AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31415

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31415.t1 MTR_2g090765 98.795 249 3 0 1 249 1 249 1.11e-179 493
MS.gene31415.t1 MTR_7g101080 46.193 197 104 2 16 210 17 213 1.52e-51 168
MS.gene31415.t1 MTR_4g059720 48.913 184 90 2 9 188 9 192 8.88e-49 161
MS.gene31415.t1 MTR_2g093990 48.649 148 76 0 38 185 41 188 4.39e-40 139
MS.gene31415.t1 MTR_4g059840 38.222 225 129 5 31 245 66 290 9.29e-40 139
MS.gene31415.t1 MTR_4g059790 40.704 199 108 3 31 227 66 256 6.34e-38 134
MS.gene31415.t1 MTR_4g053380 44.633 177 93 4 31 202 70 246 2.83e-37 133
MS.gene31415.t1 MTR_8g087460 37.255 255 136 10 14 248 66 316 9.67e-36 129
MS.gene31415.t1 MTR_8g087470 36.863 255 137 10 14 248 66 316 2.61e-35 128
MS.gene31415.t1 MTR_2g017960 40.449 178 103 2 38 214 68 243 1.01e-34 125
MS.gene31415.t1 MTR_2g017970 40.449 178 103 2 38 214 68 243 1.32e-34 125
MS.gene31415.t1 MTR_2g093980 36.323 223 134 5 29 249 60 276 3.79e-34 124
MS.gene31415.t1 MTR_8g087450 37.104 221 133 4 31 247 70 288 4.69e-32 119
MS.gene31415.t1 MTR_2g017950 36.199 221 119 6 20 220 50 268 6.36e-32 119
MS.gene31415.t1 MTR_2g093970 40.789 152 89 1 38 188 69 220 3.45e-30 114
MS.gene31415.t1 MTR_4g059780 38.650 163 99 1 27 188 79 241 7.47e-30 113
MS.gene31415.t1 MTR_7g075453 33.471 242 132 6 12 232 161 394 1.89e-28 112
MS.gene31415.t1 MTR_5g098060 34.524 168 108 2 37 203 47 213 9.79e-28 107
MS.gene31415.t1 MTR_5g098420 29.960 247 139 8 25 248 184 419 3.46e-18 83.2
MS.gene31415.t1 MTR_2g437700 29.630 189 123 6 8 190 164 348 1.75e-14 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31415.t1 AT2G20520 50.806 248 107 5 9 249 6 245 2.56e-73 224
MS.gene31415.t1 AT1G03870 53.953 215 92 3 37 249 38 247 2.08e-71 219
MS.gene31415.t1 AT5G44130 56.332 229 92 4 6 230 3 227 2.77e-68 211
MS.gene31415.t1 AT5G03170 56.667 180 75 3 27 204 25 203 2.05e-60 191
MS.gene31415.t1 AT5G60490 47.682 151 78 1 36 185 37 187 1.46e-41 142
MS.gene31415.t1 AT2G04780 34.896 192 117 4 37 224 45 232 1.26e-25 101
MS.gene31415.t1 AT2G04780 34.896 192 117 4 37 224 45 232 1.26e-25 101
MS.gene31415.t1 AT3G60900 33.333 192 122 3 18 209 171 356 6.03e-24 99.8
MS.gene31415.t1 AT2G45470 32.512 203 123 4 17 210 159 356 1.47e-18 84.3
MS.gene31415.t1 AT3G46550 31.579 171 109 5 20 185 190 357 1.87e-18 84.3
