AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene016098

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016098.t1 MTR_1g013760 96.591 176 5 1 5 179 1 176 2.70e-124 351
MS.gene016098.t1 MTR_3g106060 60.656 183 55 6 5 179 1 174 4.61e-65 201
MS.gene016098.t1 MTR_2g105060 50.323 155 67 3 28 179 58 205 1.96e-40 139
MS.gene016098.t1 MTR_2g105060 49.265 136 59 3 47 179 2 130 7.85e-33 117
MS.gene016098.t1 MTR_4g007060 43.949 157 73 3 29 179 17 164 1.46e-29 110
MS.gene016098.t1 MTR_4g007060 42.690 171 80 4 15 179 40 198 1.54e-29 108
MS.gene016098.t1 MTR_4g007060 43.860 171 78 5 15 179 40 198 2.33e-29 110
MS.gene016098.t1 MTR_1g013790 41.791 134 73 2 50 179 5 137 7.05e-25 97.4
MS.gene016098.t1 MTR_7g110720 30.978 184 111 4 10 179 71 252 1.09e-18 82.8
MS.gene016098.t1 MTR_7g110720 30.939 181 88 4 10 179 71 225 6.91e-18 80.5
MS.gene016098.t1 MTR_3g053330 27.074 229 113 5 5 179 59 287 3.14e-15 72.8
MS.gene016098.t1 MTR_4g132430 28.191 188 90 5 29 179 118 297 4.99e-15 72.4
MS.gene016098.t1 MTR_4g094412 50.877 57 28 0 123 179 223 279 1.53e-14 70.9
MS.gene016098.t1 MTR_4g094412 50.877 57 28 0 123 179 214 270 1.53e-14 70.9
MS.gene016098.t1 MTR_7g009730 51.852 54 26 0 126 179 202 255 1.68e-14 70.9
MS.gene016098.t1 MTR_4g107970 53.704 54 25 0 126 179 238 291 5.45e-14 69.3
MS.gene016098.t1 MTR_4g107970 53.704 54 25 0 126 179 161 214 6.97e-14 68.9
MS.gene016098.t1 MTR_2g045360 55.102 49 22 0 131 179 199 247 1.26e-13 68.2
MS.gene016098.t1 MTR_2g023930 51.923 52 25 0 128 179 290 341 4.67e-13 66.6
MS.gene016098.t1 MTR_4g132430 51.923 52 25 0 128 179 112 163 7.18e-13 65.9
MS.gene016098.t1 MTR_2g088000 51.923 52 25 0 128 179 334 385 9.68e-13 65.9
MS.gene016098.t1 MTR_4g049760 51.923 52 25 0 128 179 275 326 1.88e-12 65.1
MS.gene016098.t1 MTR_5g097490 56.863 51 19 2 128 178 239 286 1.04e-11 62.8
MS.gene016098.t1 MTR_5g074400 42.254 71 34 4 109 178 390 454 1.41e-11 62.4
MS.gene016098.t1 MTR_4g049790 50.980 51 25 0 128 178 297 347 2.72e-11 61.6
MS.gene016098.t1 MTR_5g094430 65.714 35 11 1 144 178 253 286 3.80e-11 61.2
MS.gene016098.t1 MTR_5g094430 65.714 35 11 1 144 178 231 264 3.90e-11 60.8
MS.gene016098.t1 MTR_5g094430 65.714 35 11 1 144 178 365 398 3.92e-11 61.2
MS.gene016098.t1 MTR_3g031220 50.980 51 22 2 128 178 352 399 5.02e-11 60.8
MS.gene016098.t1 MTR_3g056100 65.714 35 11 1 144 178 403 436 6.86e-11 60.5
MS.gene016098.t1 MTR_3g056100 65.714 35 11 1 144 178 416 449 7.02e-11 60.5
