AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene009680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009680.t1 MTR_5g075210 97.067 341 8 2 1 341 11 349 0.0 669
MS.gene009680.t1 MTR_7g072630 38.360 378 150 15 1 337 11 346 2.90e-58 192
MS.gene009680.t1 MTR_7g072875 47.368 209 94 5 145 337 76 284 2.79e-51 172
MS.gene009680.t1 MTR_4g028930 44.509 173 74 4 172 338 224 380 8.49e-34 128
MS.gene009680.t1 MTR_8g087530 42.143 140 63 4 216 338 186 324 3.49e-24 101
MS.gene009680.t1 MTR_2g018030 52.941 68 32 0 271 338 276 343 1.78e-21 94.4
MS.gene009680.t1 MTR_0907s0020 51.613 62 30 0 272 333 102 163 3.23e-16 76.3
MS.gene009680.t1 MTR_8g103520 56.452 62 27 0 272 333 224 285 5.77e-16 77.4
MS.gene009680.t1 MTR_4g052040 57.377 61 26 0 275 335 102 162 5.38e-15 72.4
MS.gene009680.t1 MTR_7g105790 48.485 66 34 0 275 340 113 178 1.17e-14 72.0
MS.gene009680.t1 MTR_3g111780 43.000 100 57 0 237 336 163 262 1.83e-13 70.1
MS.gene009680.t1 MTR_4g132740 35.165 91 56 1 249 336 55 145 5.96e-13 66.2
MS.gene009680.t1 MTR_5g079710 43.284 67 38 0 263 329 82 148 9.01e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009680.t1 AT1G06920 35.112 356 152 14 1 336 11 307 2.27e-42 149
MS.gene009680.t1 AT5G58360 35.398 339 155 11 1 338 15 290 4.58e-40 143
MS.gene009680.t1 AT2G30400 34.366 355 173 13 1 340 11 320 3.98e-35 130
MS.gene009680.t1 AT5G01840 48.214 112 50 2 226 336 158 262 1.30e-24 101
MS.gene009680.t1 AT2G18500 53.623 69 32 0 268 336 222 290 1.33e-17 82.8
MS.gene009680.t1 AT4G18830 47.126 87 42 2 253 335 259 345 1.55e-17 82.8
MS.gene009680.t1 AT5G19650 52.308 65 31 0 272 336 154 218 1.75e-15 75.1
MS.gene009680.t1 AT3G52525 52.459 61 29 0 275 335 69 129 9.18e-15 71.6
MS.gene009680.t1 AT2G36026 50.000 56 28 0 278 333 92 147 1.71e-13 68.6
MS.gene009680.t1 AT4G04025 47.619 63 33 0 270 332 111 173 1.73e-11 62.8

Find 41 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACTTGCTTTGTCAATAT+TGG 0.161919 5.2:-63067658 None:intergenic
GATTCCTTGAAATCACTTAT+TGG 0.184540 5.2:-63067961 None:intergenic
AGCTTTATACCTTGAGAATT+AGG 0.222952 5.2:-63067820 None:intergenic
CTTCTCTTTGAAGACCTTCT+TGG 0.239723 5.2:-63067346 None:intergenic
TAATGGAATGTTCAAATCTT+TGG 0.240864 5.2:-63067311 None:intergenic
TATAAGGGAATCAAAGGATT+TGG 0.325148 5.2:+63068011 MS.gene009680:CDS
CTTGGTGAATCATTAAATAA+TGG 0.325243 5.2:-63067328 None:intergenic
TGATTGTGGAGAATAATATA+AGG 0.326543 5.2:+63067995 MS.gene009680:CDS
ATTTCTCAAATGAACCAAAA+AGG 0.337952 5.2:+63067257 MS.gene009680:CDS
