AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066804

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066804.t1 MTR_4g021760 87.615 218 26 1 1 217 1 218 3.06e-138 389
MS.gene066804.t1 MTR_4g021845 80.184 217 43 0 1 217 1 217 2.86e-130 366
MS.gene066804.t1 MTR_4g021855 75.576 217 53 0 1 217 1 217 7.57e-121 345
MS.gene066804.t1 MTR_4g021790 73.272 217 58 0 1 217 1 217 2.10e-114 328
MS.gene066804.t1 MTR_5g055260 58.065 217 64 4 1 217 1 190 2.11e-81 243
MS.gene066804.t1 MTR_4g023980 76.642 137 32 0 55 191 35 171 4.91e-75 224
MS.gene066804.t1 MTR_1g032570 43.644 236 102 3 13 217 14 249 4.62e-63 206
MS.gene066804.t1 MTR_6g045327 47.534 223 109 4 1 217 1 221 2.32e-57 186
MS.gene066804.t1 MTR_3g086100 39.056 233 114 2 13 217 16 248 3.53e-54 182
MS.gene066804.t1 MTR_8g079940 38.528 231 116 2 13 217 28 258 5.56e-54 181
MS.gene066804.t1 MTR_4g121020 40.260 231 112 3 13 217 34 264 7.85e-53 180
MS.gene066804.t1 MTR_4g121020 40.260 231 112 3 13 217 34 264 8.53e-53 180
MS.gene066804.t1 MTR_2g034960 40.611 229 112 2 13 217 32 260 9.88e-53 179
MS.gene066804.t1 MTR_8g105600 41.518 224 111 2 14 217 13 236 1.57e-50 172
MS.gene066804.t1 MTR_8g093040 44.144 222 103 6 1 217 1 206 1.24e-47 158
MS.gene066804.t1 MTR_1g013170 38.197 233 116 3 13 217 8 240 1.31e-45 158
MS.gene066804.t1 MTR_4g131600 36.842 228 121 4 13 217 23 250 3.58e-45 158
MS.gene066804.t1 MTR_3g106220 37.553 237 116 3 13 217 11 247 6.10e-44 155
MS.gene066804.t1 MTR_7g117705 36.052 233 121 4 13 217 8 240 8.92e-44 152
MS.gene066804.t1 MTR_1g013180 36.910 233 119 4 13 217 159 391 6.33e-42 150
MS.gene066804.t1 MTR_3g102590 39.130 207 99 4 13 217 11 192 4.75e-41 138
MS.gene066804.t1 MTR_1g032570 40.556 180 77 2 68 217 1 180 8.92e-41 146
MS.gene066804.t1 MTR_3g102590 39.130 207 99 4 13 217 11 192 1.15e-40 139
MS.gene066804.t1 MTR_6g016850 40.828 169 97 2 4 169 3 171 6.57e-40 135
MS.gene066804.t1 MTR_4g131570 33.906 233 126 4 13 217 20 252 4.11e-39 142
MS.gene066804.t1 MTR_4g131580 33.478 230 128 4 13 217 20 249 7.09e-38 138
MS.gene066804.t1 MTR_2g450070 33.471 242 124 3 13 217 21 262 1.16e-37 138
MS.gene066804.t1 MTR_3g102600 34.884 215 102 3 4 217 4 181 1.16e-37 129
MS.gene066804.t1 MTR_2g450070 33.471 242 124 3 13 217 21 262 1.39e-37 138
MS.gene066804.t1 MTR_3g102600 34.884 215 102 3 4 217 4 181 2.35e-37 130
MS.gene066804.t1 MTR_3g086100 38.418 177 82 3 68 217 1 177 1.40e-35 131