MS.gene016098.t1 MTR_3g056100 65.714 35 11 1 144 178 259 292 7.30e-11 60.1
MS.gene016098.t1 MTR_3g056100 65.714 35 11 1 144 178 272 305 7.44e-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.gene016098.t1 AT1G80840 46.111 180 87 4 7 179 6 182 1.10e-41 142
MS.gene016098.t1 AT4G31800 39.252 214 84 7 7 179 4 212 4.02e-34 122
MS.gene016098.t1 AT4G31800 42.012 169 75 4 29 179 49 212 6.28e-34 120
MS.gene016098.t1 AT2G25000 39.286 168 70 6 23 179 36 182 2.04e-29 109
MS.gene016098.t1 AT2G25000 39.375 160 68 5 28 179 1 139 3.57e-29 107
MS.gene016098.t1 AT2G25000 39.375 160 68 5 28 179 1 139 3.57e-29 107
MS.gene016098.t1 AT2G25000 37.931 174 78 6 14 179 10 161 6.17e-29 107
MS.gene016098.t1 AT4G31800 39.735 151 68 4 47 179 2 147 4.72e-27 102
MS.gene016098.t1 AT4G01720 29.545 176 91 4 32 179 105 275 1.49e-14 70.9
MS.gene016098.t1 AT1G62300 27.513 189 99 5 29 179 160 348 1.15e-13 68.6
MS.gene016098.t1 AT4G22070 51.923 52 25 0 128 179 282 333 1.44e-13 68.2
MS.gene016098.t1 AT4G22070 51.923 52 25 0 128 179 282 333 1.44e-13 68.2
MS.gene016098.t1 AT4G22070 51.923 52 25 0 128 179 282 333 1.44e-13 68.2
MS.gene016098.t1 AT4G22070 51.923 52 25 0 128 179 282 333 1.44e-13 68.2
MS.gene016098.t1 AT5G15130 66.667 36 12 0 144 179 228 263 2.67e-13 67.4
MS.gene016098.t1 AT1G68150 50.000 62 30 1 119 179 210 271 2.93e-13 67.0
MS.gene016098.t1 AT5G15130 66.667 36 12 0 144 179 186 221 3.05e-13 67.4
MS.gene016098.t1 AT4G04450 51.923 52 25 0 128 179 183 234 4.02e-13 67.0
MS.gene016098.t1 AT4G04450 51.923 52 25 0 128 179 277 328 4.15e-13 67.0
MS.gene016098.t1 AT1G18860 66.667 36 12 0 144 179 240 275 1.58e-12 65.1
MS.gene016098.t1 AT1G69810 51.923 52 25 0 128 179 188 239 1.48e-11 62.4
MS.gene016098.t1 AT1G69810 51.923 52 25 0 128 179 130 181 1.50e-11 62.0

Find 28 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCTCACCTAAGGCTTATA+AGG 0.237117 1.2:+7843121 MS.gene016098:CDS
TCTTTCTTGATTGTTGTGTT+TGG 0.315541 1.2:-7842971 None:intergenic
GGATATCAATGGAGGAAATA+TGG 0.328462 1.2:+7843354 MS.gene016098:CDS
AATATGTTTGATACTGTTAG+AGG 0.330331 1.2:+7843020 MS.gene016098:CDS
TTATGTGCAGGACGAAGTTT+TGG 0.348061 1.2:+7842824 MS.gene016098:intron
CCTCTCCTAGAGCTTACTTT+AGG 0.371319 1.2:+7843400 MS.gene016098:CDS
ATGAAGAATCATTAATCAAA+AGG 0.454669 1.2:+7843084 MS.gene016098:CDS
ATGGAGGAAATATGGTCAAA+AGG 0.485930 1.2:+7843362 MS.gene016098:CDS
