AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051327

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051327.t1 MTR_4g119428 64.758 227 70 4 1 219 2 226 5.32e-93 273
MS.gene051327.t1 MTR_1g057270 56.140 228 91 2 1 219 1 228 6.86e-72 219
MS.gene051327.t1 MTR_7g105870 46.890 209 104 2 4 211 5 207 3.34e-48 158
MS.gene051327.t1 MTR_7g106000 38.636 220 118 4 1 213 1 210 1.78e-47 156
MS.gene051327.t1 MTR_7g106010 38.991 218 120 3 5 218 4 212 2.77e-47 155
MS.gene051327.t1 MTR_7g106030 36.073 219 126 4 5 218 7 216 3.06e-40 137
MS.gene051327.t1 MTR_7g105970 35.586 222 126 4 1 215 1 212 1.74e-36 128
MS.gene051327.t1 MTR_1g057400 35.165 182 113 2 38 214 11 192 1.59e-33 119
MS.gene051327.t1 MTR_6g071410 36.207 174 101 6 45 211 9 179 5.98e-25 97.8
MS.gene051327.t1 MTR_6g070890 36.207 174 101 6 45 211 9 179 5.98e-25 97.8
MS.gene051327.t1 MTR_6g471090 35.979 189 103 8 30 212 2 178 2.75e-24 95.9
MS.gene051327.t1 MTR_6g070900 34.483 174 103 6 47 211 8 179 8.03e-22 89.7
MS.gene051327.t1 MTR_6g071400 34.483 174 103 6 47 211 8 179 8.03e-22 89.7
MS.gene051327.t1 MTR_4g094322 75.510 49 12 0 171 219 2 50 1.57e-20 82.0
MS.gene051327.t1 MTR_2g011350 29.252 147 103 1 59 205 35 180 8.34e-20 84.0
MS.gene051327.t1 MTR_1g057290 39.333 150 86 2 72 216 52 201 3.47e-19 82.8
MS.gene051327.t1 MTR_3g078800 29.814 161 110 3 51 209 73 232 3.94e-17 78.2
MS.gene051327.t1 MTR_6g471080 37.647 170 98 6 48 211 7 174 4.40e-17 77.0
MS.gene051327.t1 MTR_2g048270 38.686 137 76 5 87 218 3 136 1.39e-16 74.7
MS.gene051327.t1 MTR_5g076170 31.410 156 103 4 63 216 96 249 1.43e-16 76.6
MS.gene051327.t1 MTR_5g087760 25.888 197 130 6 23 214 55 240 1.63e-16 76.3
MS.gene051327.t1 MTR_3g063310 30.872 149 93 3 66 209 87 230 1.66e-15 73.6
MS.gene051327.t1 MTR_7g106100 32.203 118 73 3 42 153 64 180 1.97e-13 67.8
MS.gene051327.t1 MTR_2g100060 25.170 147 108 2 61 206 78 223 4.30e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051327.t1 AT2G35460 38.182 220 128 3 4 215 3 222 6.43e-55 175
MS.gene051327.t1 AT2G35980 38.679 212 120 3 2 211 3 206 1.05e-52 169
MS.gene051327.t1 AT3G11650 37.443 219 129 3 6 217 8 225 3.46e-51 166
MS.gene051327.t1 AT5G06320 39.450 218 127 3 1 215 1 216 1.01e-47 157
MS.gene051327.t1 AT1G32270 33.775 151 98 1 69 217 1 151 1.42e-21 91.3
MS.gene051327.t1 AT1G32270 33.775 151 98 1 69 217 1 151 3.93e-21 90.9