MS.gene31415.t1 AT4G12730 34.123 211 122 9 25 229 178 377 7.10e-18 82.4
MS.gene31415.t1 AT5G55730 31.169 154 100 3 37 189 185 333 6.23e-13 68.2
MS.gene31415.t1 AT5G55730 31.169 154 100 3 37 189 185 333 6.23e-13 68.2

Find 61 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGCCTGAGGGTGCTGGTGC+TGG 0.134067 2.4:-9640337 None:intergenic
AGGGTGCTGGTGCTGGGGCT+TGG 0.151988 2.4:-9640330 None:intergenic
CTGGTGCTGGGGCTTGGGCT+TGG 0.184032 2.4:-9640324 None:intergenic
GGCCTGAGGGTGCTGGTGCT+GGG 0.229466 2.4:-9640336 None:intergenic
AAGATTGATGTGATGTTTAT+TGG 0.232703 2.4:-9640358 None:intergenic
TAATACCTGATGGAAGATTT+TGG 0.242668 2.4:-9640510 None:intergenic
CTTCTGGTAAAGAAGGTAAT+TGG 0.246525 2.4:+9640763 MS.gene31415:CDS
GGGTGCTGGTGCTGGGGCTT+GGG 0.247233 2.4:-9640329 None:intergenic
TCGGAAAGAGAGTAGTATTT+TGG 0.290230 2.4:-9640705 None:intergenic
GGGGCTTGGGCTTGGATTTG+TGG 0.297552 2.4:-9640316 None:intergenic
CCAGAAGCTTGTGTTCTAAC+TGG 0.300644 2.4:-9640747 None:intergenic
GCTGGAAGGAATGTTGGTTT+TGG 0.343086 2.4:+9641053 MS.gene31415:CDS
TCCTTTGGCTGTTTATCAAT+TGG 0.345240 2.4:+9640875 MS.gene31415:CDS
TTTGGATTTGTTGCTGGGCT+TGG 0.356493 2.4:+9641071 MS.gene31415:CDS
TTCTGGTAAAGAAGGTAATT+GGG 0.362073 2.4:+9640764 MS.gene31415:CDS
ATTTGAAACTGTTAAGAAAT+CGG 0.370630 2.4:-9640724 None:intergenic
TTTGGAAGGCATTGTCTGTT+GGG 0.376563 2.4:-9640492 None:intergenic
AGATTGATGTGATGTTTATT+GGG 0.381794 2.4:-9640357 None:intergenic
TTTGAGACAACAATTTCCTT+TGG 0.394518 2.4:+9640860 MS.gene31415:CDS
TGTCTCAAAGCATTGTTGAT+AGG 0.394899 2.4:-9640846 None:intergenic
AACCAAGTCAATGTTTCAAC+TGG 0.415400 2.4:+9640810 MS.gene31415:CDS
CTTCAGAAGTTGAGTTGAGT+TGG 0.431445 2.4:-9640453 None:intergenic
AAGTTGAGTTGAGTTGGGTT+TGG 0.439465 2.4:-9640447 None:intergenic
CCAGTTAGAACACAAGCTTC+TGG 0.442793 2.4:+9640747 MS.gene31415:CDS
TTTATTGGGCCTGAGGGTGC+TGG 0.445785 2.4:-9640343 None:intergenic
GCCTGAGGGTGCTGGTGCTG+GGG 0.448279 2.4:-9640335 None:intergenic
TTGGATTTGTGGAGTTAAGA+AGG 0.451732 2.4:-9640305 None:intergenic
TTCAGAAGTTGAGTTGAGTT+GGG 0.456224 2.4:-9640452 None:intergenic
TGGGCTTGGTTTGATTTGCA+TGG 0.457325 2.4:+9641085 MS.gene31415:CDS
GCCCCAGCACCAGCACCCTC+AGG 0.463369 2.4:+9640334 MS.gene31415:CDS
AAGAAGGATGATAGTGCAGC+TGG 0.464254 2.4:+9641035 MS.gene31415:CDS
