AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene041078

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene041078.t1 MTR_5g017210 92.430 251 13 2 1 249 1 247 3.99e-142 398
MS.gene041078.t1 MTR_3g101810 55.024 209 75 8 25 214 40 248 5.68e-58 185
MS.gene041078.t1 MTR_8g093500 74.725 91 23 0 112 202 87 177 4.54e-46 155
MS.gene041078.t1 MTR_2g100490 64.486 107 36 2 100 205 251 356 9.40e-32 120
MS.gene041078.t1 MTR_8g015450 63.636 99 32 1 111 205 296 394 4.26e-29 114
MS.gene041078.t1 MTR_7g069590 68.966 58 18 0 145 202 32 89 4.03e-23 92.0
MS.gene041078.t1 MTR_5g079500 55.696 79 33 1 125 201 202 280 2.17e-20 88.6
MS.gene041078.t1 MTR_1g106460 53.731 67 31 0 135 201 234 300 1.23e-17 80.9
MS.gene041078.t1 MTR_1g018090 62.963 54 20 0 148 201 283 336 3.61e-17 80.1
MS.gene041078.t1 MTR_5g005110 62.963 54 20 0 148 201 233 286 5.73e-17 79.3
MS.gene041078.t1 MTR_1g106470 51.948 77 32 2 130 201 182 258 8.43e-17 78.2
MS.gene041078.t1 MTR_3g103030 55.556 63 28 0 139 201 229 291 3.09e-16 77.0
MS.gene041078.t1 MTR_4g131160 54.286 70 27 1 146 210 203 272 8.02e-15 73.6
MS.gene041078.t1 MTR_4g131160 43.564 101 47 3 120 210 175 275 8.33e-15 73.6
MS.gene041078.t1 MTR_1g080890 51.429 70 34 0 132 201 186 255 1.04e-14 72.8
MS.gene041078.t1 MTR_1g106480 64.444 45 16 0 157 201 87 131 1.12e-13 67.0
MS.gene041078.t1 MTR_2g067000 46.667 75 33 1 135 202 146 220 1.12e-12 66.6
MS.gene041078.t1 MTR_1g060700 57.407 54 23 0 149 202 357 410 4.43e-12 65.9
MS.gene041078.t1 MTR_4g033295 50.769 65 31 1 140 203 119 183 5.54e-12 63.2
MS.gene041078.t1 MTR_4g033295 50.000 66 32 1 140 204 119 184 1.03e-11 62.4
MS.gene041078.t1 MTR_2g089070 48.148 54 28 0 149 202 146 199 9.08e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene041078.t1 AT5G67060 56.771 192 69 4 17 203 4 186 1.94e-50 165
MS.gene041078.t1 AT3G50330 54.587 218 68 7 14 222 4 199 2.60e-50 164
MS.gene041078.t1 AT5G67060 56.284 183 67 3 25 203 1 174 2.03e-47 157
MS.gene041078.t1 AT4G00120 66.667 96 29 1 114 206 87 182 3.63e-39 135
MS.gene041078.t1 AT3G21330 54.472 123 48 1 90 204 212 334 4.01e-38 137
MS.gene041078.t1 AT5G09750 75.556 90 22 0 112 201 92 181 6.80e-35 124
MS.gene041078.t1 AT5G01305 69.492 59 18 0 140 198 38 96 7.24e-22 89.4
MS.gene041078.t1 AT5G43175 50.725 69 34 0 133 201 126 194 7.75e-19 82.8
MS.gene041078.t1 AT4G33880 59.677 62 25 0 140 201 267 328 1.47e-18 84.0
MS.gene041078.t1 AT5G37800 56.164 73 25 1 136 201 191 263 3.51e-18 82.4
MS.gene041078.t1 AT1G27740 51.471 68 33 0 134 201 162 229 5.02e-18 81.3
MS.gene041078.t1 AT1G66470 67.273 55 18 0 147 201 203 257 5.21e-18 81.6