MS.gene051327.t1 AT5G22870 25.767 163 117 3 46 205 24 185 6.20e-16 73.9
MS.gene051327.t1 AT4G01410 27.607 163 112 2 48 207 44 203 2.02e-15 72.8
MS.gene051327.t1 AT4G05220 22.051 195 149 3 16 209 14 206 3.74e-15 72.0
MS.gene051327.t1 AT3G52470 28.000 150 106 2 34 182 5 153 4.26e-15 71.6
MS.gene051327.t1 AT5G53730 29.825 171 103 5 61 217 40 207 7.03e-15 70.9
MS.gene051327.t1 AT2G27080 25.248 202 133 6 15 209 49 239 2.82e-14 70.1
MS.gene051327.t1 AT2G27080 25.248 202 133 6 15 209 49 239 2.82e-14 70.1
MS.gene051327.t1 AT4G09590 25.000 160 118 2 48 206 22 180 6.15e-13 65.9
MS.gene051327.t1 AT5G21130 25.743 202 132 6 15 209 70 260 1.99e-12 65.1
MS.gene051327.t1 AT1G61760 23.353 167 125 3 44 209 40 204 5.27e-12 63.2
MS.gene051327.t1 AT1G65690 25.444 169 122 4 49 215 71 237 1.09e-11 62.8
MS.gene051327.t1 AT2G35970 24.375 160 119 2 48 206 22 180 5.20e-11 60.5
MS.gene051327.t1 AT5G36970 25.828 151 109 3 60 209 78 226 5.70e-11 60.8

Find 43 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATAATTGGTTTCCTCTTT+TGG 0.148150 4.1:-19300689 MS.gene051327:CDS
GCAAAACACTTGTATTCTTA+TGG 0.189397 4.1:+19300445 None:intergenic
CAAAACACTTGTATTCTTAT+GGG 0.307477 4.1:+19300446 None:intergenic
TTCAAATCGCAATGAAGTTT+AGG 0.324721 4.1:+19300267 None:intergenic
CAAGGGATTCATTTGAGTTC+AGG 0.328368 4.1:-19300402 MS.gene051327:CDS
ATTGTCATAGTAGCAATAAT+TGG 0.352334 4.1:-19300702 MS.gene051327:CDS
TAAACTTCATTGCGATTTGA+AGG 0.374826 4.1:-19300265 MS.gene051327:CDS
CGCTGGGCTTGTTTAGGTCT+AGG 0.393225 4.1:-19300299 MS.gene051327:CDS
CTTCACTAACGCTGAATTTG+AGG 0.395049 4.1:+19300646 None:intergenic
TCTAAATTTGAGGTGTACGC+TGG 0.411534 4.1:-19300316 MS.gene051327:CDS
GGTGTACGCTGGGCTTGTTT+AGG 0.415997 4.1:-19300305 MS.gene051327:CDS
AAGTTTGTTTCTCAAACCTT+AGG 0.419715 4.1:-19300483 MS.gene051327:CDS
TCAAATGTTAGAGTTCAATA+AGG 0.431524 4.1:-19300379 MS.gene051327:CDS
GCAGAAGCCGCAACCATTGT+TGG 0.436398 4.1:+19300788 None:intergenic
CAAAACCCTAATCGAAAAGT+TGG 0.457401 4.1:-19300552 MS.gene051327:CDS
TGCAGTTGCTTCAGAGGATG+TGG 0.464777 4.1:-19300768 MS.gene051327:CDS
TTCGACGGCGAGGGGATGGA+AGG 0.471157 4.1:+19300831 None:intergenic
ACGCTGAATTTGAGGACGTA+GGG 0.476124 4.1:+19300654 None:intergenic
AACCATTGTTGGTGTGGCGT+CGG 0.479384 4.1:+19300799 None:intergenic
CGGTCAGATTTCGACGGCGA+GGG 0.491291 4.1:+19300822 None:intergenic