GGGCTTGGTTTGATTTGCAT+GGG 0.469150 2.4:+9641086 MS.gene31415:CDS
CCGAGCAGCAGCGACGTTGA+AGG 0.470821 2.4:+9640987 MS.gene31415:CDS
GACGAATGAGGAAGGTGTAT+TGG 0.472056 2.4:-9640393 None:intergenic
GCCTTCCAAAATCTTCCATC+AGG 0.478103 2.4:+9640505 MS.gene31415:CDS
GTGAGAAGAATGAGTGCAAG+AGG 0.488921 2.4:-9640274 None:intergenic
CTCCAGTTGAAACATTGACT+TGG 0.506376 2.4:-9640812 None:intergenic
GAATGAGTTGAACTTTCTGT+TGG 0.508496 2.4:-9640668 None:intergenic
CCTTCAACGTCGCTGCTGCT+CGG 0.510769 2.4:-9640987 None:intergenic
ACACAAGCTTCTGGTAAAGA+AGG 0.515910 2.4:+9640756 MS.gene31415:CDS
ATCTCCAGCGTCTAGTAAGA+AGG 0.521844 2.4:+9641019 MS.gene31415:CDS
TGGATTTGTGGAGTTAAGAA+GGG 0.522153 2.4:-9640304 None:intergenic
TTCTTACTAGACGCTGGAGA+TGG 0.526597 2.4:-9641017 None:intergenic
CAACTCAACTCAACTTCTGA+AGG 0.527769 2.4:+9640454 MS.gene31415:CDS
TAAGTCTCCATCTTCATCTC+CGG 0.540687 2.4:+9640932 MS.gene31415:CDS
TTGGAAGGCATTGTCTGTTG+GGG 0.549695 2.4:-9640491 None:intergenic
TTTCATTGAGGAGACGAATG+AGG 0.550194 2.4:-9640405 None:intergenic
TTAGGAGCCGGAGATGAAGA+TGG 0.552898 2.4:-9640939 None:intergenic
TCCAATTGATAAACAGCCAA+AGG 0.570662 2.4:-9640876 None:intergenic
GTGATGTTTATTGGGCCTGA+GGG 0.572050 2.4:-9640349 None:intergenic
GGCTGTTTATCAATTGGACA+AGG 0.577680 2.4:+9640881 MS.gene31415:CDS
ATTGAGGAGACGAATGAGGA+AGG 0.579677 2.4:-9640401 None:intergenic
GAACTTTCTGTTGGTCTGAG+AGG 0.589738 2.4:-9640659 None:intergenic
GGTCTTCACTTCACTTCACA+AGG 0.592303 2.4:+9640786 MS.gene31415:CDS
AGTGCAGCTGGAAGGAATGT+TGG 0.593131 2.4:+9641047 MS.gene31415:CDS
TCATCCTTCTTACTAGACGC+TGG 0.596871 2.4:-9641023 None:intergenic
TGTGATGTTTATTGGGCCTG+AGG 0.598868 2.4:-9640350 None:intergenic
TCTGGTAAAGAAGGTAATTG+GGG 0.623440 2.4:+9640765 MS.gene31415:CDS
GAGTGCAAGAGGTGTTGTAG+TGG 0.624287 2.4:-9640263 None:intergenic
AGGATGATAGTGCAGCTGGA+AGG 0.628901 2.4:+9641039 MS.gene31415:CDS
TGAGTTGTTGAGTTTCATTG+AGG 0.637415 2.4:-9640417 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAATTATAATACCTGA+TGG - chr2.4:9640523-9640542 None:intergenic 15.0%
!! CATGCAAGTTATAATTATAT+AGG - chr2.4:9640587-9640606 None:intergenic 20.0%
!! TAACATTTATGTCTATTATC+AGG + chr2.4:9640624-9640643 MS.gene31415:intron 20.0%
!!! ATTTGAAACTGTTAAGAAAT+CGG - chr2.4:9640727-9640746 None:intergenic 20.0%
! AAGATTGATGTGATGTTTAT+TGG - chr2.4:9640361-9640380 None:intergenic 25.0%