MS.gene066804.t1 MTR_0450s0040 31.019 216 132 3 14 217 8 218 1.49e-30 115
MS.gene066804.t1 MTR_3g102600 33.537 164 74 1 54 217 4 132 6.78e-30 108
MS.gene066804.t1 MTR_3g102600 33.537 164 74 1 54 217 4 132 1.10e-29 108
MS.gene066804.t1 MTR_7g026400 33.514 185 92 3 54 217 32 206 5.34e-29 114
MS.gene066804.t1 MTR_4g121020 38.710 155 70 2 88 217 6 160 1.05e-27 110
MS.gene066804.t1 MTR_1g013160 33.108 148 72 2 71 191 1 148 3.63e-18 78.6
MS.gene066804.t1 MTR_5g041350 52.941 51 23 1 168 217 15 65 1.01e-11 63.5
MS.gene066804.t1 MTR_8g024260 28.455 123 84 2 13 131 35 157 4.62e-11 62.0
MS.gene066804.t1 MTR_6g032990 52.941 51 23 1 168 217 42 92 5.57e-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.gene066804.t1 AT2G01760 38.430 242 110 5 13 217 10 249 1.41e-51 171
MS.gene066804.t1 AT1G67710 40.171 234 111 4 13 217 10 243 1.00e-50 172
MS.gene066804.t1 AT3G16857 37.450 251 111 5 13 217 36 286 6.07e-46 161
MS.gene066804.t1 AT3G16857 37.450 251 111 5 13 217 36 286 9.51e-46 160
MS.gene066804.t1 AT2G01760 34.444 270 110 6 13 217 10 277 1.22e-45 156
MS.gene066804.t1 AT4G31920 38.532 218 120 4 13 217 16 232 3.70e-42 149
MS.gene066804.t1 AT2G25180 35.808 229 123 3 13 217 16 244 5.62e-41 147
MS.gene066804.t1 AT5G58080 37.118 229 118 5 13 217 17 243 2.51e-36 134
MS.gene066804.t1 AT3G16857 35.814 215 92 5 49 217 2 216 3.10e-35 131
MS.gene066804.t1 AT2G01760 36.022 186 81 4 68 217 1 184 2.19e-34 125
MS.gene066804.t1 AT1G67710 39.326 178 80 3 68 217 1 178 8.55e-32 120
MS.gene066804.t1 AT5G49240 29.289 239 136 3 9 217 37 272 4.20e-30 113
MS.gene066804.t1 AT1G49190 28.755 233 135 5 16 217 36 268 3.23e-25 102
MS.gene066804.t1 AT1G67710 37.975 158 70 3 88 217 12 169 8.08e-24 98.6
MS.gene066804.t1 AT3G62670 28.444 225 134 6 16 217 45 265 1.07e-23 98.2
MS.gene066804.t1 AT5G07210 27.132 258 132 8 14 217 16 271 7.18e-21 90.5
MS.gene066804.t1 AT5G07210 26.316 266 132 9 14 217 16 279 2.52e-18 83.2
MS.gene066804.t1 AT1G68210 24.812 266 143 6 8 217 7 271 1.84e-15 75.1
MS.gene066804.t1 AT1G49190 31.933 119 80 1 16 133 36 154 4.02e-15 73.9
MS.gene066804.t1 AT2G27070 24.138 261 139 9 14 217 16 274 8.70e-15 72.8
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 6.05e-12 64.7
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 8.56e-12 63.9
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 8.56e-12 63.9
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 8.56e-12 63.9
