AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01273

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01273.t1 MTR_2g010600 90.184 163 15 1 1 163 1 162 1.88e-108 306
MS.gene01273.t1 MTR_4g050762 84.049 163 25 1 1 163 1 162 1.50e-94 271
MS.gene01273.t1 MTR_2g012370 84.049 163 25 1 1 163 1 162 1.50e-94 271
MS.gene01273.t1 MTR_2g010590 74.847 163 37 2 1 163 1 159 7.01e-89 256
MS.gene01273.t1 MTR_2g010650 67.647 170 43 7 1 163 1 165 2.28e-73 217
MS.gene01273.t1 MTR_2g010610 72.393 163 20 3 1 163 1 138 3.40e-72 213
MS.gene01273.t1 MTR_2g010630 69.872 156 39 5 13 163 13 165 9.33e-72 213
MS.gene01273.t1 MTR_2g010700 59.412 170 60 5 1 163 1 168 1.79e-65 197
MS.gene01273.t1 MTR_2g435490 54.717 159 68 2 6 163 9 164 4.96e-63 192
MS.gene01273.t1 MTR_2g010640 60.479 167 58 6 1 163 1 163 7.38e-61 186
MS.gene01273.t1 MTR_2g010670 57.738 168 62 6 1 163 1 164 1.16e-55 172
MS.gene01273.t1 MTR_2g010690 54.762 168 67 6 1 163 1 164 4.43e-53 166
MS.gene01273.t1 MTR_2g010580 50.331 151 70 3 13 163 19 164 5.72e-52 163
MS.gene01273.t1 MTR_4g092540 45.122 164 84 4 1 163 1 159 8.92e-45 145
MS.gene01273.t1 MTR_4g128750 50.735 136 63 2 29 163 41 173 2.17e-44 144
MS.gene01273.t1 MTR_4g128770 44.203 138 74 3 28 163 70 206 1.37e-38 130
MS.gene01273.t1 MTR_1g067290 42.029 138 74 4 28 162 73 207 6.19e-33 116
MS.gene01273.t1 MTR_8g078770 38.129 139 81 4 28 163 36 172 8.12e-26 97.1
MS.gene01273.t1 MTR_5g018770 31.844 179 103 4 4 163 7 185 1.14e-24 94.4
MS.gene01273.t1 MTR_4g092515 55.789 95 36 4 1 94 7 96 7.27e-23 88.2
MS.gene01273.t1 MTR_5g018755 38.462 91 51 4 78 163 13 103 1.13e-13 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01273.t1 AT2G14580 64.242 165 51 4 1 163 3 161 5.09e-70 209
MS.gene01273.t1 AT4G33720 59.259 162 62 2 2 163 6 163 5.18e-66 199
MS.gene01273.t1 AT2G14610 58.788 165 60 4 1 163 3 161 4.65e-64 194
MS.gene01273.t1 AT5G26130 58.228 158 64 2 6 163 11 166 1.35e-59 182
MS.gene01273.t1 AT3G19690 53.333 165 71 3 1 163 1 161 4.94e-59 181
MS.gene01273.t1 AT4G33710 59.859 142 55 2 22 163 27 166 1.95e-55 172
MS.gene01273.t1 AT2G19990 54.962 131 56 1 33 163 49 176 4.18e-50 159
MS.gene01273.t1 AT1G50060 52.410 166 71 5 1 163 1 161 7.84e-50 157
MS.gene01273.t1 AT4G25790 49.640 139 66 2 26 163 75 210 9.41e-48 154
MS.gene01273.t1 AT3G09590 48.551 138 66 2 28 163 52 186 4.63e-46 149
MS.gene01273.t1 AT5G57625 49.265 136 65 2 29 163 75 207 7.36e-46 149
MS.gene01273.t1 AT1G50050 53.012 166 71 5 1 163 1 162 9.81e-46 147