AATGATGCAGGGTTTGTAGA+TGG 0.356794 5.2:+63067910 MS.gene009680:CDS
TGGTTGAGAAGGCTTGTAAA+TGG 0.361373 5.2:-63067383 None:intergenic
TTCAAATCTTTGGTCTGAAT+TGG 0.372756 5.2:-63067301 None:intergenic
AAGATCTTTACATTCTAAGT+TGG 0.393025 5.2:-63068125 None:intergenic
AGCTTGTAAAACCAAGCATT+TGG 0.394500 5.2:-63067121 None:intergenic
AGTTGAACTACTTCGCGATT+CGG 0.396798 5.2:-63067707 None:intergenic
CAACTGCAGTTAAGCAAATC+AGG 0.411925 5.2:-63067523 None:intergenic
TGATCCAATAAGTGATTTCA+AGG 0.412491 5.2:+63067957 MS.gene009680:CDS
TCTCCTTCTTTGACTGACTT+TGG 0.424881 5.2:-63067767 None:intergenic
AGATCTTTACATTCTAAGTT+GGG 0.428724 5.2:-63068124 None:intergenic
AGTATTTCAAAGAATGATGC+AGG 0.439556 5.2:+63067898 MS.gene009680:CDS
TGTGATTGAACTTGATCAAA+TGG 0.456333 5.2:-63067403 None:intergenic
CAGACATGATACCAAATGCT+TGG 0.494027 5.2:+63067110 None:intergenic
AAATCATCAAGGAAGAGAAA+TGG 0.497520 5.2:+63067157 MS.gene009680:CDS
AAGGGAATCAAAGGATTTGG+AGG 0.497577 5.2:+63068014 MS.gene009680:CDS
TGAGACCTTTGAGATGTTGT+TGG 0.501197 5.2:-63067217 None:intergenic
AAGTGATTTCAAGGAATCAA+TGG 0.509939 5.2:+63067966 MS.gene009680:CDS
GATTGTGGAGAATAATATAA+GGG 0.512687 5.2:+63067996 MS.gene009680:CDS
ACTTGATCAAATGGTTGAGA+AGG 0.519734 5.2:-63067394 None:intergenic
CTACCAAAGTCAGTCAAAGA+AGG 0.522505 5.2:+63067764 MS.gene009680:CDS
GAATAATATAAGGGAATCAA+AGG 0.538128 5.2:+63068005 MS.gene009680:CDS
TATTTAATGATTCACCAAGA+AGG 0.540531 5.2:+63067332 MS.gene009680:CDS
AAAACTTCTCCTAATTCTCA+AGG 0.546162 5.2:+63067811 MS.gene009680:CDS
CAAGAAGGTCTTCAAAGAGA+AGG 0.551446 5.2:+63067347 MS.gene009680:CDS
ATTTGAAGAAAAGATTGCTA+AGG 0.566943 5.2:+63067681 MS.gene009680:CDS
AAGATATGAGCAAATCATCA+AGG 0.573800 5.2:+63067146 MS.gene009680:CDS
AAGAAGGTCTTCAAAGAGAA+GGG 0.575024 5.2:+63067348 MS.gene009680:CDS
TGAGCAAATTTGGTATGACA+TGG 0.588029 5.2:+63068101 MS.gene009680:CDS
ATCAATGGTGGAGATGATTG+TGG 0.597753 5.2:+63067981 MS.gene009680:CDS
CTTCACCAACAACATCTCAA+AGG 0.609838 5.2:+63067212 MS.gene009680:CDS
GTATTTCAAAGAATGATGCA+GGG 0.644805 5.2:+63067899 MS.gene009680:CDS
TGATTTCAAGGAATCAATGG+TGG 0.655951 5.2:+63067969 MS.gene009680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTGCTAACAAGTTT+TGG - chr5.2:63067859-63067878 None:intergenic 20.0%
! ATTTCTCAAATGAACCAAAA+AGG + chr5.2:63067257-63067276 MS.gene009680:CDS 25.0%
! ATTTGAAGAAAAGATTGCTA+AGG + chr5.2:63067681-63067700 MS.gene009680:CDS 25.0%
! CTTGGTGAATCATTAAATAA+TGG - chr5.2:63067331-63067350 None:intergenic 25.0%