ACAAGAACCTTATAAGCCTT+AGG 0.486641 1.2:-7843128 None:intergenic
CATTAATCAAAAGGCCATGT+AGG 0.493040 1.2:+7843093 MS.gene016098:CDS
TAGGGATATTTCCTCACCTA+AGG 0.500791 1.2:+7843112 MS.gene016098:CDS
AACTGGGCAGCTTGGAGCAT+AGG 0.506437 1.2:-7843427 None:intergenic
TAGTGCTTCTTCTATACTCA+AGG 0.512134 1.2:+7842355 MS.gene016098:CDS
GAGCACCTAAAGTAAGCTCT+AGG 0.538868 1.2:-7843405 None:intergenic
ATTAATCAAAAGGCCATGTA+GGG 0.538909 1.2:+7843094 MS.gene016098:CDS
CCTAAAGTAAGCTCTAGGAG+AGG 0.548395 1.2:-7843400 None:intergenic
CTCATAGTTCTCACACATGT+TGG 0.554828 1.2:-7842901 None:intergenic
CTTTCAGCAGCAAATAACAA+TGG 0.558973 1.2:+7842295 None:intergenic
CTAAAGTAAGCTCTAGGAGA+GGG 0.569732 1.2:-7843399 None:intergenic
GTCTCAGTTCTGAGAACAAG+AGG 0.575865 1.2:+7842862 MS.gene016098:CDS
AACAATGGAATCAACATGCG+TGG 0.589289 1.2:+7842310 MS.gene016098:CDS
GGTATAAAGTATGTGATGGA+TGG 0.592987 1.2:+7843333 MS.gene016098:intron
ATGTGATGGATGGATATCAA+TGG 0.593080 1.2:+7843343 MS.gene016098:CDS
TTGTGGTATAAAGTATGTGA+TGG 0.595565 1.2:+7843329 MS.gene016098:intron
GGTGAGGAAATATCCCTACA+TGG 0.620508 1.2:-7843107 None:intergenic
AACCTTATAAGCCTTAGGTG+AGG 0.658225 1.2:-7843123 None:intergenic
TAAAGTAAGCTCTAGGAGAG+GGG 0.664718 1.2:-7843398 None:intergenic
TGATGGATGGATATCAATGG+AGG 0.669535 1.2:+7843346 MS.gene016098:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTAATATACAATACTTA+GGG - chr1.2:7842635-7842654 None:intergenic 10.0%
!! TATATTAATTTCACTAAAAA+TGG + chr1.2:7842644-7842663 MS.gene016098:intron 10.0%
!! GAAATTAATATACAATACTT+AGG - chr1.2:7842636-7842655 None:intergenic 15.0%
!! TAATTCAATAATGTTGAAAT+TGG + chr1.2:7842667-7842686 MS.gene016098:intron 15.0%
!! TACAAATTCAAAATTAATCA+AGG - chr1.2:7843308-7843327 None:intergenic 15.0%
!!! TAATTTTGAATTTGTATTTG+TGG + chr1.2:7843312-7843331 MS.gene016098:intron 15.0%
!! AATACTTAGGGATATAATAA+AGG - chr1.2:7842623-7842642 None:intergenic 20.0%
!! ATACTTAGGGATATAATAAA+GGG - chr1.2:7842622-7842641 None:intergenic 20.0%
!! ATGAAGAATCATTAATCAAA+AGG + chr1.2:7843084-7843103 MS.gene016098:CDS 20.0%
!!! AATGTCATTCTAAGAAATTT+AGG - chr1.2:7842797-7842816 None:intergenic 20.0%
!!! ATGTCATTCTAAGAAATTTA+GGG - chr1.2:7842796-7842815 None:intergenic 20.0%
! AATATGTTTGATACTGTTAG+AGG + chr1.2:7843020-7843039 MS.gene016098:CDS 25.0%
! CAGTTAATGAAGTAAAATTG+TGG + chr1.2:7843262-7843281 MS.gene016098:intron 25.0%
! TAATACACAATGTCGTATTT+AGG - chr1.2:7842539-7842558 None:intergenic 25.0%