MS.gene01273.t1 AT4G30320 45.033 151 78 3 14 163 15 161 6.19e-44 142
MS.gene01273.t1 AT4G25780 50.000 138 66 3 28 163 54 190 3.49e-43 142
MS.gene01273.t1 AT4G33730 48.428 159 68 5 14 163 19 172 3.82e-43 141
MS.gene01273.t1 AT1G50050 51.829 164 72 5 1 161 1 160 1.66e-42 141
MS.gene01273.t1 AT5G02730 47.482 139 68 2 27 163 58 193 2.13e-42 140
MS.gene01273.t1 AT1G01310 46.715 137 68 3 28 163 87 219 1.14e-39 134
MS.gene01273.t1 AT4G31470 44.604 139 72 3 26 163 51 185 2.28e-38 129
MS.gene01273.t1 AT4G07820 46.479 142 70 4 22 163 25 160 1.08e-37 127
MS.gene01273.t1 AT5G66590 42.336 137 77 1 29 163 49 185 5.00e-34 118
MS.gene01273.t1 AT2G19970 43.262 141 71 5 30 163 39 177 1.27e-29 107
MS.gene01273.t1 AT2G19980 37.427 171 85 8 3 163 7 165 6.46e-26 97.1

Find 38 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGGCGGTGATAAACATTA+TGG 0.283064 2.2:-70887458 MS.gene01273:CDS
GCTGGGCTTATCCCTCATTA+TGG 0.334186 2.2:-70887645 MS.gene01273:CDS
CATAGTCTGCTTGTGAGTCT+TGG 0.335837 2.2:+70887606 None:intergenic
TATTAAGCATGCACTTAGTA+TGG 0.353177 2.2:+70887188 None:intergenic
GCCATTATACTCAGGTGGTT+TGG 0.358578 2.2:-70887316 MS.gene01273:CDS
TCCAAACCACCTGAGTATAA+TGG 0.398812 2.2:+70887315 None:intergenic
ATAGTCTGCTTGTGAGTCTT+GGG 0.401577 2.2:+70887607 None:intergenic
TTGGTGTTGCAAATATTGTT+TGG 0.407510 2.2:-70887553 MS.gene01273:CDS
GTTACTATTATAATCATAGT+TGG 0.429625 2.2:+70887364 None:intergenic
TGGTGTTGCAAATATTGTTT+GGG 0.451345 2.2:-70887552 MS.gene01273:CDS
TTGACGTCTTGCATCGTTGT+GGG 0.459049 2.2:+70887577 None:intergenic
GTGGCGGTGATAAACATTAT+GGG 0.460708 2.2:-70887457 MS.gene01273:CDS
ATTATTATCACATCTCACTT+TGG 0.463790 2.2:+70887268 None:intergenic
CGTTATTATAGTTGCCTGGT+GGG 0.465282 2.2:+70887216 None:intergenic
GAGAATCTAGCGTGGAGCTC+CGG 0.490150 2.2:-70887434 MS.gene01273:CDS
GTGAGATGTGATAATAATAG+AGG 0.514467 2.2:-70887263 MS.gene01273:CDS
ATCTGAGCCACTCATGTCGC+CGG 0.523273 2.2:+70887415 None:intergenic
CTTGACGTCTTGCATCGTTG+TGG 0.543312 2.2:+70887576 None:intergenic
GCTCAGATGCAGTGAAGTTG+TGG 0.543630 2.2:-70887400 MS.gene01273:CDS
CTCAGATGCAGTGAAGTTGT+GGG 0.551141 2.2:-70887399 MS.gene01273:CDS
TGGAGCTCCGGCGACATGAG+TGG 0.557633 2.2:-70887422 MS.gene01273:CDS
GTGTAACATGAACCATAATG+AGG 0.566235 2.2:+70887633 None:intergenic
ATAATGTTTATCACCGCCAC+CGG 0.571825 2.2:+70887460 None:intergenic
TCGTTATTATAGTTGCCTGG+TGG 0.573306 2.2:+70887215 None:intergenic
AAACTATGCTAATCAACGCA+AGG 0.596763 2.2:-70887504 MS.gene01273:CDS
TGGAGAAACTCAGTACGTGT+TGG 0.598633 2.2:-70887296 MS.gene01273:CDS