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 9.87e-12 63.9
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 9.87e-12 63.9
MS.gene066804.t1 AT5G60100 30.894 123 79 3 14 131 64 185 9.87e-12 63.9
MS.gene066804.t1 AT5G44190 49.057 53 27 0 165 217 144 196 2.04e-11 62.8
MS.gene066804.t1 AT5G44190 49.057 53 27 0 165 217 144 196 2.18e-11 62.8
MS.gene066804.t1 AT5G24470 27.778 126 81 3 13 131 49 171 2.62e-11 62.8
MS.gene066804.t1 AT3G04030 52.941 51 23 1 168 217 45 95 3.32e-11 62.4
MS.gene066804.t1 AT3G04030 52.941 51 23 1 168 217 45 95 3.72e-11 62.0

Find 39 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATGTTGCCAGCCATTTAC+AGG 0.283862 4.1:+76380289 MS.gene066804:CDS
GTGTAATCGATGCAATTATA+AGG 0.312923 4.1:+76379467 MS.gene066804:CDS
ACATCTCCTCGACGAAATTA+AGG 0.321564 4.1:-76379446 None:intergenic
TGAGTTGTAGGGTAACATTT+TGG 0.373812 4.1:-76379707 None:intergenic
CGAATATTGGACCAAGCCTT+TGG 0.374007 4.1:+76379896 MS.gene066804:CDS
AATGTGGGGCTTGCGAATAT+TGG 0.387677 4.1:+76379883 MS.gene066804:CDS
ATCAGAAGCCATGCTACATT+TGG 0.418312 4.1:-76379598 None:intergenic
CAAAGAAGGCCCGTTTGTCT+TGG 0.418636 4.1:+76380066 MS.gene066804:CDS
GTTTCAAGAAAATAGAAAAC+GGG 0.418887 4.1:+76380007 MS.gene066804:CDS
CTTTCTTTCCAACATGTTGA+AGG 0.419409 4.1:-76379622 None:intergenic
TGGCAACATGTTATAAGAAA+AGG 0.422808 4.1:+76379942 MS.gene066804:CDS
TGATGGTTTGTCGGTGAAAA+GGG 0.427097 4.1:-76379376 None:intergenic
ATATGAAATTGTTGGAAGCT+TGG 0.446291 4.1:+76379983 MS.gene066804:CDS
AAAAGAAACACTTGCAAAGA+AGG 0.446990 4.1:+76380052 MS.gene066804:CDS
ATGATGGTTTGTCGGTGAAA+AGG 0.455733 4.1:-76379377 None:intergenic
CTTCAACATGTTGGAAAGAA+AGG 0.459586 4.1:+76379623 MS.gene066804:CDS
AATAAATTCTTACTAATGAC+AGG 0.461511 4.1:-76379735 None:intergenic
TTCTCGCGACCAAGACAAAC+GGG 0.470376 4.1:-76380075 None:intergenic
TGTAATCGATGCAATTATAA+GGG 0.476930 4.1:+76379468 MS.gene066804:CDS
TTGAGACCTTCTGATAATGA+TGG 0.479264 4.1:-76379393 None:intergenic
TTCTGATAATGATGGTTTGT+CGG 0.493949 4.1:-76379385 None:intergenic
AAGTCGTAAACATCCATGTT+TGG 0.494866 4.1:-76379681 None:intergenic
TGTTTCAAGAAAATAGAAAA+CGG 0.510078 4.1:+76380006 MS.gene066804:CDS
AGGAAAGAATCATACTATCA+AGG 0.510494 4.1:-76380136 None:intergenic
ATTATGAAGTCTATTGAATG+TGG 0.513075 4.1:+76379867 MS.gene066804:CDS
TTCTGATGCCTTCAACATGT+TGG 0.527887 4.1:+76379614 MS.gene066804:CDS
TTATGAAGTCTATTGAATGT+GGG 0.532174 4.1:+76379868 MS.gene066804:CDS
AAAACGAACCTGTAAATGGC+TGG 0.538065 4.1:-76380297 None:intergenic