AGATTTCGACGGCGAGGGGA+TGG 0.498045 4.1:+19300827 None:intergenic
GGCTTCTGCAGTTGCTTCAG+AGG 0.506618 4.1:-19300774 MS.gene051327:CDS
AACAATGGAACTTCTTCGTA+GGG 0.531313 4.1:-19300228 None:intergenic
CATTGTTGGTGTGGCGTCGG+CGG 0.541260 4.1:+19300802 None:intergenic
GTTCCATTGTTTGATGTCAA+CGG 0.541893 4.1:+19300240 None:intergenic
CTAAATTTGAGGTGTACGCT+GGG 0.543006 4.1:-19300315 MS.gene051327:CDS
CGCCACACCAACAATGGTTG+CGG 0.544206 4.1:-19300795 MS.gene051327:CDS
AAACAATGGAACTTCTTCGT+AGG 0.544398 4.1:-19300229 None:intergenic
CGCCGACGCCACACCAACAA+TGG 0.545022 4.1:-19300801 MS.gene051327:CDS
AAAACACTTGTATTCTTATG+GGG 0.553234 4.1:+19300447 None:intergenic
GGCGCACAATAAACCAAAAG+AGG 0.561827 4.1:+19300676 None:intergenic
AGCCGCAACCATTGTTGGTG+TGG 0.573197 4.1:+19300793 None:intergenic
TCGACGGCGAGGGGATGGAA+GGG 0.573313 4.1:+19300832 None:intergenic
CAACTCCACAATGCTTACTA+CGG 0.575454 4.1:-19300855 MS.gene051327:CDS
GGTCAGATTTCGACGGCGAG+GGG 0.601595 4.1:+19300823 None:intergenic
TGCTACTATGACAATGATTG+TGG 0.622752 4.1:+19300710 None:intergenic
GCGGTCAGATTTCGACGGCG+AGG 0.623861 4.1:+19300821 None:intergenic
CGTCGGCGGTCAGATTTCGA+CGG 0.641839 4.1:+19300816 None:intergenic
CGCTGAATTTGAGGACGTAG+GGG 0.649005 4.1:+19300655 None:intergenic
AGTTGCTTCAGAGGATGTGG+TGG 0.654726 4.1:-19300765 MS.gene051327:CDS
AAGGGCCGTAGTAAGCATTG+TGG 0.684765 4.1:+19300850 None:intergenic
GTTCCGTTGACATCAAACAA+TGG 0.691708 4.1:-19300243 MS.gene051327:CDS
AACGCTGAATTTGAGGACGT+AGG 0.716355 4.1:+19300653 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAACACTTGTATTCTTATG+GGG + chr4.1:19300653-19300672 None:intergenic 25.0%
! ATTGTCATAGTAGCAATAAT+TGG - chr4.1:19300395-19300414 MS.gene051327:CDS 25.0%
! CAAAACACTTGTATTCTTAT+GGG + chr4.1:19300654-19300673 None:intergenic 25.0%
! TCAAATGTTAGAGTTCAATA+AGG - chr4.1:19300718-19300737 MS.gene051327:CDS 25.0%
! TTCAATAAGGAGAAAAATGA+TGG - chr4.1:19300731-19300750 MS.gene051327:CDS 25.0%
!! ATAAGAATACAAGTGTTTTG+CGG - chr4.1:19300654-19300673 MS.gene051327:CDS 25.0%
!! TGAAGGTTTTTCTAAATTTG+AGG - chr4.1:19300771-19300790 MS.gene051327:CDS 25.0%
GCAAAACACTTGTATTCTTA+TGG + chr4.1:19300655-19300674 None:intergenic 30.0%
TAAACTTCATTGCGATTTGA+AGG - chr4.1:19300832-19300851 MS.gene051327:CDS 30.0%
TTCAAATCGCAATGAAGTTT+AGG + chr4.1:19300833-19300852 None:intergenic 30.0%