!! AAGCGTTTTTAACAATTTGT+TGG + chr1.2:7842472-7842491 MS.gene016098:intron 25.0%
!! ACATTGAAAATTTTATGTGC+AGG + chr1.2:7842812-7842831 MS.gene016098:intron 25.0%
ATTAATCAAAAGGCCATGTA+GGG + chr1.2:7843094-7843113 MS.gene016098:CDS 30.0%
TCTTTCTTGATTGTTGTGTT+TGG - chr1.2:7842974-7842993 None:intergenic 30.0%
TTGTGGTATAAAGTATGTGA+TGG + chr1.2:7843329-7843348 MS.gene016098:intron 30.0%
ACAAGAACCTTATAAGCCTT+AGG - chr1.2:7843131-7843150 None:intergenic 35.0%
ATGGAGGAAATATGGTCAAA+AGG + chr1.2:7843362-7843381 MS.gene016098:CDS 35.0%
CATTAATCAAAAGGCCATGT+AGG + chr1.2:7843093-7843112 MS.gene016098:CDS 35.0%
GGATATCAATGGAGGAAATA+TGG + chr1.2:7843354-7843373 MS.gene016098:CDS 35.0%
TAGTGCTTCTTCTATACTCA+AGG + chr1.2:7842355-7842374 MS.gene016098:CDS 35.0%
! GGTATAAAGTATGTGATGGA+TGG + chr1.2:7843333-7843352 MS.gene016098:intron 35.0%
!! ATGTGATGGATGGATATCAA+TGG + chr1.2:7843343-7843362 MS.gene016098:CDS 35.0%
!! TTGTTGGTAATAACCCACTT+AGG + chr1.2:7842488-7842507 MS.gene016098:intron 35.0%
AACAATGGAATCAACATGCG+TGG + chr1.2:7842310-7842329 MS.gene016098:CDS 40.0%
AACCTTATAAGCCTTAGGTG+AGG - chr1.2:7843126-7843145 None:intergenic 40.0%
CTCATAGTTCTCACACATGT+TGG - chr1.2:7842904-7842923 None:intergenic 40.0%
TAGGGATATTTCCTCACCTA+AGG + chr1.2:7843112-7843131 MS.gene016098:CDS 40.0%
TGGTAATAACCCACTTAGGT+TGG + chr1.2:7842492-7842511 MS.gene016098:intron 40.0%
TTCCTCACCTAAGGCTTATA+AGG + chr1.2:7843121-7843140 MS.gene016098:CDS 40.0%
TTGGCCTAATGGTATTAGCT+TGG + chr1.2:7842511-7842530 MS.gene016098:intron 40.0%
! TGATGGATGGATATCAATGG+AGG + chr1.2:7843346-7843365 MS.gene016098:CDS 40.0%
! TGGCCTAATGGTATTAGCTT+GGG + chr1.2:7842512-7842531 MS.gene016098:intron 40.0%
! TTATGTGCAGGACGAAGTTT+TGG + chr1.2:7842824-7842843 MS.gene016098:intron 40.0%
!! CTAAAGTAAGCTCTAGGAGA+GGG - chr1.2:7843402-7843421 None:intergenic 40.0%
!! TAAAGTAAGCTCTAGGAGAG+GGG - chr1.2:7843401-7843420 None:intergenic 40.0%
!! TTCTTTTTAACTGGGCAGCT+TGG - chr1.2:7843438-7843457 None:intergenic 40.0%
ACCATTAGGCCAACCTAAGT+GGG - chr1.2:7842504-7842523 None:intergenic 45.0%
CCTCTCCTAGAGCTTACTTT+AGG + chr1.2:7843400-7843419 MS.gene016098:CDS 45.0%
GAGCACCTAAAGTAAGCTCT+AGG - chr1.2:7843408-7843427 None:intergenic 45.0%
GGTCCCAAGCTAATACCATT+AGG - chr1.2:7842518-7842537 None:intergenic 45.0%
GGTGAGGAAATATCCCTACA+TGG - chr1.2:7843110-7843129 None:intergenic 45.0%
TACCATTAGGCCAACCTAAG+TGG - chr1.2:7842505-7842524 None:intergenic 45.0%
