AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98432

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98432.t1 MTR_5g027570 69.626 214 44 5 3 207 30 231 1.06e-88 261
MS.gene98432.t1 MTR_5g088010 57.977 257 50 6 1 207 1 249 6.71e-85 251
MS.gene98432.t1 MTR_5g088060 57.588 257 46 7 1 207 218 461 6.20e-80 246
MS.gene98432.t1 MTR_5g488160 57.588 257 46 7 1 207 218 461 6.20e-80 246
MS.gene98432.t1 MTR_5g027550 57.143 224 56 9 1 207 29 229 2.36e-66 204
MS.gene98432.t1 MTR_3g462790 43.478 138 58 4 61 184 143 274 1.04e-24 99.0
MS.gene98432.t1 MTR_1g111830 42.748 131 69 4 11 139 72 198 3.04e-24 96.3
MS.gene98432.t1 MTR_5g081860 43.243 148 67 5 26 161 75 217 9.68e-23 92.8
MS.gene98432.t1 MTR_4g111975 53.846 78 34 2 61 137 134 210 5.03e-22 91.7
MS.gene98432.t1 MTR_5g069710 60.811 74 27 2 61 133 128 200 5.43e-22 91.7
MS.gene98432.t1 MTR_4g100630 40.517 116 57 3 15 126 47 154 1.07e-21 90.9
MS.gene98432.t1 MTR_8g063600 55.263 76 33 1 61 135 102 177 1.57e-21 90.1
MS.gene98432.t1 MTR_7g067080 46.364 110 54 3 57 164 132 238 2.80e-21 89.7
MS.gene98432.t1 MTR_8g063870 60.563 71 27 1 66 135 93 163 5.48e-21 88.2
MS.gene98432.t1 MTR_3g104370 35.503 169 84 8 38 186 67 230 1.11e-19 84.0
MS.gene98432.t1 MTR_2g100930 55.556 72 28 2 57 126 99 168 1.27e-19 85.5
MS.gene98432.t1 MTR_4g107230 38.000 150 68 5 48 196 66 191 3.77e-19 83.6
MS.gene98432.t1 MTR_8g101650 52.174 69 31 1 61 129 101 167 1.04e-18 82.0
MS.gene98432.t1 MTR_1g048660 51.429 70 33 1 67 136 14 82 4.29e-18 76.3
MS.gene98432.t1 MTR_6g092540 54.545 66 28 1 61 126 93 156 9.85e-18 79.7
MS.gene98432.t1 MTR_4g015130 48.780 82 39 2 75 156 3 81 1.37e-17 74.7
MS.gene98432.t1 MTR_5g037080 61.111 54 21 0 59 112 96 149 2.56e-17 79.0
MS.gene98432.t1 MTR_1g033620 50.704 71 33 2 80 149 20 89 4.77e-16 74.3
MS.gene98432.t1 MTR_1g083180 52.703 74 32 2 66 137 62 134 8.91e-16 72.4
MS.gene98432.t1 MTR_5g075760 43.299 97 47 3 66 155 106 201 2.57e-15 72.0
MS.gene98432.t1 MTR_0036s0260 40.000 85 50 1 67 151 30 113 6.21e-15 70.9
MS.gene98432.t1 MTR_2g090305 40.909 88 51 1 67 154 30 116 1.15e-14 69.7
MS.gene98432.t1 MTR_5g075790 32.394 142 84 4 25 155 69 209 4.96e-14 68.6
MS.gene98432.t1 MTR_3g070110 45.833 72 33 1 66 131 96 167 1.78e-13 67.0
MS.gene98432.t1 MTR_8g072990 44.615 65 33 1 62 123 97 161 1.15e-12 65.1