TTCAGTTACCAAATGTAGCA+TGG 0.538628 4.1:+76379590 MS.gene066804:intron
ATTCTCGCGACCAAGACAAA+CGG 0.543227 4.1:-76380076 None:intergenic
CTACGTGCAGTCAATCAACT+AGG 0.547867 4.1:+76380113 MS.gene066804:CDS
ATCATTATCAGAAGGTCTCA+AGG 0.582734 4.1:+76379395 MS.gene066804:CDS
AGAACTTTCTGCAGAATCAA+CGG 0.593830 4.1:-76379844 None:intergenic
TCTTATAACATGTTGCCACA+TGG 0.594344 4.1:-76379937 None:intergenic
TATGAAGTCTATTGAATGTG+GGG 0.598969 4.1:+76379869 MS.gene066804:CDS
TGATGCTCATATGCCAAACA+TGG 0.604750 4.1:+76379668 MS.gene066804:CDS
CACTCTCCTTAATTTCGTCG+AGG 0.625060 4.1:+76379440 MS.gene066804:CDS
GACAAACCATCATTATCAGA+AGG 0.636966 4.1:+76379387 MS.gene066804:CDS
TTTCAAGAAAATAGAAAACG+GGG 0.722642 4.1:+76380008 MS.gene066804:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAAAATATGAAATTGT+TGG + chr4.1:76379975-76379994 MS.gene066804:CDS 15.0%
!! AACATAGTAAAAAAGTAATT+AGG - chr4.1:76380159-76380178 None:intergenic 15.0%
!! AATAAATTCTTACTAATGAC+AGG - chr4.1:76379738-76379757 None:intergenic 20.0%
!! ATAGATGAAAACTTTGAATA+AGG - chr4.1:76379511-76379530 None:intergenic 20.0%
!! TGAAAAATAAGAGAAAAACA+TGG - chr4.1:76380213-76380232 None:intergenic 20.0%
!! TGTTTCAAGAAAATAGAAAA+CGG + chr4.1:76380006-76380025 MS.gene066804:CDS 20.0%
!!! AAAAAAGATTCTGAAAATCA+TGG + chr4.1:76380244-76380263 MS.gene066804:CDS 20.0%
!!! AACATGTTCTTTTTTCATAT+CGG - chr4.1:76380276-76380295 None:intergenic 20.0%
!!! ATGATTTTCAGAATCTTTTT+TGG - chr4.1:76380245-76380264 None:intergenic 20.0%
!!! ATGTTTTTCTCTTATTTTTC+AGG + chr4.1:76380212-76380231 MS.gene066804:intron 20.0%
!!! TGTTTTTCTCTTATTTTTCA+GGG + chr4.1:76380213-76380232 MS.gene066804:intron 20.0%
!!! TTATTTCTTTTTTGTAGTGA+TGG + chr4.1:76379821-76379840 MS.gene066804:intron 20.0%
!!! TTCAAAGTTTTCATCTATTT+TGG + chr4.1:76379513-76379532 MS.gene066804:intron 20.0%
! ATTATGAAGTCTATTGAATG+TGG + chr4.1:76379867-76379886 MS.gene066804:CDS 25.0%
! GTTTCAAGAAAATAGAAAAC+GGG + chr4.1:76380007-76380026 MS.gene066804:CDS 25.0%
! TGTAATCGATGCAATTATAA+GGG + chr4.1:76379468-76379487 MS.gene066804:CDS 25.0%
! TTATGAAGTCTATTGAATGT+GGG + chr4.1:76379868-76379887 MS.gene066804:CDS 25.0%
! TTTCAAGAAAATAGAAAACG+GGG + chr4.1:76380008-76380027 MS.gene066804:CDS 25.0%
!!! ACATGTTCTTTTTTCATATC+GGG - chr4.1:76380275-76380294 None:intergenic 25.0%
!!! GTTTTTCTCTTATTTTTCAG+GGG + chr4.1:76380214-76380233 MS.gene066804:intron 25.0%