! AAGTTTGTTTCTCAAACCTT+AGG - chr4.1:19300614-19300633 MS.gene051327:CDS 30.0%
! TAAGAATACAAGTGTTTTGC+GGG - chr4.1:19300655-19300674 MS.gene051327:CDS 30.0%
!! CAATAATTGGTTTCCTCTTT+TGG - chr4.1:19300408-19300427 MS.gene051327:CDS 30.0%
CAAAACCCTAATCGAAAAGT+TGG - chr4.1:19300545-19300564 MS.gene051327:CDS 35.0%
GTTCCATTGTTTGATGTCAA+CGG + chr4.1:19300860-19300879 None:intergenic 35.0%
TGCTACTATGACAATGATTG+TGG + chr4.1:19300390-19300409 None:intergenic 35.0%
! CAACTTTTCGATTAGGGTTT+TGG + chr4.1:19300547-19300566 None:intergenic 35.0%
! CGATACCAACTTTTCGATTA+GGG + chr4.1:19300553-19300572 None:intergenic 35.0%
! GGGTTGAAAGAATTTTCCTA+AGG + chr4.1:19300633-19300652 None:intergenic 35.0%
! TCGATACCAACTTTTCGATT+AGG + chr4.1:19300554-19300573 None:intergenic 35.0%
!! CTGCTTTTAAAGGTAAGCAA+GGG - chr4.1:19300678-19300697 MS.gene051327:CDS 35.0%
!! GAGAAAAATGATGGCGTTTT+TGG - chr4.1:19300740-19300759 MS.gene051327:CDS 35.0%
!!! CGTTTTTGGAATTGACTTGA+AGG - chr4.1:19300754-19300773 MS.gene051327:CDS 35.0%
CAACTCCACAATGCTTACTA+CGG - chr4.1:19300242-19300261 MS.gene051327:CDS 40.0%
CTTCACTAACGCTGAATTTG+AGG + chr4.1:19300454-19300473 None:intergenic 40.0%
GTTCCGTTGACATCAAACAA+TGG - chr4.1:19300854-19300873 MS.gene051327:CDS 40.0%
! CAAGGGATTCATTTGAGTTC+AGG - chr4.1:19300695-19300714 MS.gene051327:CDS 40.0%
! CTAAATTTGAGGTGTACGCT+GGG - chr4.1:19300782-19300801 MS.gene051327:CDS 40.0%
! TCTAAATTTGAGGTGTACGC+TGG - chr4.1:19300781-19300800 MS.gene051327:CDS 40.0%
!!! GCTGCTTTTAAAGGTAAGCA+AGG - chr4.1:19300677-19300696 MS.gene051327:CDS 40.0%
AACGCTGAATTTGAGGACGT+AGG + chr4.1:19300447-19300466 None:intergenic 45.0%
ACGCTGAATTTGAGGACGTA+GGG + chr4.1:19300446-19300465 None:intergenic 45.0%
GGCGCACAATAAACCAAAAG+AGG + chr4.1:19300424-19300443 None:intergenic 45.0%
!!! GTTTTGCGGGCTGCTTTTAA+AGG - chr4.1:19300668-19300687 MS.gene051327:CDS 45.0%
AACCATTGTTGGTGTGGCGT+CGG + chr4.1:19300301-19300320 None:intergenic 50.0%
AGTTGCTTCAGAGGATGTGG+TGG - chr4.1:19300332-19300351 MS.gene051327:CDS 50.0%
CGCTGAATTTGAGGACGTAG+GGG + chr4.1:19300445-19300464 None:intergenic 50.0%
TGCAGTTGCTTCAGAGGATG+TGG - chr4.1:19300329-19300348 MS.gene051327:CDS 50.0%
! AAGGGCCGTAGTAAGCATTG+TGG + chr4.1:19300250-19300269 None:intergenic 50.0%
AGCCGCAACCATTGTTGGTG+TGG + chr4.1:19300307-19300326 None:intergenic 55.0%