MS.gene041078.t1 AT2G14760 58.065 62 26 0 140 201 238 299 1.51e-17 80.9
MS.gene041078.t1 AT4G30980 40.000 115 68 1 87 201 79 192 7.47e-17 78.6
MS.gene041078.t1 AT2G24260 52.703 74 29 1 134 201 24 97 1.19e-16 77.0
MS.gene041078.t1 AT4G30980 40.000 115 68 1 87 201 127 240 1.76e-16 78.2
MS.gene041078.t1 AT2G24260 52.703 74 29 1 134 201 127 200 2.99e-16 77.4
MS.gene041078.t1 AT5G58010 54.545 66 30 0 136 201 96 161 8.46e-15 72.8
MS.gene041078.t1 AT2G14760 48.000 75 26 1 140 201 238 312 3.29e-14 71.6
MS.gene041078.t1 AT4G09180 43.210 81 45 1 122 201 167 247 7.26e-11 61.2

Find 58 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGTGGTTTAATGGTTTC+TGG 0.032783 5.2:-9337716 None:intergenic
CTTTCTCTTTGGTGGTTTAA+TGG 0.129321 5.2:-9337723 None:intergenic
ACAAACAATGATTTCCCTTA+TGG 0.235794 5.2:+9337467 MS.gene041078:CDS
ATCTTCACATTCTTTCTCTT+TGG 0.246196 5.2:-9337734 None:intergenic
AATTATTCTTCTTTGCTTAG+AGG 0.274535 5.2:+9337995 MS.gene041078:CDS
GAGATTGAGAGTGTTGTTAT+TGG 0.283226 5.2:-9337438 None:intergenic
AAAGAATTAGTGAAAGAATA+AGG 0.285456 5.2:+9337798 MS.gene041078:CDS
TTATTGGTGTTGCTATAAAA+AGG 0.298991 5.2:-9337422 None:intergenic
TTGGTGGTTTAATGGTTTCT+GGG 0.314323 5.2:-9337715 None:intergenic
TGTCTTGCTGCTACACTTTG+TGG 0.337683 5.2:-9337767 None:intergenic
TTCACATTCTTTCTCTTTGG+TGG 0.352271 5.2:-9337731 None:intergenic
TGAAGCGACGGCGGTGTCAT+TGG 0.364263 5.2:-9337560 None:intergenic
TTCAAACGTTGGAACAAGTT+GGG 0.370508 5.2:+9337915 MS.gene041078:CDS
TTGAATGTTGTTGGGTTTCA+AGG 0.375435 5.2:+9337950 MS.gene041078:CDS
GTTTCTGGGTCTATGTTAAT+CGG 0.384832 5.2:-9337701 None:intergenic
TGATGGGATTTGAACTCTGT+TGG 0.387374 5.2:-9337585 None:intergenic
GCCATTGAATTCTTCTTCTC+CGG 0.399282 5.2:-9337638 None:intergenic
ACTAAGCATTTGTTTGGAAG+TGG 0.402015 5.2:-9338047 None:intergenic
AATAGACCTTTGAATGTTGT+TGG 0.403761 5.2:+9337941 MS.gene041078:CDS
GTTACATTTGAGTTTCCATA+AGG 0.409196 5.2:-9337482 None:intergenic
TGAGGACATACTGAAAACTT+TGG 0.409321 5.2:+9337328 MS.gene041078:CDS
TGGAAGTGGGACCCACCATT+TGG 0.414540 5.2:-9338033 None:intergenic
GATGGGATTTGAACTCTGTT+GGG 0.418955 5.2:-9337584 None:intergenic
GTGTCAACTAAGCATTTGTT+TGG 0.421668 5.2:-9338053 None:intergenic
CAATTCTTCATTCTCCTATC+CGG 0.438986 5.2:+9337619 MS.gene041078:CDS
TTCATCACCTTGCCAAATGG+TGG 0.447650 5.2:+9338021 MS.gene041078:CDS
GAGGACATACTGAAAACTTT+GGG 0.447841 5.2:+9337329 MS.gene041078:CDS
ATAGACCTTTGAATGTTGTT+GGG 0.458742 5.2:+9337942 MS.gene041078:CDS
ATAGGAGAATGAAGAATTGT+TGG 0.471030 5.2:-9337615 None:intergenic
TTACATTTGAGTTTCCATAA+GGG 0.484501 5.2:-9337481 None:intergenic