AAAAGAAACACTTGCAAAGA+AGG + chr4.1:76380052-76380071 MS.gene066804:CDS 30.0%
AGGAAAGAATCATACTATCA+AGG - chr4.1:76380139-76380158 None:intergenic 30.0%
ATATGAAATTGTTGGAAGCT+TGG + chr4.1:76379983-76380002 MS.gene066804:CDS 30.0%
GTGTAATCGATGCAATTATA+AGG + chr4.1:76379467-76379486 MS.gene066804:CDS 30.0%
TATGAAGTCTATTGAATGTG+GGG + chr4.1:76379869-76379888 MS.gene066804:CDS 30.0%
TGGCAACATGTTATAAGAAA+AGG + chr4.1:76379942-76379961 MS.gene066804:CDS 30.0%
! CTTTGCAAGTGTTTCTTTTA+AGG - chr4.1:76380051-76380070 None:intergenic 30.0%
! TTCTGATAATGATGGTTTGT+CGG - chr4.1:76379388-76379407 None:intergenic 30.0%
!! TTGAACTGTTTTTCAACCAA+AGG - chr4.1:76379915-76379934 None:intergenic 30.0%
AAAAACAGTTCAAGACCATG+TGG + chr4.1:76379922-76379941 MS.gene066804:CDS 35.0%
AAGTCGTAAACATCCATGTT+TGG - chr4.1:76379684-76379703 None:intergenic 35.0%
AGAACTTTCTGCAGAATCAA+CGG - chr4.1:76379847-76379866 None:intergenic 35.0%
ATCATTATCAGAAGGTCTCA+AGG + chr4.1:76379395-76379414 MS.gene066804:CDS 35.0%
CTTCAACATGTTGGAAAGAA+AGG + chr4.1:76379623-76379642 MS.gene066804:CDS 35.0%
CTTTCTTTCCAACATGTTGA+AGG - chr4.1:76379625-76379644 None:intergenic 35.0%
GACAAACCATCATTATCAGA+AGG + chr4.1:76379387-76379406 MS.gene066804:CDS 35.0%
TCTTATAACATGTTGCCACA+TGG - chr4.1:76379940-76379959 None:intergenic 35.0%
TTCAGTTACCAAATGTAGCA+TGG + chr4.1:76379590-76379609 MS.gene066804:intron 35.0%
! TGAGTTGTAGGGTAACATTT+TGG - chr4.1:76379710-76379729 None:intergenic 35.0%
! TTGAGACCTTCTGATAATGA+TGG - chr4.1:76379396-76379415 None:intergenic 35.0%
!!! GACAGGAATTTTGAGTTGTA+GGG - chr4.1:76379721-76379740 None:intergenic 35.0%
!!! TGACAGGAATTTTGAGTTGT+AGG - chr4.1:76379722-76379741 None:intergenic 35.0%
ACATCTCCTCGACGAAATTA+AGG - chr4.1:76379449-76379468 None:intergenic 40.0%
ATCAGAAGCCATGCTACATT+TGG - chr4.1:76379601-76379620 None:intergenic 40.0%
TGATGCTCATATGCCAAACA+TGG + chr4.1:76379668-76379687 MS.gene066804:CDS 40.0%
TTCTGATGCCTTCAACATGT+TGG + chr4.1:76379614-76379633 MS.gene066804:CDS 40.0%
! ATGATGGTTTGTCGGTGAAA+AGG - chr4.1:76379380-76379399 None:intergenic 40.0%
! TGATGGTTTGTCGGTGAAAA+GGG - chr4.1:76379379-76379398 None:intergenic 40.0%
!! CTGTTTTTCAACCAAAGGCT+TGG - chr4.1:76379910-76379929 None:intergenic 40.0%
AATGTGGGGCTTGCGAATAT+TGG + chr4.1:76379883-76379902 MS.gene066804:CDS 45.0%
ATTCTCGCGACCAAGACAAA+CGG - chr4.1:76380079-76380098 None:intergenic 45.0%
CACTCTCCTTAATTTCGTCG+AGG + chr4.1:76379440-76379459 MS.gene066804:CDS 45.0%