ACATGCAATTACGACCCACC+AGG 0.608369 2.2:-70887230 MS.gene01273:CDS
AACTATGCTAATCAACGCAA+GGG 0.616329 2.2:-70887503 MS.gene01273:CDS
TGTAACATGAACCATAATGA+GGG 0.618907 2.2:+70887634 None:intergenic
AACGATGCAAGACGTCAAGT+TGG 0.620216 2.2:-70887572 MS.gene01273:CDS
AAACTGATGCACTCCGGTGG+CGG 0.623369 2.2:-70887473 MS.gene01273:CDS
GTGTGGCCATTATACTCAGG+TGG 0.627875 2.2:-70887321 MS.gene01273:CDS
TGGCGGTGATAAACATTATG+GGG 0.629775 2.2:-70887456 MS.gene01273:CDS
AGTGTGTGGCCATTATACTC+AGG 0.651003 2.2:-70887324 MS.gene01273:CDS
GATTGTAAACTGATGCACTC+CGG 0.660976 2.2:-70887479 MS.gene01273:CDS
TGTAAACTGATGCACTCCGG+TGG 0.705347 2.2:-70887476 MS.gene01273:CDS
ATTATGGGGAGAATCTAGCG+TGG 0.720756 2.2:-70887442 MS.gene01273:CDS
TGTGCTGCTAATAAAGTGTG+TGG 0.730769 2.2:-70887338 MS.gene01273:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTACTATTATAATCATAGT+TGG + chr2.2:70887512-70887531 None:intergenic 20.0%
! ATTATTATCACATCTCACTT+TGG + chr2.2:70887608-70887627 None:intergenic 25.0%
GTGAGATGTGATAATAATAG+AGG - chr2.2:70887610-70887629 MS.gene01273:CDS 30.0%
TGTAACATGAACCATAATGA+GGG + chr2.2:70887242-70887261 None:intergenic 30.0%
! TTTTCGTTATTATAGTTGCC+TGG + chr2.2:70887664-70887683 None:intergenic 30.0%
!! TGGTGTTGCAAATATTGTTT+GGG - chr2.2:70887321-70887340 MS.gene01273:CDS 30.0%
!! TTGGTGTTGCAAATATTGTT+TGG - chr2.2:70887320-70887339 MS.gene01273:CDS 30.0%
AAACTATGCTAATCAACGCA+AGG - chr2.2:70887369-70887388 MS.gene01273:CDS 35.0%
AACTATGCTAATCAACGCAA+GGG - chr2.2:70887370-70887389 MS.gene01273:CDS 35.0%
GTGTAACATGAACCATAATG+AGG + chr2.2:70887243-70887262 None:intergenic 35.0%
! ATTTTCTCTATTGTGTGTGC+TGG - chr2.2:70887210-70887229 MS.gene01273:CDS 35.0%
! TTTTCTCTATTGTGTGTGCT+GGG - chr2.2:70887211-70887230 MS.gene01273:CDS 35.0%
ATAATGTTTATCACCGCCAC+CGG + chr2.2:70887416-70887435 None:intergenic 40.0%
ATAGTCTGCTTGTGAGTCTT+GGG + chr2.2:70887269-70887288 None:intergenic 40.0%
CGTTATTATAGTTGCCTGGT+GGG + chr2.2:70887660-70887679 None:intergenic 40.0%
GATTGTAAACTGATGCACTC+CGG - chr2.2:70887394-70887413 MS.gene01273:CDS 40.0%
GTGGCGGTGATAAACATTAT+GGG - chr2.2:70887416-70887435 MS.gene01273:CDS 40.0%
TCCAAACCACCTGAGTATAA+TGG + chr2.2:70887561-70887580 None:intergenic 40.0%
TCGTTATTATAGTTGCCTGG+TGG + chr2.2:70887661-70887680 None:intergenic 40.0%
TGGCGGTGATAAACATTATG+GGG - chr2.2:70887417-70887436 MS.gene01273:CDS 40.0%
! TGTGCTGCTAATAAAGTGTG+TGG - chr2.2:70887535-70887554 MS.gene01273:CDS 40.0%