MS.gene98432.t1 MTR_6g043490 42.029 69 37 1 62 127 104 172 3.73e-12 63.5
MS.gene98432.t1 MTR_6g043480 40.580 69 38 1 62 127 104 172 1.59e-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.gene98432.t1 AT5G08520 50.515 97 47 1 35 131 88 183 7.83e-25 99.0
MS.gene98432.t1 AT1G49010 51.190 84 40 1 57 140 126 208 2.31e-23 95.5
MS.gene98432.t1 AT2G38090 46.847 111 51 4 35 138 105 214 2.69e-23 94.7
MS.gene98432.t1 AT5G23650 47.748 111 54 2 25 135 83 189 2.73e-23 95.5
MS.gene98432.t1 AT5G58900 47.664 107 52 3 61 164 137 242 7.98e-23 93.6
MS.gene98432.t1 AT5G04760 57.500 80 31 2 53 131 87 164 1.08e-22 91.7
MS.gene98432.t1 AT3G10580 51.765 85 35 2 67 148 97 178 7.93e-21 87.4
MS.gene98432.t1 AT5G01200 53.947 76 33 2 59 133 140 214 1.04e-20 87.4
MS.gene98432.t1 AT3G10580 51.765 85 35 2 67 148 97 178 1.10e-20 87.8
MS.gene98432.t1 AT3G11280 50.562 89 39 2 51 135 113 200 3.28e-20 85.9
MS.gene98432.t1 AT3G11280 50.562 89 39 2 51 135 113 200 3.28e-20 85.9
MS.gene98432.t1 AT5G47390 52.857 70 31 1 57 126 88 155 1.20e-19 85.9
MS.gene98432.t1 AT5G05790 50.000 90 40 2 50 135 116 204 1.86e-19 84.3
MS.gene98432.t1 AT5G05790 50.000 90 40 2 50 135 116 204 1.86e-19 84.3
MS.gene98432.t1 AT5G61620 54.878 82 30 3 52 132 99 174 3.78e-19 84.0
MS.gene98432.t1 AT5G56840 53.623 69 32 0 61 129 87 155 4.22e-19 82.4
MS.gene98432.t1 AT1G70000 47.059 102 43 4 57 154 87 181 1.63e-18 81.3
MS.gene98432.t1 AT1G70000 47.059 102 43 4 57 154 87 181 1.63e-18 81.3
MS.gene98432.t1 AT1G74840 56.250 64 28 0 48 111 79 142 4.11e-18 80.1
MS.gene98432.t1 AT1G74840 56.250 64 28 0 48 111 79 142 5.13e-18 80.1
MS.gene98432.t1 AT3G16350 49.315 73 37 0 40 112 112 184 1.57e-17 80.1
MS.gene98432.t1 AT1G19000 45.055 91 42 3 29 111 58 148 1.12e-16 76.6
MS.gene98432.t1 AT1G19000 45.055 91 42 3 29 111 58 148 1.12e-16 76.6
MS.gene98432.t1 AT3G10590 46.875 96 46 4 39 132 84 176 3.13e-16 74.3
MS.gene98432.t1 AT4G09450 48.193 83 41 2 67 148 93 174 6.11e-16 73.2

Find 41 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTATATCTTTCACATTT+TGG 0.095253 5.4:-18514759 None:intergenic
TGGTGTGTCATTCTTGTTTA+AGG 0.172573 5.4:-18514812 None:intergenic
TGTGATGTATAGGTTGTTTC+TGG 0.210646 5.4:+18514627 MS.gene98432:intron
TTTGCTTCATGACTTCCTTT+TGG 0.294411 5.4:-18514029 None:intergenic
TCCTTTAGTCACTTCTCCTA+TGG 0.384449 5.4:+18514876 MS.gene98432:CDS