CGAATATTGGACCAAGCCTT+TGG + chr4.1:76379896-76379915 MS.gene066804:CDS 45.0%
CTACGTGCAGTCAATCAACT+AGG + chr4.1:76380113-76380132 MS.gene066804:CDS 45.0%
CAAAGAAGGCCCGTTTGTCT+TGG + chr4.1:76380066-76380085 MS.gene066804:CDS 50.0%
TTCTCGCGACCAAGACAAAC+GGG - chr4.1:76380078-76380097 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 76379372 76380310 76379372 ID=MS.gene066804
chr4.1 mRNA 76379372 76380310 76379372 ID=MS.gene066804.t1;Parent=MS.gene066804
chr4.1 exon 76379372 76379489 76379372 ID=MS.gene066804.t1.exon1;Parent=MS.gene066804.t1
chr4.1 CDS 76379372 76379489 76379372 ID=cds.MS.gene066804.t1;Parent=MS.gene066804.t1
chr4.1 exon 76379595 76379744 76379595 ID=MS.gene066804.t1.exon2;Parent=MS.gene066804.t1
chr4.1 CDS 76379595 76379744 76379595 ID=cds.MS.gene066804.t1;Parent=MS.gene066804.t1
chr4.1 exon 76379838 76380143 76379838 ID=MS.gene066804.t1.exon3;Parent=MS.gene066804.t1
chr4.1 CDS 76379838 76380143 76379838 ID=cds.MS.gene066804.t1;Parent=MS.gene066804.t1
chr4.1 exon 76380234 76380310 76380234 ID=MS.gene066804.t1.exon4;Parent=MS.gene066804.t1
chr4.1 CDS 76380234 76380310 76380234 ID=cds.MS.gene066804.t1;Parent=MS.gene066804.t1
Gene Sequence

>MS.gene066804

ATGGCCCTTTTCACCGACAAACCATCATTATCAGAAGGTCTCAAGGTTCTTGCAATTGATCATGACATCACTCTCCTTAATTTCGTCGAGGAGATGTGTAATCGATGCAATTATAAGGGTTAGTAACTGAATCACACCTTATTCAAAGTTTTCATCTATTTTGGTAAAAATTCTGACTTTTATATGTTTTCATGTTTGCTTATTCTGATATTGTTTATTTCAGTTACCAAATGTAGCATGGCTTCTGATGCCTTCAACATGTTGGAAAGAAAGGACTGTTTCGATGTAATGTTGATTGATGCTCATATGCCAAACATGGATGTTTACGACTTTGTCCAAAATGTTACCCTACAACTCAAAATTCCTGTCATTAGTAAGAATTTATTCAACTTTGCACAATTCAAATGATTCATTCATATTATGTACTTAATAAGTGTGAACTTACATTATTATTTCTTTTTTGTAGTGATGGCCGTTGATTCTGCAGAAAGTTCTATTATGAAGTCTATTGAATGTGGGGCTTGCGAATATTGGACCAAGCCTTTGGTTGAAAAACAGTTCAAGACCATGTGGCAACATGTTATAAGAAAAGGTTTGACTCAAAACAAAAAATATGAAATTGTTGGAAGCTTGGTGTTTCAAGAAAATAGAAAACGGGGTAGAGAAGATGCTAATGCCTTAAAAGAAACACTTGCAAAGAAGGCCCGTTTGTCTTGGTCGCGAGAATTGCATCAGCAGTTTCTACGTGCAGTCAATCAACTAGGCCTTGATAGTATGATTCTTTCCTAATTACTTTTTTACTATGTTTTATTGCATTCTTCAACAGTTGAACTTATGTCCATGTTTTTCTCTTATTTTTCAGGGGCAACGCCAAAAAAGATTCTGAAAATCATGGATGTTCCCGATATGAAAAAAGAACATGTTGCCAGCCATTTACAG
Protein sequence

>MS.gene066804.t1

MALFTDKPSLSEGLKVLAIDHDITLLNFVEEMCNRCNYKVTKCSMASDAFNMLERKDCFDVMLIDAHMPNMDVYDFVQNVTLQLKIPVIMMAVDSAESSIMKSIECGACEYWTKPLVEKQFKTMWQHVIRKGLTQNKKYEIVGSLVFQENRKRGREDANALKETLAKKARLSWSRELHQQFLRAVNQLGLDRATPKKILKIMDVPDMKKEHVASHLQ