! GAATAATATAAGGGAATCAA+AGG + chr5.2:63068005-63068024 MS.gene009680:CDS 25.0%
! GATTGTGGAGAATAATATAA+GGG + chr5.2:63067996-63068015 MS.gene009680:CDS 25.0%
! TAATGGAATGTTCAAATCTT+TGG - chr5.2:63067314-63067333 None:intergenic 25.0%
! TATTTAATGATTCACCAAGA+AGG + chr5.2:63067332-63067351 MS.gene009680:CDS 25.0%
! TGATTGTGGAGAATAATATA+AGG + chr5.2:63067995-63068014 MS.gene009680:CDS 25.0%
!! AATAACTTACCATTCCTTTT+TGG - chr5.2:63067274-63067293 None:intergenic 25.0%
!! ATGAACAATGAATCTTTTCA+AGG + chr5.2:63067583-63067602 MS.gene009680:CDS 25.0%
!! TTAAAGCTTTTGAGCAAATT+TGG + chr5.2:63068091-63068110 MS.gene009680:CDS 25.0%
AAAACTTCTCCTAATTCTCA+AGG + chr5.2:63067811-63067830 MS.gene009680:CDS 30.0%
AAATCATCAAGGAAGAGAAA+TGG + chr5.2:63067157-63067176 MS.gene009680:CDS 30.0%
AAGATATGAGCAAATCATCA+AGG + chr5.2:63067146-63067165 MS.gene009680:CDS 30.0%
AAGTGATTTCAAGGAATCAA+TGG + chr5.2:63067966-63067985 MS.gene009680:CDS 30.0%
AGTATTTCAAAGAATGATGC+AGG + chr5.2:63067898-63067917 MS.gene009680:CDS 30.0%
GATTCCTTGAAATCACTTAT+TGG - chr5.2:63067964-63067983 None:intergenic 30.0%
GTATTTCAAAGAATGATGCA+GGG + chr5.2:63067899-63067918 MS.gene009680:CDS 30.0%
TATAAGGGAATCAAAGGATT+TGG + chr5.2:63068011-63068030 MS.gene009680:CDS 30.0%
TCAAATGAACCAAAAAGGAA+TGG + chr5.2:63067262-63067281 MS.gene009680:CDS 30.0%
TGATCCAATAAGTGATTTCA+AGG + chr5.2:63067957-63067976 MS.gene009680:CDS 30.0%
TGTGATTGAACTTGATCAAA+TGG - chr5.2:63067406-63067425 None:intergenic 30.0%
TTCAAATCTTTGGTCTGAAT+TGG - chr5.2:63067304-63067323 None:intergenic 30.0%
TTCACTTGCTTTGTCAATAT+TGG - chr5.2:63067661-63067680 None:intergenic 30.0%
! AGCTTTATACCTTGAGAATT+AGG - chr5.2:63067823-63067842 None:intergenic 30.0%
! GGCAATTCTAAAAACTTAGA+TGG + chr5.2:63067604-63067623 MS.gene009680:CDS 30.0%
! TTTGATGCATTTTCACAACT+TGG + chr5.2:63067628-63067647 MS.gene009680:CDS 30.0%
AAGAAGGTCTTCAAAGAGAA+GGG + chr5.2:63067348-63067367 MS.gene009680:CDS 35.0%
ACTTGATCAAATGGTTGAGA+AGG - chr5.2:63067397-63067416 None:intergenic 35.0%
AGCTTGTAAAACCAAGCATT+TGG - chr5.2:63067124-63067143 None:intergenic 35.0%
TGAGCAAATTTGGTATGACA+TGG + chr5.2:63068101-63068120 MS.gene009680:CDS 35.0%
TGATTTCAAGGAATCAATGG+TGG + chr5.2:63067969-63067988 MS.gene009680:CDS 35.0%
AAGGGAATCAAAGGATTTGG+AGG + chr5.2:63068014-63068033 MS.gene009680:CDS 40.0%
AATGATGCAGGGTTTGTAGA+TGG + chr5.2:63067910-63067929 MS.gene009680:CDS 40.0%
AGTTGAACTACTTCGCGATT+CGG - chr5.2:63067710-63067729 None:intergenic 40.0%