! AGATTGATGTGATGTTTATT+GGG - chr2.4:9640360-9640379 None:intergenic 25.0%
TTCTGGTAAAGAAGGTAATT+GGG + chr2.4:9640764-9640783 MS.gene31415:CDS 30.0%
! ACATCAATCTTTGAAAAAGC+TGG + chr2.4:9640370-9640389 MS.gene31415:CDS 30.0%
! TAATACCTGATGGAAGATTT+TGG - chr2.4:9640513-9640532 None:intergenic 30.0%
! TTGTTACCTTCTGAACTTTT+TGG + chr2.4:9640906-9640925 MS.gene31415:CDS 30.0%
! TTTGAGACAACAATTTCCTT+TGG + chr2.4:9640860-9640879 MS.gene31415:CDS 30.0%
!!! AGTAGTATTTTGGTGTAACA+TGG - chr2.4:9640698-9640717 None:intergenic 30.0%
AACCAAGTCAATGTTTCAAC+TGG + chr2.4:9640810-9640829 MS.gene31415:CDS 35.0%
CTTCTGGTAAAGAAGGTAAT+TGG + chr2.4:9640763-9640782 MS.gene31415:CDS 35.0%
TCCAATTGATAAACAGCCAA+AGG - chr2.4:9640879-9640898 None:intergenic 35.0%
TCCTTTGGCTGTTTATCAAT+TGG + chr2.4:9640875-9640894 MS.gene31415:CDS 35.0%
TCTGGTAAAGAAGGTAATTG+GGG + chr2.4:9640765-9640784 MS.gene31415:CDS 35.0%
TGAGTTGTTGAGTTTCATTG+AGG - chr2.4:9640420-9640439 None:intergenic 35.0%
TGGATTTGTGGAGTTAAGAA+GGG - chr2.4:9640307-9640326 None:intergenic 35.0%
TTAGCACCAAAAAGTTCAGA+AGG - chr2.4:9640915-9640934 None:intergenic 35.0%
TTGGATTTGTGGAGTTAAGA+AGG - chr2.4:9640308-9640327 None:intergenic 35.0%
! GAATGAGTTGAACTTTCTGT+TGG - chr2.4:9640671-9640690 None:intergenic 35.0%
! TCGGAAAGAGAGTAGTATTT+TGG - chr2.4:9640708-9640727 None:intergenic 35.0%
!! TGTCTCAAAGCATTGTTGAT+AGG - chr2.4:9640849-9640868 None:intergenic 35.0%
!! TTCAGAAGTTGAGTTGAGTT+GGG - chr2.4:9640455-9640474 None:intergenic 35.0%
!!! TTGGTTTTGGATTTGTTGCT+GGG + chr2.4:9641066-9641085 MS.gene31415:CDS 35.0%
ACACAAGCTTCTGGTAAAGA+AGG + chr2.4:9640756-9640775 MS.gene31415:CDS 40.0%
CAACTCAACTCAACTTCTGA+AGG + chr2.4:9640454-9640473 MS.gene31415:CDS 40.0%
GGCTGTTTATCAATTGGACA+AGG + chr2.4:9640881-9640900 MS.gene31415:CDS 40.0%
TAAGTCTCCATCTTCATCTC+CGG + chr2.4:9640932-9640951 MS.gene31415:CDS 40.0%
TTTCATTGAGGAGACGAATG+AGG - chr2.4:9640408-9640427 None:intergenic 40.0%
! ACCTGATGGAAGATTTTGGA+AGG - chr2.4:9640509-9640528 None:intergenic 40.0%
! CTCCAGTTGAAACATTGACT+TGG - chr2.4:9640815-9640834 None:intergenic 40.0%
!! AAGTTGAGTTGAGTTGGGTT+TGG - chr2.4:9640450-9640469 None:intergenic 40.0%
!! CTTCAGAAGTTGAGTTGAGT+TGG - chr2.4:9640456-9640475 None:intergenic 40.0%
!! TTTGGAAGGCATTGTCTGTT+GGG - chr2.4:9640495-9640514 None:intergenic 40.0%