CGCCACACCAACAATGGTTG+CGG - chr4.1:19300302-19300321 MS.gene051327:CDS 55.0%
GCAGAAGCCGCAACCATTGT+TGG + chr4.1:19300312-19300331 None:intergenic 55.0%
GGCTTCTGCAGTTGCTTCAG+AGG - chr4.1:19300323-19300342 MS.gene051327:CDS 55.0%
! CGCTGGGCTTGTTTAGGTCT+AGG - chr4.1:19300798-19300817 MS.gene051327:CDS 55.0%
! GGTGTACGCTGGGCTTGTTT+AGG - chr4.1:19300792-19300811 MS.gene051327:CDS 55.0%
AGATTTCGACGGCGAGGGGA+TGG + chr4.1:19300273-19300292 None:intergenic 60.0%
CGGTCAGATTTCGACGGCGA+GGG + chr4.1:19300278-19300297 None:intergenic 60.0%
CGTCGGCGGTCAGATTTCGA+CGG + chr4.1:19300284-19300303 None:intergenic 60.0%
GGTCAGATTTCGACGGCGAG+GGG + chr4.1:19300277-19300296 None:intergenic 60.0%
! CATTGTTGGTGTGGCGTCGG+CGG + chr4.1:19300298-19300317 None:intergenic 60.0%
CGCCGACGCCACACCAACAA+TGG - chr4.1:19300296-19300315 MS.gene051327:CDS 65.0%
GCGGTCAGATTTCGACGGCG+AGG + chr4.1:19300279-19300298 None:intergenic 65.0%
TCGACGGCGAGGGGATGGAA+GGG + chr4.1:19300268-19300287 None:intergenic 65.0%
TTCGACGGCGAGGGGATGGA+AGG + chr4.1:19300269-19300288 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 19300230 19300889 19300230 ID=MS.gene051327
chr4.1 mRNA 19300230 19300889 19300230 ID=MS.gene051327.t1;Parent=MS.gene051327
chr4.1 exon 19300230 19300889 19300230 ID=MS.gene051327.t1.exon1;Parent=MS.gene051327.t1
chr4.1 CDS 19300230 19300889 19300230 ID=cds.MS.gene051327.t1;Parent=MS.gene051327.t1
Gene Sequence

>MS.gene051327

ATGGCAGATAATCAACTCCACAATGCTTACTACGGCCCTTCCATCCCCTCGCCGTCGAAATCTGACCGCCGACGCCACACCAACAATGGTTGCGGCTTCTGCAGTTGCTTCAGAGGATGTGGTGGTTGCATCTTCAGCTTCTTATGCAAAATCATTACCACAATCATTGTCATAGTAGCAATAATTGGTTTCCTCTTTTGGTTTATTGTGCGCCCCTACGTCCTCAAATTCAGCGTTAGTGAAGCATCACTTACACTATTCAATTTCACAAACAACAACACATTTAACTATGATCTTTCTGTCAACATATCGATCCAAAACCCTAATCGAAAAGTTGGTATCGATTATGAAGACATCGAAATGTTTGCATTTTATAAAGATCTTAAGTTTGTTTCTCAAACCTTAGGAAAATTCTTTCAACCCCATAAGAATACAAGTGTTTTGCGGGCTGCTTTTAAAGGTAAGCAAGGGATTCATTTGAGTTCAGGTCAAATGTTAGAGTTCAATAAGGAGAAAAATGATGGCGTTTTTGGAATTGACTTGAAGGTTTTTCTAAATTTGAGGTGTACGCTGGGCTTGTTTAGGTCTAGGAATGTGAAACCTAAACTTCATTGCGATTTGAAGGTTCCGTTGACATCAAACAATGGAACTTCTTCGTAG
Protein sequence

>MS.gene051327.t1

MADNQLHNAYYGPSIPSPSKSDRRRHTNNGCGFCSCFRGCGGCIFSFLCKIITTIIVIVAIIGFLFWFIVRPYVLKFSVSEASLTLFNFTNNNTFNYDLSVNISIQNPNRKVGIDYEDIEMFAFYKDLKFVSQTLGKFFQPHKNTSVLRAAFKGKQGIHLSSGQMLEFNKEKNDGVFGIDLKVFLNLRCTLGLFRSRNVKPKLHCDLKVPLTSNNGTSS