GTTCAAACGTTGGAACAAGT+TGG 0.486495 5.2:+9337914 MS.gene041078:CDS
GATGACAATGATGATGCAAA+TGG 0.498844 5.2:+9337376 MS.gene041078:CDS
AATTGTTGGTTCTTCCTGAT+GGG 0.499420 5.2:-9337601 None:intergenic
TGAATTCTTCTTCTCCGGAT+AGG 0.501360 5.2:-9337633 None:intergenic
GAATTGTTGGTTCTTCCTGA+TGG 0.503297 5.2:-9337602 None:intergenic
TTGTTCATCACCTTGCCAAA+TGG 0.505893 5.2:+9338018 MS.gene041078:CDS
AACAGAGTTCAAATCCCATC+AGG 0.513806 5.2:+9337587 MS.gene041078:CDS
TGTTGTTGGGTTTCAAGGAG+TGG 0.515205 5.2:+9337955 MS.gene041078:CDS
TCTGAAAACATTCATGGATG+AGG 0.543834 5.2:+9337310 None:intergenic
CTAAGCATTTGTTTGGAAGT+GGG 0.548242 5.2:-9338046 None:intergenic
GGTGTCATTGGTTGTTGAAG+AGG 0.548657 5.2:-9337548 None:intergenic
GAGAGAGATGATATTTCGTA+TGG 0.550671 5.2:+9337667 MS.gene041078:CDS
GAAGAAACAAGTTCAAACGT+TGG 0.554879 5.2:+9337904 MS.gene041078:CDS
TCATCACCTTGCCAAATGGT+GGG 0.555921 5.2:+9338022 MS.gene041078:CDS
TGAAACCCAACAACATTCAA+AGG 0.560330 5.2:-9337947 None:intergenic
TCAAACGTTGGAACAAGTTG+GGG 0.569007 5.2:+9337916 MS.gene041078:CDS
ACTCTGTTGGGTTGAAGCGA+CGG 0.575367 5.2:-9337572 None:intergenic
AAAGAATGTGAAGATTTCAA+AGG 0.590303 5.2:+9337742 MS.gene041078:CDS
TGAAGAGGATAAGACAATGG+TGG 0.592428 5.2:-9337533 None:intergenic
TCCGGAGAAGAAGAATTCAA+TGG 0.605617 5.2:+9337637 MS.gene041078:CDS
AATGGTGGATTGATCAATGA+AGG 0.629442 5.2:-9337518 None:intergenic
AGAGATGATATTTCGTATGG+CGG 0.630427 5.2:+9337670 MS.gene041078:CDS
GGGAAATGTTGAAAGTAACA+TGG 0.631569 5.2:+9337349 MS.gene041078:CDS
GTGGGACCCACCATTTGGCA+AGG 0.634945 5.2:-9338028 None:intergenic
CTGTTGGGTTGAAGCGACGG+CGG 0.671897 5.2:-9337569 None:intergenic
ATATTACAAAGATTAGTACC+TGG 0.683168 5.2:+9337821 MS.gene041078:CDS
TTACAAAGATTAGTACCTGG+TGG 0.689802 5.2:+9337824 MS.gene041078:CDS
TGTTGAAGAGGATAAGACAA+TGG 0.700529 5.2:-9337536 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAATTAGTGAAAGAATA+AGG + chr5.2:9337798-9337817 MS.gene041078:CDS 20.0%
! AAAAAGGTTCATATGAATCA+GGG - chr5.2:9337409-9337428 None:intergenic 25.0%
! AAAGAATGTGAAGATTTCAA+AGG + chr5.2:9337742-9337761 MS.gene041078:CDS 25.0%
! AATTATTCTTCTTTGCTTAG+AGG + chr5.2:9337995-9338014 MS.gene041078:CDS 25.0%
! ATATTACAAAGATTAGTACC+TGG + chr5.2:9337821-9337840 MS.gene041078:CDS 25.0%
! TAAAAAGGTTCATATGAATC+AGG - chr5.2:9337410-9337429 None:intergenic 25.0%
!! TTACATTTGAGTTTCCATAA+GGG - chr5.2:9337484-9337503 None:intergenic 25.0%
!!! TTATTGGTGTTGCTATAAAA+AGG - chr5.2:9337425-9337444 None:intergenic 25.0%
AATAGACCTTTGAATGTTGT+TGG + chr5.2:9337941-9337960 MS.gene041078:CDS 30.0%
ACAAACAATGATTTCCCTTA+TGG + chr5.2:9337467-9337486 MS.gene041078:CDS 30.0%