GCATGGCTAGCAATTTGAAT+TGG 0.406712 5.4:-18514718 None:intergenic
GTGCAACTTGTTCAACTTGT+TGG 0.431038 5.4:+18515008 MS.gene98432:CDS
AACTTAGTTCAAGCCGGGTC+AGG 0.434416 5.4:+18513960 MS.gene98432:CDS
GAACAACAACAGGAGAAAAC+TGG 0.441684 5.4:+18513882 MS.gene98432:CDS
AGATATTTCAAAAGAATTTG+TGG 0.448838 5.4:+18514684 MS.gene98432:CDS
AAAGAGAAGGCGTAGGGAAA+GGG 0.451763 5.4:+18514049 MS.gene98432:CDS
ACTTCCTTCTGCTCCTGACC+CGG 0.468451 5.4:-18513973 None:intergenic
ATGACCCGACTCACTGATAT+CGG 0.474612 5.4:-18513907 None:intergenic
GATAATAACTTAGTTCAAGC+CGG 0.482726 5.4:+18513954 MS.gene98432:CDS
CAAAGAGAAGGCGTAGGGAA+AGG 0.485224 5.4:+18514048 MS.gene98432:CDS
GCATAGCATGGAACAACAAC+AGG 0.485938 5.4:+18513872 None:intergenic
TTGGTGCTGCTCTGTCCAAT+CGG 0.496082 5.4:+18514949 MS.gene98432:CDS
GGATTCTCATGTTGTTCCAT+AGG 0.496486 5.4:-18514892 None:intergenic
CTTGAGGTGGCTGTGTCTTG+AGG 0.504065 5.4:-18514916 None:intergenic
GGCACCGATATCAGTGAGTC+GGG 0.505895 5.4:+18513903 MS.gene98432:CDS
CACCAACTGCATTTGTCTTG+AGG 0.508085 5.4:-18514932 None:intergenic
CAAGCTGAGTCAGTACCAAA+AGG 0.521750 5.4:+18514014 MS.gene98432:CDS
ATGTATAGGTTGTTTCTGGA+GGG 0.542704 5.4:+18514631 MS.gene98432:intron
CAACTGCATTTGTCTTGAGG+TGG 0.545901 5.4:-18514929 None:intergenic
TCAGTACGTGTAGGACCGAT+TGG 0.557328 5.4:-18514964 None:intergenic
ACTGAAGGAATCTCAGTGAC+TGG 0.562057 5.4:-18514832 None:intergenic
TGTATAGGTTGTTTCTGGAG+GGG 0.562950 5.4:+18514632 MS.gene98432:intron
CACCTCAAGACAAATGCAGT+TGG 0.567812 5.4:+18514930 MS.gene98432:CDS
CAAGCCGGGTCAGGAGCAGA+AGG 0.568635 5.4:+18513969 MS.gene98432:CDS
ATAATAACTTAGTTCAAGCC+GGG 0.570276 5.4:+18513955 MS.gene98432:CDS
GAGGTGGCTGTGTCTTGAGG+AGG 0.576603 5.4:-18514913 None:intergenic
ATGAAGCAAAGAGAAGGCGT+AGG 0.578502 5.4:+18514042 MS.gene98432:CDS
GAAAGGGCACATTGGACAGA+AGG 0.581957 5.4:+18514065 MS.gene98432:CDS
TCCATAGGAGAAGTGACTAA+AGG 0.586339 5.4:-18514877 None:intergenic
GGCGTAGGGAAAGGGCACAT+TGG 0.587387 5.4:+18514057 MS.gene98432:CDS
TGGCACCGATATCAGTGAGT+CGG 0.599539 5.4:+18513902 MS.gene98432:CDS
GAAGTCATGAAGCAAAGAGA+AGG 0.600109 5.4:+18514036 MS.gene98432:CDS
ATTAGAGTTTAGATTTGCGA+CGG 0.604472 5.4:-18513931 None:intergenic
GATGTATAGGTTGTTTCTGG+AGG 0.607647 5.4:+18514630 MS.gene98432:intron
TGAAGCAAAGAGAAGGCGTA+GGG 0.634488 5.4:+18514043 MS.gene98432:CDS