!!! GTTGGTTTTGGATTTGTTGC+TGG + chr2.4:9641065-9641084 MS.gene31415:CDS 40.0%
!!! TTTTGGAAGGCATTGTCTGT+TGG - chr2.4:9640496-9640515 None:intergenic 40.0%
ATCTCCAGCGTCTAGTAAGA+AGG + chr2.4:9641019-9641038 MS.gene31415:CDS 45.0%
ATTGAGGAGACGAATGAGGA+AGG - chr2.4:9640404-9640423 None:intergenic 45.0%
CCAGAAGCTTGTGTTCTAAC+TGG - chr2.4:9640750-9640769 None:intergenic 45.0%
CCAGTTAGAACACAAGCTTC+TGG + chr2.4:9640747-9640766 MS.gene31415:CDS 45.0%
GCCTTCCAAAATCTTCCATC+AGG + chr2.4:9640505-9640524 MS.gene31415:CDS 45.0%
GGTCTTCACTTCACTTCACA+AGG + chr2.4:9640786-9640805 MS.gene31415:CDS 45.0%
GTGAGAAGAATGAGTGCAAG+AGG - chr2.4:9640277-9640296 None:intergenic 45.0%
GTGATGTTTATTGGGCCTGA+GGG - chr2.4:9640352-9640371 None:intergenic 45.0%
TCATCCTTCTTACTAGACGC+TGG - chr2.4:9641026-9641045 None:intergenic 45.0%
TGTGATGTTTATTGGGCCTG+AGG - chr2.4:9640353-9640372 None:intergenic 45.0%
TTCTTACTAGACGCTGGAGA+TGG - chr2.4:9641020-9641039 None:intergenic 45.0%
! AAGAAGGATGATAGTGCAGC+TGG + chr2.4:9641035-9641054 MS.gene31415:CDS 45.0%
! GAACTTTCTGTTGGTCTGAG+AGG - chr2.4:9640662-9640681 None:intergenic 45.0%
! GAAGGAGTTTTCGACGACTT+AGG - chr2.4:9640960-9640979 None:intergenic 45.0%
! GACGAATGAGGAAGGTGTAT+TGG - chr2.4:9640396-9640415 None:intergenic 45.0%
!! GGGCTTGGTTTGATTTGCAT+GGG + chr2.4:9641086-9641105 MS.gene31415:CDS 45.0%
!! TGGGCTTGGTTTGATTTGCA+TGG + chr2.4:9641085-9641104 MS.gene31415:CDS 45.0%
!! TTGGAAGGCATTGTCTGTTG+GGG - chr2.4:9640494-9640513 None:intergenic 45.0%
!! TTTGGATTTGTTGCTGGGCT+TGG + chr2.4:9641071-9641090 MS.gene31415:CDS 45.0%
!!! GCTGGAAGGAATGTTGGTTT+TGG + chr2.4:9641053-9641072 MS.gene31415:CDS 45.0%
AGTGCAGCTGGAAGGAATGT+TGG + chr2.4:9641047-9641066 MS.gene31415:CDS 50.0%
TTAGGAGCCGGAGATGAAGA+TGG - chr2.4:9640942-9640961 None:intergenic 50.0%
! AGGATGATAGTGCAGCTGGA+AGG + chr2.4:9641039-9641058 MS.gene31415:CDS 50.0%
! GTTTTCGACGACTTAGGAGC+CGG - chr2.4:9640954-9640973 None:intergenic 50.0%
!! GAGTGCAAGAGGTGTTGTAG+TGG - chr2.4:9640266-9640285 None:intergenic 50.0%
!!! CTGCTGCTCGGTGTTTTAGA+AGG - chr2.4:9640978-9640997 None:intergenic 50.0%
! TTTATTGGGCCTGAGGGTGC+TGG - chr2.4:9640346-9640365 None:intergenic 55.0%
CCTTCAACGTCGCTGCTGCT+CGG - chr2.4:9640990-9641009 None:intergenic 60.0%
GGGGCTTGGGCTTGGATTTG+TGG - chr2.4:9640319-9640338 None:intergenic 60.0%