!! CCTAAAGTAAGCTCTAGGAG+AGG - chr1.2:7843403-7843422 None:intergenic 45.0%
!! GTCTCAGTTCTGAGAACAAG+AGG + chr1.2:7842862-7842881 MS.gene016098:CDS 45.0%
!! ACCCACTTAGGTTGGCCTAA+TGG + chr1.2:7842500-7842519 MS.gene016098:intron 50.0%
AACTGGGCAGCTTGGAGCAT+AGG - chr1.2:7843430-7843449 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 7842302 7843458 7842302 ID=MS.gene016098
chr1.2 mRNA 7842302 7843458 7842302 ID=MS.gene016098.t1;Parent=MS.gene016098
chr1.2 exon 7842302 7842376 7842302 ID=MS.gene016098.t1.exon1;Parent=MS.gene016098.t1
chr1.2 CDS 7842302 7842376 7842302 ID=cds.MS.gene016098.t1;Parent=MS.gene016098.t1
chr1.2 exon 7842834 7843178 7842834 ID=MS.gene016098.t1.exon2;Parent=MS.gene016098.t1
chr1.2 CDS 7842834 7843178 7842834 ID=cds.MS.gene016098.t1;Parent=MS.gene016098.t1
chr1.2 exon 7843342 7843458 7843342 ID=MS.gene016098.t1.exon3;Parent=MS.gene016098.t1
chr1.2 CDS 7843342 7843458 7843342 ID=cds.MS.gene016098.t1;Parent=MS.gene016098.t1
Gene Sequence

>MS.gene016098

CAGCAAATAACAATGGAATCAACATGCGTGGATACTTCACTCAATCTTAACGTTAGTGCTTCTTCTATACTCAAGGTTCGTATACAAATACAGTTAAAGAGTTAAATTTTCATATTTTTAAACATCAAAATCAATCACGCGTGACTTTAAAAATAGTTATCATAAAAGTCAAGCGTTTTTAACAATTTGTTGGTAATAACCCACTTAGGTTGGCCTAATGGTATTAGCTTGGGACCTAAATACGACATTGTGTATTATATATATCTACAAAAATTGAATTAACGATGAAAATTTATTAATGAAAGATTTAAAATCTACCCTTTATTATATCCCTAAGTATTGTATATTAATTTCACTAAAAATGGTAATTCAATAATGTTGAAATTGGATACTAATTTCATTCTAATTATTTTTATTTTTGTTGATAATTTAACTGTTTTTACTAGTAGTATTTGCATATATATGTAATAAATTTTAGTTATTTCATGTGTCCCTAAATTTCTTAGAATGACATTGAAAATTTTATGTGCAGGACGAAGTTTTGGTTGAAGAGTTACATCGTCTCAGTTCTGAGAACAAGAGGCTAAATGAAACATTGACCAACATGTGTGAGAACTATGAGACTATGCAAAAGCAATTGAATCAATTGATGAATCAAAATTTTGAACACCAAACACAACAATCAAGAAAGAGAAAAGCTGAGAGTGAAAGTTGCATCAATATGTTTGATACTGTTAGAGGCATTAATATTAGCAATAATAATGAGTGCAGCACTGTTACTGATGAAGAATCATTAATCAAAAGGCCATGTAGGGATATTTCCTCACCTAAGGCTTATAAGGTTCTTGTGAAGACAGAAGCATCTAGTAATAGCTTAGTAAGTTAATTTCTTTATTATTTTGATGTATAAATTTAATTTTTCTAGCAACTTCAATAGTGTGTTTAGTTGTGTCTATATTACAGTTAATGAAGTAAAATTGTGGAGCTTAATCACAAGTACTAACCTTGATTAATTTTGAATTTGTATTTGTGGTATAAAGTATGTGATGGATGGATATCAATGGAGGAAATATGGTCAAAAGGTTACTAGAGATAACCCCTCTCCTAGAGCTTACTTTAGGTGCTCCTATGCTCCAAGCTGCCCAGTTAAAAAGAAG
Protein sequence

>MS.gene016098.t1

QQITMESTCVDTSLNLNVSASSILKDEVLVEELHRLSSENKRLNETLTNMCENYETMQKQLNQLMNQNFEHQTQQSRKRKAESESCINMFDTVRGINISNNNECSTVTDEESLIKRPCRDISSPKAYKVLVKTEASSNSLYVMDGYQWRKYGQKVTRDNPSPRAYFRCSYAPSCPVKKK