CAACTGCAGTTAAGCAAATC+AGG - chr5.2:63067526-63067545 None:intergenic 40.0%
CAAGAAGGTCTTCAAAGAGA+AGG + chr5.2:63067347-63067366 MS.gene009680:CDS 40.0%
CTACCAAAGTCAGTCAAAGA+AGG + chr5.2:63067764-63067783 MS.gene009680:CDS 40.0%
CTTCACCAACAACATCTCAA+AGG + chr5.2:63067212-63067231 MS.gene009680:CDS 40.0%
TGGTTGAGAAGGCTTGTAAA+TGG - chr5.2:63067386-63067405 None:intergenic 40.0%
! ATCAATGGTGGAGATGATTG+TGG + chr5.2:63067981-63068000 MS.gene009680:CDS 40.0%
! CTTCTCTTTGAAGACCTTCT+TGG - chr5.2:63067349-63067368 None:intergenic 40.0%
! TCTCCTTCTTTGACTGACTT+TGG - chr5.2:63067770-63067789 None:intergenic 40.0%
!! TGAGACCTTTGAGATGTTGT+TGG - chr5.2:63067220-63067239 None:intergenic 40.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 63067115 63068140 63067115 ID=MS.gene009680
chr5.2 mRNA 63067115 63068140 63067115 ID=MS.gene009680.t1;Parent=MS.gene009680
chr5.2 exon 63067115 63068140 63067115 ID=MS.gene009680.t1.exon1;Parent=MS.gene009680.t1
chr5.2 CDS 63067115 63068140 63067115 ID=cds.MS.gene009680.t1;Parent=MS.gene009680.t1
Gene Sequence

>MS.gene009680

ATGATACCAAATGCTTGGTTTTACAAGCTAAAAGATATGAGCAAATCATCAAGGAAGAGAAATGGTTCTCATCATGTTATGAAGAACAAAGTTACATCTTCACCAACAACATCTCAAAGGTCTCATTCAAGCTATTCACAATATTTCTCAAATGAACCAAAAAGGAATGGTAAGTTATTCAACACACCAATTCAGACCAAAGATTTGAACATTCCATTATTTAATGATTCACCAAGAAGGTCTTCAAAGAGAAGGGCTAAAAGAAAAACCATTTACAAGCCTTCTCAACCATTTGATCAAGTTCAATCACAAGAACATGATTTGTCTTCAATAGAAAATTCTTCTTCTGAGTCTTATCATAATCAATGTGTTTCTTCTGAATCTGAATTTTGTGATAGCTTTTCTGTTCCTGATTTGCTTAACTGCAGTTGTAGAGTTAGTTCTTCTACTAATGATATCATCATAGACATGAACAATGAATCTTTTCAAGGCAATTCTAAAAACTTAGATGGTTTTGATGCATTTTCACAACTTGGTTTAGCTCCAATATTGACAAAGCAAGTGAAATTTGAAGAAAAGATTGCTAAGGTGACCGAATCGCGAAGTAGTTCAACTGAATCAGACGAGCGAAAAATCGATCATTCATTCTCTACCAAAGTCAGTCAAAGAAGGAGAAGAAAAAGTCAGATAGCTAGAAAAACTTCTCCTAATTCTCAAGGTATAAAGCTTAGAGTGAATTCTCCAAAACTTGTTAGCAAAAAAATTCAAGCTAGTGCAAGAAAGAGTATTTCAAAGAATGATGCAGGGTTTGTAGATGGATTTGCTGTTGTTAAGTCTTCAATTGATCCAATAAGTGATTTCAAGGAATCAATGGTGGAGATGATTGTGGAGAATAATATAAGGGAATCAAAGGATTTGGAGGATTTACTTGCTTGCTATCTTTCTCTTAATTCAAGTGAATATCATGATGTTATAGTTAAAGCTTTTGAGCAAATTTGGTATGACATGGCCCAACTTAGAATGTAA
Protein sequence

>MS.gene009680.t1

MIPNAWFYKLKDMSKSSRKRNGSHHVMKNKVTSSPTTSQRSHSSYSQYFSNEPKRNGKLFNTPIQTKDLNIPLFNDSPRRSSKRRAKRKTIYKPSQPFDQVQSQEHDLSSIENSSSESYHNQCVSSESEFCDSFSVPDLLNCSCRVSSSTNDIIIDMNNESFQGNSKNLDGFDAFSQLGLAPILTKQVKFEEKIAKVTESRSSSTESDERKIDHSFSTKVSQRRRRKSQIARKTSPNSQGIKLRVNSPKLVSKKIQASARKSISKNDAGFVDGFAVVKSSIDPISDFKESMVEMIVENNIRESKDLEDLLACYLSLNSSEYHDVIVKAFEQIWYDMAQLRM