CCGAGCAGCAGCGACGTTGA+AGG + chr2.4:9640987-9641006 MS.gene31415:CDS 65.0%
! CTGGTGCTGGGGCTTGGGCT+TGG - chr2.4:9640327-9640346 None:intergenic 70.0%
!! AGGGTGCTGGTGCTGGGGCT+TGG - chr2.4:9640333-9640352 None:intergenic 70.0%
!! GCCTGAGGGTGCTGGTGCTG+GGG - chr2.4:9640338-9640357 None:intergenic 70.0%
!! GGCCTGAGGGTGCTGGTGCT+GGG - chr2.4:9640339-9640358 None:intergenic 70.0%
!! GGGTGCTGGTGCTGGGGCTT+GGG - chr2.4:9640332-9640351 None:intergenic 70.0%
GCCCCAGCACCAGCACCCTC+AGG + chr2.4:9640334-9640353 MS.gene31415:CDS 75.0%
!! GGGCCTGAGGGTGCTGGTGC+TGG - chr2.4:9640340-9640359 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 9640253 9641121 9640253 ID=MS.gene31415
chr2.4 mRNA 9640253 9641121 9640253 ID=MS.gene31415.t1;Parent=MS.gene31415
chr2.4 exon 9640253 9640526 9640253 ID=MS.gene31415.t1.exon1;Parent=MS.gene31415.t1
chr2.4 CDS 9640253 9640526 9640253 ID=cds.MS.gene31415.t1;Parent=MS.gene31415.t1
chr2.4 exon 9640646 9641121 9640646 ID=MS.gene31415.t1.exon2;Parent=MS.gene31415.t1
chr2.4 CDS 9640646 9641121 9640646 ID=cds.MS.gene31415.t1;Parent=MS.gene31415.t1
Gene Sequence

>MS.gene31415

ATGGCACTCACCACTACAACACCTCTTGCACTCATTCTTCTCACTCTCATTCCCTTCTTAACTCCACAAATCCAAGCCCAAGCCCCAGCACCAGCACCCTCAGGCCCAATAAACATCACATCAATCTTTGAAAAAGCTGGCCAATACACCTTCCTCATTCGTCTCCTCAATGAAACTCAACAACTCACTCAAATCCAAACCCAACTCAACTCAACTTCTGAAGGTTTCACAATCTTTGCCCCAACAGACAATGCCTTCCAAAATCTTCCATCAGGTATTATAATTTATATATATAAAACAAATTTATCTACGTTCATAATATGTTTTTACTCCTATATAATTATAACTTGCATGTAACTAATTAGTATAACTAACATTTATGTCTATTATCAGGAGCAATCAACGACCTCTCAGACCAACAGAAAGTTCAACTCATTCTCTACCATGTTACACCAAAATACTACTCTCTTTCCGATTTCTTAACAGTTTCAAATCCAGTTAGAACACAAGCTTCTGGTAAAGAAGGTAATTGGGGTCTTCACTTCACTTCACAAGGTAACCAAGTCAATGTTTCAACTGGAGTTGTTACTGTACCTATCAACAATGCTTTGAGACAACAATTTCCTTTGGCTGTTTATCAATTGGACAAGGTTTTGTTACCTTCTGAACTTTTTGGTGCTAAGTCTCCATCTTCATCTCCGGCTCCTAAGTCGTCGAAAACTCCTTCTAAAACACCGAGCAGCAGCGACGTTGAAGGTGATGCTCCATCTCCAGCGTCTAGTAAGAAGGATGATAGTGCAGCTGGAAGGAATGTTGGTTTTGGATTTGTTGCTGGGCTTGGTTTGATTTGCATGGGAGTTCTTTTTTGA
Protein sequence

>MS.gene31415.t1

MALTTTTPLALILLTLIPFLTPQIQAQAPAPAPSGPINITSIFEKAGQYTFLIRLLNETQQLTQIQTQLNSTSEGFTIFAPTDNAFQNLPSGAINDLSDQQKVQLILYHVTPKYYSLSDFLTVSNPVRTQASGKEGNWGLHFTSQGNQVNVSTGVVTVPINNALRQQFPLAVYQLDKVLLPSELFGAKSPSSSPAPKSSKTPSKTPSSSDVEGDAPSPASSKKDDSAAGRNVGFGFVAGLGLICMGVLF