS.gene043346:CDS 45.0%
!! GAAGAAGTGTTGGAGGGTTA+AGG + chr2.2:10243976-10243995 None:intergenic 45.0%
!! GGTTGGTGATGGAAGTGAAT+TGG + chr2.2:10243817-10243836 None:intergenic 45.0%
!! TCGTGAAGAAGTGTTGTACG+CGG - chr2.2:10244559-10244578 MS.gene043346:CDS 45.0%
AAAGTGAGAGGGAGAGTGGT+TGG + chr2.2:10243834-10243853 None:intergenic 50.0%
CAGCGACATGGTTGTAAGTG+AGG + chr2.2:10244265-10244284 None:intergenic 50.0%
GAAGAAAGTGAGAGGGAGAG+TGG + chr2.2:10243838-10243857 None:intergenic 50.0%
GATGGAAGTGAATTGGGTGG+TGG + chr2.2:10243810-10243829 None:intergenic 50.0%
GGGAATTTGGAGGGATGATG+AGG + chr2.2:10244013-10244032 None:intergenic 50.0%
GTCTGCTGAAGATTCGGCAA+CGG + chr2.2:10244087-10244106 None:intergenic 50.0%
TACAACCATGTCGCTGCAGA+CGG - chr2.2:10244269-10244288 MS.gene043346:CDS 50.0%
TGAAGATTCGGCAACGGTGA+AGG + chr2.2:10244081-10244100 None:intergenic 50.0%
TGCATCTCGAACGAGACTTG+TGG + chr2.2:10244501-10244520 None:intergenic 50.0%
TGGGAAGGAAGATCAAGAGG+CGG + chr2.2:10244389-10244408 None:intergenic 50.0%
TGGTGAGTTTAGGAGCCGTT+GGG + chr2.2:10244436-10244455 None:intergenic 50.0%
TTGGTGAGTTTAGGAGCCGT+TGG + chr2.2:10244437-10244456 None:intergenic 50.0%
! AATTGGGTGGTGGTGCAACT+TGG + chr2.2:10243800-10243819 None:intergenic 50.0%
! ATTTTCCGTCTGCAGCGACA+TGG + chr2.2:10244277-10244296 None:intergenic 50.0%
! GGGGTGTTATGGGAATTTGG+AGG + chr2.2:10244023-10244042 None:intergenic 50.0%
!! GGAGGGGTGTTATGGGAATT+TGG + chr2.2:10244026-10244045 None:intergenic 50.0%
!! GGTGATGGAAGTGAATTGGG+TGG + chr2.2:10243813-10243832 None:intergenic 50.0%
TGGAGGGATGATGAGGTTGG+AGG + chr2.2:10244006-10244025 None:intergenic 55.0%
!! AGAGGGAGAGTGGTTGGTGA+TGG + chr2.2:10243828-10243847 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 10243774 10244589 10243774 ID=MS.gene043346
chr2.2 mRNA 10243774 10244589 10243774 ID=MS.gene043346.t1;Parent=MS.gene043346
chr2.2 exon 10243774 10244589 10243774 ID=MS.gene043346.t1.exon1;Parent=MS.gene043346.t1
chr2.2 CDS 10243774 10244589 10243774 ID=cds.MS.gene043346.t1;Parent=MS.gene043346.t1
Gene Sequence

>MS.gene043346

ATGTTGAAGGTAATTGAACATAGCCAAGTTGCACCACCACCCAATTCACTTCCATCACCAACCACTCTCCCTCTCACTTTCTTCGACATTTCATGGCTTTACTGTCAATCCGCTGTTAAACGTATCTTCTTCTACCATTTTCCTCATCCAACTCATCACTTCCTACAAACAACACTTCCCATTCTCAAACACTCACTTTCCTTAACCCTCCAACACTTCTTCCCTTTTTCCTCCAACCTCATCATCCCTCCAAATTCCCATAACACCCCTCCTTATATACGTTACCTTGATGAAGACTCTATCTCCTTCACCGTTGCCGAATCTTCAGCAGACTTCAACATCCTCGTATCTGATTCACAAGATGCTCTAAATTGGCACCATCTTGTTCCTAACTTGCCTTCACCTCATACAGAACAAAACGGTACATGTATCGTTCCTCTCATGGCCATTCAAATCACCATTCTACCAAACTCTGGCTTCTCTATCTGCCTCACTTACAACCATGTCGCTGCAGACGGAAAATCACTTCATCATTTCATGAAATTTTGGGCCTCTCTTTCAAAAGCCATAGCAAAAAACAATAACAACAATAATTTGTCTCTTGAATACTCTCCGCCTCTTGATCTTCCTTCCCATGAAAGAGATGGAGTGCTTAAACACCCAACGGCTCCTAAACTCACCAACTTACAAGAAATACAAGATTTTGTTTTGGAAGTCATGGAATCCACAAGTCTCGTTCGAGATGCAGCTTACGCTAACAAGGTACGAACTAGTTTAGTATTGAGTCGTGAAGAAGTGTTGTACGCGGATGACTGA
Protein sequence

>MS.gene043346.t1

MLKVIEHSQVAPPPNSLPSPTTLPLTFFDISWLYCQSAVKRIFFYHFPHPTHHFLQTTLPILKHSLSLTLQHFFPFSSNLIIPPNSHNTPPYIRYLDEDSISFTVAESSADFNILVSDSQDALNWHHLVPNLPSPHTEQNGTCIVPLMAIQITILPNSGFSICLTYNHVAADGKSLHHFMKFWASLSKAIAKNNNNNNLSLEYSPPLDLPSHERDGVLKHPTAPKLTNLQEIQDFVLEVMESTSLVRDAAYANKVRTSLVLSREEVLYADD