TTGTTCATATCAGTACGTGT+AGG 0.642020 5.4:-18514973 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAAATAATAAAGAAATG+AGG - chr5.4:18514559-18514578 None:intergenic 15.0%
!! TATTGTAAATACATATCAAT+TGG - chr5.4:18514339-18514358 None:intergenic 15.0%
!!! TTCTTTTTCAATTCTATTTT+AGG + chr5.4:18514135-18514154 MS.gene98432:intron 15.0%
!! AAAAAAAGATATAACTTCCA+AGG - chr5.4:18514117-18514136 None:intergenic 20.0%
!! AGATATTTCAAAAGAATTTG+TGG + chr5.4:18514684-18514703 MS.gene98432:CDS 20.0%
!!! TTCTATAATTTGTGATGTAT+AGG + chr5.4:18514617-18514636 MS.gene98432:intron 20.0%
!! TCTCTATATCTTTCACATTT+TGG - chr5.4:18514762-18514781 None:intergenic 25.0%
!!! TTGGTGGATAAAGTATTTTT+GGG - chr5.4:18514743-18514762 None:intergenic 25.0%
!!! TTTGGTGGATAAAGTATTTT+TGG - chr5.4:18514744-18514763 None:intergenic 25.0%
AGATGCAAATTAATCGTTCT+AGG + chr5.4:18514455-18514474 MS.gene98432:intron 30.0%
ATAATAACTTAGTTCAAGCC+GGG + chr5.4:18513955-18513974 MS.gene98432:CDS 30.0%
ATTAGAGTTTAGATTTGCGA+CGG - chr5.4:18513934-18513953 None:intergenic 30.0%
GAAATGAGGTAACTATATCT+TGG - chr5.4:18514545-18514564 None:intergenic 30.0%
GATAATAACTTAGTTCAAGC+CGG + chr5.4:18513954-18513973 MS.gene98432:CDS 30.0%
GTAAGTATTCAATCTATCCT+TGG + chr5.4:18514097-18514116 MS.gene98432:intron 30.0%
TTGGTATGTATCCAAAACAA+TGG - chr5.4:18514526-18514545 None:intergenic 30.0%
! CTATATCTTTCACATTTTGG+TGG - chr5.4:18514759-18514778 None:intergenic 30.0%
AAAAATATGGTAAGGGACGT+TGG + chr5.4:18514659-18514678 MS.gene98432:CDS 35.0%
AGTGACTAGATACTCAACTA+TGG + chr5.4:18514258-18514277 MS.gene98432:intron 35.0%
GGGCTAGAAAAATATGGTAA+GGG + chr5.4:18514652-18514671 MS.gene98432:CDS 35.0%
TTGTTCATATCAGTACGTGT+AGG - chr5.4:18514976-18514995 None:intergenic 35.0%
! CATATCAATTGGTAGCTACA+AGG - chr5.4:18514328-18514347 None:intergenic 35.0%
! TCATTTTGTTGCTCAACTGA+AGG - chr5.4:18514850-18514869 None:intergenic 35.0%
! TGCAAGTGTTTCCATTGTTT+TGG + chr5.4:18514512-18514531 MS.gene98432:intron 35.0%
! TGGTGTGTCATTCTTGTTTA+AGG - chr5.4:18514815-18514834 None:intergenic 35.0%
! TGTGATGTATAGGTTGTTTC+TGG + chr5.4:18514627-18514646 MS.gene98432:intron 35.0%
! TTTGCTTCATGACTTCCTTT+TGG - chr5.4:18514032-18514051 None:intergenic 35.0%
!! ATGTATAGGTTGTTTCTGGA+GGG + chr5.4:18514631-18514650 MS.gene98432:intron 35.0%