ATAGACCTTTGAATGTTGTT+GGG + chr5.2:9337942-9337961 MS.gene041078:CDS 30.0%
ATAGGAGAATGAAGAATTGT+TGG - chr5.2:9337618-9337637 None:intergenic 30.0%
ATCTTCACATTCTTTCTCTT+TGG - chr5.2:9337737-9337756 None:intergenic 30.0%
! GTTACATTTGAGTTTCCATA+AGG - chr5.2:9337485-9337504 None:intergenic 30.0%
ACTAAGCATTTGTTTGGAAG+TGG - chr5.2:9338050-9338069 None:intergenic 35.0%
AGAGATGATATTTCGTATGG+CGG + chr5.2:9337670-9337689 MS.gene041078:CDS 35.0%
CAATTCTTCATTCTCCTATC+CGG + chr5.2:9337619-9337638 MS.gene041078:CDS 35.0%
CTAAGCATTTGTTTGGAAGT+GGG - chr5.2:9338049-9338068 None:intergenic 35.0%
GAAGAAACAAGTTCAAACGT+TGG + chr5.2:9337904-9337923 MS.gene041078:CDS 35.0%
GAGAGAGATGATATTTCGTA+TGG + chr5.2:9337667-9337686 MS.gene041078:CDS 35.0%
GAGGACATACTGAAAACTTT+GGG + chr5.2:9337329-9337348 MS.gene041078:CDS 35.0%
GGGAAATGTTGAAAGTAACA+TGG + chr5.2:9337349-9337368 MS.gene041078:CDS 35.0%
TGAAACCCAACAACATTCAA+AGG - chr5.2:9337950-9337969 None:intergenic 35.0%
TGAGGACATACTGAAAACTT+TGG + chr5.2:9337328-9337347 MS.gene041078:CDS 35.0%
TGTTGAAGAGGATAAGACAA+TGG - chr5.2:9337539-9337558 None:intergenic 35.0%
TTACAAAGATTAGTACCTGG+TGG + chr5.2:9337824-9337843 MS.gene041078:CDS 35.0%
TTCAAACGTTGGAACAAGTT+GGG + chr5.2:9337915-9337934 MS.gene041078:CDS 35.0%
TTCACATTCTTTCTCTTTGG+TGG - chr5.2:9337734-9337753 None:intergenic 35.0%
TTGAATGTTGTTGGGTTTCA+AGG + chr5.2:9337950-9337969 MS.gene041078:CDS 35.0%
! CTTTCTCTTTGGTGGTTTAA+TGG - chr5.2:9337726-9337745 None:intergenic 35.0%
! GATGACAATGATGATGCAAA+TGG + chr5.2:9337376-9337395 MS.gene041078:CDS 35.0%
! GTTTCTGGGTCTATGTTAAT+CGG - chr5.2:9337704-9337723 None:intergenic 35.0%
! TTGGTGGTTTAATGGTTTCT+GGG - chr5.2:9337718-9337737 None:intergenic 35.0%
! TTTGGTGGTTTAATGGTTTC+TGG - chr5.2:9337719-9337738 None:intergenic 35.0%
!! AATGGTGGATTGATCAATGA+AGG - chr5.2:9337521-9337540 None:intergenic 35.0%
!! AATTGTTGGTTCTTCCTGAT+GGG - chr5.2:9337604-9337623 None:intergenic 35.0%
!! GAGATTGAGAGTGTTGTTAT+TGG - chr5.2:9337441-9337460 None:intergenic 35.0%
AACAGAGTTCAAATCCCATC+AGG + chr5.2:9337587-9337606 MS.gene041078:CDS 40.0%
AGTACCTGGTGGAACAAAAA+TGG + chr5.2:9337835-9337854 MS.gene041078:CDS 40.0%
GATGGGATTTGAACTCTGTT+GGG - chr5.2:9337587-9337606 None:intergenic 40.0%
GCCATTGAATTCTTCTTCTC+CGG - chr5.2:9337641-9337660 None:intergenic 40.0%
GTTCAAACGTTGGAACAAGT+TGG + chr5.2:9337914-9337933 MS.gene041078:CDS 40.0%
TCAAACGTTGGAACAAGTTG+GGG + chr5.2:9337916-9337935 MS.gene041078:CDS 40.0%
TCCGGAGAAGAAGAATTCAA+TGG + chr5.2:9337637-9337656 MS.gene041078:CDS 40.0%