AACGATGCAAGACGTCAAGT+TGG - chr2.2:70887301-70887320 MS.gene01273:CDS 45.0%
AGTGTGTGGCCATTATACTC+AGG - chr2.2:70887549-70887568 MS.gene01273:CDS 45.0%
ATTATGGGGAGAATCTAGCG+TGG - chr2.2:70887431-70887450 MS.gene01273:CDS 45.0%
CATAGTCTGCTTGTGAGTCT+TGG + chr2.2:70887270-70887289 None:intergenic 45.0%
CTCAGATGCAGTGAAGTTGT+GGG - chr2.2:70887474-70887493 MS.gene01273:CDS 45.0%
GCCATTATACTCAGGTGGTT+TGG - chr2.2:70887557-70887576 MS.gene01273:CDS 45.0%
TGGAGAAACTCAGTACGTGT+TGG - chr2.2:70887577-70887596 MS.gene01273:CDS 45.0%
TTGACGTCTTGCATCGTTGT+GGG + chr2.2:70887299-70887318 None:intergenic 45.0%
! GGTGGCGGTGATAAACATTA+TGG - chr2.2:70887415-70887434 MS.gene01273:CDS 45.0%
ACATGCAATTACGACCCACC+AGG - chr2.2:70887643-70887662 MS.gene01273:CDS 50.0%
CTTGACGTCTTGCATCGTTG+TGG + chr2.2:70887300-70887319 None:intergenic 50.0%
GCTCAGATGCAGTGAAGTTG+TGG - chr2.2:70887473-70887492 MS.gene01273:CDS 50.0%
GCTGGGCTTATCCCTCATTA+TGG - chr2.2:70887228-70887247 MS.gene01273:CDS 50.0%
GTGTGGCCATTATACTCAGG+TGG - chr2.2:70887552-70887571 MS.gene01273:CDS 50.0%
TGTAAACTGATGCACTCCGG+TGG - chr2.2:70887397-70887416 MS.gene01273:CDS 50.0%
AAACTGATGCACTCCGGTGG+CGG - chr2.2:70887400-70887419 MS.gene01273:CDS 55.0%
ATCTGAGCCACTCATGTCGC+CGG + chr2.2:70887461-70887480 None:intergenic 55.0%
GAGAATCTAGCGTGGAGCTC+CGG - chr2.2:70887439-70887458 MS.gene01273:CDS 55.0%
TGGAGCTCCGGCGACATGAG+TGG - chr2.2:70887451-70887470 MS.gene01273:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 70887202 70887693 70887202 ID=MS.gene01273
chr2.2 mRNA 70887202 70887693 70887202 ID=MS.gene01273.t1;Parent=MS.gene01273
chr2.2 exon 70887202 70887693 70887202 ID=MS.gene01273.t1.exon1;Parent=MS.gene01273.t1
chr2.2 CDS 70887202 70887693 70887202 ID=cds.MS.gene01273.t1;Parent=MS.gene01273.t1
Gene Sequence

>MS.gene01273

ATGAGTTCATTTTCTCTATTGTGTGTGCTGGGCTTATCCCTCATTATGGTTCATGTTACACATGCCCAAGACTCACAAGCAGACTATGTGAACGCCCACAACGATGCAAGACGTCAAGTTGGTGTTGCAAATATTGTTTGGGACAATACTGTTGCTGCTTTTGCACAAAACTATGCTAATCAACGCAAGGGTGATTGTAAACTGATGCACTCCGGTGGCGGTGATAAACATTATGGGGAGAATCTAGCGTGGAGCTCCGGCGACATGAGTGGCTCAGATGCAGTGAAGTTGTGGGTGAACGAGAAAGCCAACTATGATTATAATAGTAACACATGTGCTGCTAATAAAGTGTGTGGCCATTATACTCAGGTGGTTTGGAGAAACTCAGTACGTGTTGGATGTGCCAAAGTGAGATGTGATAATAATAGAGGAACATTCATTACATGCAATTACGACCCACCAGGCAACTATAATAACGAAAAGCCATACTAA
Protein sequence

>MS.gene01273.t1

MSSFSLLCVLGLSLIMVHVTHAQDSQADYVNAHNDARRQVGVANIVWDNTVAAFAQNYANQRKGDCKLMHSGGGDKHYGENLAWSSGDMSGSDAVKLWVNEKANYDYNSNTCAANKVCGHYTQVVWRNSVRVGCAKVRCDNNRGTFITCNYDPPGNYNNEKPY