!!! GGATAAAGTATTTTTGGGCA+TGG - chr5.4:18514738-18514757 None:intergenic 35.0%
CAAGGACGTTTATCTACATG+CGG - chr5.4:18514310-18514329 None:intergenic 40.0%
GAACAACAACAGGAGAAAAC+TGG + chr5.4:18513882-18513901 MS.gene98432:CDS 40.0%
GAAGTCATGAAGCAAAGAGA+AGG + chr5.4:18514036-18514055 MS.gene98432:CDS 40.0%
GATACTCAACTATGGAGAAG+TGG + chr5.4:18514266-18514285 MS.gene98432:intron 40.0%
GCATGGCTAGCAATTTGAAT+TGG - chr5.4:18514721-18514740 None:intergenic 40.0%
GGATTCTCATGTTGTTCCAT+AGG - chr5.4:18514895-18514914 None:intergenic 40.0%
GGGGCTAGAAAAATATGGTA+AGG + chr5.4:18514651-18514670 MS.gene98432:CDS 40.0%
TCCATAGGAGAAGTGACTAA+AGG - chr5.4:18514880-18514899 None:intergenic 40.0%
TCCTTTAGTCACTTCTCCTA+TGG + chr5.4:18514876-18514895 MS.gene98432:CDS 40.0%
! GTGCAACTTGTTCAACTTGT+TGG + chr5.4:18515008-18515027 MS.gene98432:CDS 40.0%
!! GATGTATAGGTTGTTTCTGG+AGG + chr5.4:18514630-18514649 MS.gene98432:intron 40.0%
!! TGTATAGGTTGTTTCTGGAG+GGG + chr5.4:18514632-18514651 MS.gene98432:intron 40.0%
ACTGAAGGAATCTCAGTGAC+TGG - chr5.4:18514835-18514854 None:intergenic 45.0%
ATGACCCGACTCACTGATAT+CGG - chr5.4:18513910-18513929 None:intergenic 45.0%
CAACTGCATTTGTCTTGAGG+TGG - chr5.4:18514932-18514951 None:intergenic 45.0%
CAAGCTGAGTCAGTACCAAA+AGG + chr5.4:18514014-18514033 MS.gene98432:CDS 45.0%
CACCAACTGCATTTGTCTTG+AGG - chr5.4:18514935-18514954 None:intergenic 45.0%
CACCTCAAGACAAATGCAGT+TGG + chr5.4:18514930-18514949 MS.gene98432:CDS 45.0%
CTGGAGGGGCTAGAAAAATA+TGG + chr5.4:18514646-18514665 MS.gene98432:CDS 45.0%
! AAAGAGAAGGCGTAGGGAAA+GGG + chr5.4:18514049-18514068 MS.gene98432:CDS 45.0%
! ATGAAGCAAAGAGAAGGCGT+AGG + chr5.4:18514042-18514061 MS.gene98432:CDS 45.0%
! TGAAGCAAAGAGAAGGCGTA+GGG + chr5.4:18514043-18514062 MS.gene98432:CDS 45.0%
AACTTAGTTCAAGCCGGGTC+AGG + chr5.4:18513960-18513979 MS.gene98432:CDS 50.0%
TCAGTACGTGTAGGACCGAT+TGG - chr5.4:18514967-18514986 None:intergenic 50.0%
! CAAAGAGAAGGCGTAGGGAA+AGG + chr5.4:18514048-18514067 MS.gene98432:CDS 50.0%
! GAAAGGGCACATTGGACAGA+AGG + chr5.4:18514065-18514084 MS.gene98432:CDS 50.0%
!! TGGCACCGATATCAGTGAGT+CGG + chr5.4:18513902-18513921 MS.gene98432:CDS 50.0%
!! TTGGTGCTGCTCTGTCCAAT+CGG + chr5.4:18514949-18514968 MS.gene98432:CDS 50.0%
ACTTCCTTCTGCTCCTGACC+CGG - chr5.4:18513976-18513995 None:intergenic 55.0%
CTTGAGGTGGCTGTGTCTTG+AGG - chr5.4:18514919-18514938 None:intergenic 55.0%