TGAAGAGGATAAGACAATGG+TGG - chr5.2:9337536-9337555 None:intergenic 40.0%
TGAATTCTTCTTCTCCGGAT+AGG - chr5.2:9337636-9337655 None:intergenic 40.0%
TGATGGGATTTGAACTCTGT+TGG - chr5.2:9337588-9337607 None:intergenic 40.0%
TTGTTCATCACCTTGCCAAA+TGG + chr5.2:9338018-9338037 MS.gene041078:CDS 40.0%
!! GAATTGTTGGTTCTTCCTGA+TGG - chr5.2:9337605-9337624 None:intergenic 40.0%
TCATCACCTTGCCAAATGGT+GGG + chr5.2:9338022-9338041 MS.gene041078:CDS 45.0%
TGTCTTGCTGCTACACTTTG+TGG - chr5.2:9337770-9337789 None:intergenic 45.0%
TGTTGTTGGGTTTCAAGGAG+TGG + chr5.2:9337955-9337974 MS.gene041078:CDS 45.0%
TTCATCACCTTGCCAAATGG+TGG + chr5.2:9338021-9338040 MS.gene041078:CDS 45.0%
!! GGTGTCATTGGTTGTTGAAG+AGG - chr5.2:9337551-9337570 None:intergenic 45.0%
!! GTGTCCATTTTTGTTCCACC+AGG - chr5.2:9337842-9337861 None:intergenic 45.0%
!! ACTCTGTTGGGTTGAAGCGA+CGG - chr5.2:9337575-9337594 None:intergenic 50.0%
TGGAAGTGGGACCCACCATT+TGG - chr5.2:9338036-9338055 None:intergenic 55.0%
GTGGGACCCACCATTTGGCA+AGG - chr5.2:9338031-9338050 None:intergenic 60.0%
!! CTGTTGGGTTGAAGCGACGG+CGG - chr5.2:9337572-9337591 None:intergenic 60.0%
!! TGAAGCGACGGCGGTGTCAT+TGG - chr5.2:9337563-9337582 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 9337323 9338072 9337323 ID=MS.gene041078
chr5.2 mRNA 9337323 9338072 9337323 ID=MS.gene041078.t1;Parent=MS.gene041078
chr5.2 exon 9337323 9338072 9337323 ID=MS.gene041078.t1.exon1;Parent=MS.gene041078.t1
chr5.2 CDS 9337323 9338072 9337323 ID=cds.MS.gene041078.t1;Parent=MS.gene041078.t1
Gene Sequence

>MS.gene041078

ATGGATGAGGACATACTGAAAACTTTGGGAAATGTTGAAAGTAACATGGACATGATGACAATGATGATGCAAATGGAAAAGTTCCCTGATTCATATGAACCTTTTTATAGCAACACCAATAACAACACTCTCAATCTCAATCTCACAAACAATGATTTCCCTTATGGAAACTCAAATGTAACTTCATCACTCACACCTTCATTGATCAATCCACCATTGTCTTATCCTCTTCAACAACCAATGACACCGCCGTCGCTTCAACCCAACAGAGTTCAAATCCCATCAGGAAGAACCAACAATTCTTCATTCTCCTATCCGGAGAAGAAGAATTCAATGGCAGCAATGAGAGAGATGATATTTCGTATGGCGGTTATGCAACCGATTAACATAGACCCAGAAACCATTAAACCACCAAAGAGAAAGAATGTGAAGATTTCAAAGGATCCACAAAGTGTAGCAGCAAGACATAGAAGAGAAAGAATTAGTGAAAGAATAAGGATATTACAAAGATTAGTACCTGGTGGAACAAAAATGGACACTGCTTCTATGTTAGATGAAGCAATACATTATGTGAAGTTTTTGAAGAAACAAGTTCAAACGTTGGAACAAGTTGGGGCAAATAGACCTTTGAATGTTGTTGGGTTTCAAGGAGTGGTTTCTAATGCTAATTTTAATTATTCTTCTTTGCTTAGAGGTTGTTCATCACCTTGCCAAATGGTGGGTCCCACTTCCAAACAAATGCTTAGTTGA
Protein sequence

>MS.gene041078.t1

MDEDILKTLGNVESNMDMMTMMMQMEKFPDSYEPFYSNTNNNTLNLNLTNNDFPYGNSNVTSSLTPSLINPPLSYPLQQPMTPPSLQPNRVQIPSGRTNNSSFSYPEKKNSMAAMREMIFRMAVMQPINIDPETIKPPKRKNVKISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQVQTLEQVGANRPLNVVGFQGVVSNANFNYSSLLRGCSSPCQMVGPTSKQMLS