!! GGCACCGATATCAGTGAGTC+GGG + chr5.4:18513903-18513922 MS.gene98432:CDS 55.0%
GAGGTGGCTGTGTCTTGAGG+AGG - chr5.4:18514916-18514935 None:intergenic 60.0%
! GGCGTAGGGAAAGGGCACAT+TGG + chr5.4:18514057-18514076 MS.gene98432:CDS 60.0%
CAAGCCGGGTCAGGAGCAGA+AGG + chr5.4:18513969-18513988 MS.gene98432:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 18513879 18515044 18513879 ID=MS.gene98432
chr5.4 mRNA 18513879 18515044 18513879 ID=MS.gene98432.t1;Parent=MS.gene98432
chr5.4 exon 18513879 18514096 18513879 ID=MS.gene98432.t1.exon1;Parent=MS.gene98432.t1
chr5.4 CDS 18513879 18514096 18513879 ID=cds.MS.gene98432.t1;Parent=MS.gene98432.t1
chr5.4 exon 18514639 18515044 18514639 ID=MS.gene98432.t1.exon2;Parent=MS.gene98432.t1
chr5.4 CDS 18514639 18515044 18514639 ID=cds.MS.gene98432.t1;Parent=MS.gene98432.t1
Gene Sequence

>MS.gene98432

ATGGAACAACAACAGGAGAAAACTGGCACCGATATCAGTGAGTCGGGTCATGCCGTCGCAAATCTAAACTCTAATGATAATAACTTAGTTCAAGCCGGGTCAGGAGCAGAAGGAAGTAATGAAGCTAACTTAGTTCAAGCTGAGTCAGTACCAAAAGGAAGTCATGAAGCAAAGAGAAGGCGTAGGGAAAGGGCACATTGGACAGAAGGTGAACATAAGTAAGTATTCAATCTATCCTTGGAAGTTATATCTTTTTTTCTTTTTCAATTCTATTTTAGGTTAAATATATTCTTTTCAATTTAAATTAATAGATGAAGTATTAAATAGTTGTTAGATCGCATAACTACGAAATTATATTTTTATTTTAGACGAATAGTCTAGTGACTAGATACTCAACTATGGAGAAGTGGAAAATTTTACGATTCGAACCGCATGTAGATAAACGTCCTTGTAGCTACCAATTGATATGTATTTACAATACATTAAATAAAAAACACATTTATAGCTTTTTAGTTTGTATGATGTATATAAGAAATAATTCAGTTCTAGAAAAACAAAAATGATATTTATGTTCATAGATGCAAATTAATCGTTCTAGGTTGCATATCAACAAAGAAAAGAGAAAAAAATCAATGCAAGTGTTTCCATTGTTTTGGATACATACCAAGATATAGTTACCTCATTTCTTTATTATTTTCTTCTCTTATTATTTAATTGAATTTGAATATTTCACATTCATTCTATAATTTGTGATGTATAGGTTGTTTCTGGAGGGGCTAGAAAAATATGGTAAGGGACGTTGGAAAGATATTTCAAAAGAATTTGTGGTGACAAAGACTCCAATTCAAATTGCTAGCCATGCCCAAAAATACTTTATCCACCAAAATGTGAAAGATATAGAGAAGAGAAAACAGAGAAGTATACACGACACAACCTTAAACAAGAATGACACACCAGTCACTGAGATTCCTTCAGTTGAGCAACAAAATGAGCTTACTCCTTTAGTCACTTCTCCTATGGAACAACATGAGAATCCTCCTCAAGACACAGCCACCTCAAGACAAATGCAGTTGGTGCTGCTCTGTCCAATCGGTCCTACACGTACTGATATGAACAAACTTGAGAAGATGTGCAACTTGTTCAACTTGTTGGCAAAAGAACTTTGA
Protein sequence

>MS.gene98432.t1

MEQQQEKTGTDISESGHAVANLNSNDNNLVQAGSGAEGSNEANLVQAESVPKGSHEAKRRRRERAHWTEGEHKLFLEGLEKYGKGRWKDISKEFVVTKTPIQIASHAQKYFIHQNVKDIEKRKQRSIHDTTLNKNDTPVTEIPSVEQQNELTPLVTSPMEQHENPPQDTATSRQMQLVLLCPIGPTRTDMNKLEKMCNLFNLLAKEL