AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40393

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40393.t1 MTR_7g095150 84.135 208 25 3 1 207 1 201 1.74e-112 320
MS.gene40393.t1 MTR_1g072110 50.427 234 78 7 12 209 6 237 1.29e-61 192
MS.gene40393.t1 MTR_1g103640 46.617 133 51 4 75 206 66 179 6.81e-30 111
MS.gene40393.t1 MTR_2g102140 38.028 142 74 3 88 216 142 282 2.70e-20 87.4
MS.gene40393.t1 MTR_7g105780 35.032 157 79 5 50 206 66 199 1.76e-18 82.0
MS.gene40393.t1 MTR_4g012060 46.914 81 40 2 135 215 183 260 2.23e-15 73.6
MS.gene40393.t1 MTR_1g111640 48.529 68 29 2 137 204 138 199 1.49e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40393.t1 AT2G32100 43.056 144 70 4 77 208 95 238 4.01e-28 107
MS.gene40393.t1 AT1G05420 42.857 133 55 4 78 208 107 220 3.55e-25 98.6
MS.gene40393.t1 AT1G05420 42.857 133 55 4 78 208 123 236 4.58e-25 99.0
MS.gene40393.t1 AT4G14860 50.000 78 36 2 133 208 96 172 9.29e-20 83.2
MS.gene40393.t1 AT5G04820 35.616 146 80 5 63 206 79 212 1.09e-17 79.3
MS.gene40393.t1 AT1G79960 41.026 117 49 4 90 206 164 260 7.11e-17 77.8
MS.gene40393.t1 AT2G36050 31.452 124 58 2 83 206 77 173 6.21e-14 69.3

Find 58 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGGTTCGGGTTTGGAATC+TGG 0.244871 7.2:-14582447 None:intergenic
ATGTCGGCGGGTTGAGGTTC+GGG 0.249268 7.2:-14582459 None:intergenic
AATAAACTTGTGAGTGTTCT+TGG 0.269260 7.2:-14582811 None:intergenic
AATGTCGGCGGGTTGAGGTT+CGG 0.312904 7.2:-14582460 None:intergenic
CTTCTTGTTCTAAGTGTAGT+TGG 0.316838 7.2:-14582252 None:intergenic
AGAAGATGAGGAGGAGGAGG+AGG 0.357794 7.2:-14582562 None:intergenic
GGCGGGTTGAGGTTCGGGTT+TGG 0.367644 7.2:-14582454 None:intergenic
TGTGATCAATTTGGTGATGT+TGG 0.393032 7.2:-14582350 None:intergenic
ATGGAGGATTGTGATCAATT+TGG 0.401416 7.2:-14582359 None:intergenic
GGAAGAAGATGAGGAGGAGG+AGG 0.404203 7.2:-14582565 None:intergenic
TGAAAGACGTGAAGTCCAAC+TGG 0.409296 7.2:+14582745 MS.gene40393:CDS
TTAGAATCATTTGTCGGTGC+TGG 0.428480 7.2:-14582609 None:intergenic
CTCATCTTCTTCCTCCTCGT+TGG 0.428907 7.2:+14582575 MS.gene40393:CDS
GACTGCCGAAAATCCATGTA+AGG 0.436850 7.2:-14582687 None:intergenic
ATAAACTTGTGAGTGTTCTT+GGG 0.441701 7.2:-14582810 None:intergenic
GTGGCAATGTCGGCGGGTTG+AGG 0.442171 7.2:-14582465 None:intergenic
GGAGGAAGAAGATGAGGAGG+AGG 0.444956 7.2:-14582568 None:intergenic
ATAGGTAATTGAGGTGTTTG+AGG 0.446472 7.2:-14582284 None:intergenic
ATACTCACCGGACCCTTACA+TGG 0.446488 7.2:+14582674 MS.gene40393:CDS
GGATGAGGTGGATTCAACTA+TGG 0.452726 7.2:-14582538 None:intergenic
TGTTCTAAGTGTAGTTGGCA+TGG 0.478635 7.2:-14582247 None:intergenic
TGTTGAAGAGGAGGAGATTG+AGG 0.483301 7.2:-14582327 None:intergenic
TTCACGTCTTTCATCAACTC+TGG 0.488171 7.2:-14582735 None:intergenic
GGGTTTGGAATCTGGTTCGA+TGG 0.501378 7.2:-14582439 None:intergenic
TTTGATCATGGTTGATGACT+TGG 0.504706 7.2:-14582388 None:intergenic
TTGAGAAACATAGGTAATTG+AGG 0.507591 7.2:-14582293 None:intergenic
GCTAAGAAGAAGCTCGTGTA+AGG 0.508873 7.2:-14582772 None:intergenic
CGAAAATCCATGTAAGGGTC+CGG 0.511393 7.2:-14582681 None:intergenic
GGCGATAGCGGTGGCAATGT+CGG 0.513648 7.2:-14582475 None:intergenic
ATAGCGGTGGCAATGTCGGC+GGG 0.519957 7.2:-14582471 None:intergenic
TGGAATCTGGTTCGATGGAG+TGG 0.523377 7.2:-14582434 None:intergenic
GGTGGATTCAACTATGGAGT+TGG 0.526250 7.2:-14582532 None:intergenic
GTATGAAAGTTGAGAAACAT+AGG 0.539754 7.2:-14582302 None:intergenic
CGAGGAGGAAGAAGATGAGG+AGG 0.566205 7.2:-14582571 None:intergenic
CTCGTGTAAGGTATCCCAGT+TGG 0.568383 7.2:-14582760 None:intergenic
GGCGGTGCCAACATACTCAC+CGG 0.568623 7.2:+14582662 MS.gene40393:CDS
ATCATTTGTCGGTGCTGGCA+CGG 0.571546 7.2:-14582604 None:intergenic
TGGTGATGTTGGTGTTGAAG+AGG 0.571921 7.2:-14582339 None:intergenic
CTGGTTCGATGGAGTGGTGG+TGG 0.576085 7.2:-14582428 None:intergenic
GATAGCGGTGGCAATGTCGG+CGG 0.576430 7.2:-14582472 None:intergenic
GATGACTTGGAGAGTGATGG+AGG 0.578578 7.2:-14582375 None:intergenic
CAACGAGGAGGAAGAAGATG+AGG 0.579217 7.2:-14582574 None:intergenic
ATACACTATCACGAAGAAGA+TGG 0.579944 7.2:-14582891 None:intergenic
TCGGCAGTCAATGCAAGAGA+TGG 0.582966 7.2:+14582701 MS.gene40393:CDS
GCAGTCAATGCAAGAGATGG+TGG 0.593765 7.2:+14582704 MS.gene40393:CDS
GAAGCGGTTGGAGGCGATAG+CGG 0.600134 7.2:-14582487 None:intergenic
TAAGGGTCCGGTGAGTATGT+TGG 0.613914 7.2:-14582669 None:intergenic
GTTGATGACTTGGAGAGTGA+TGG 0.615673 7.2:-14582378 None:intergenic
TGATGTTGGTGTTGAAGAGG+AGG 0.624026 7.2:-14582336 None:intergenic
GCGGTTGGAGGCGATAGCGG+TGG 0.625107 7.2:-14582484 None:intergenic
AATCTGGTTCGATGGAGTGG+TGG 0.632867 7.2:-14582431 None:intergenic
ACTGCCGAAAATCCATGTAA+GGG 0.646543 7.2:-14582686 None:intergenic
ACTATGGAGTTGGAACGCCC+CGG 0.655856 7.2:-14582522 None:intergenic
GGAGTTGGAACGCCCCGGAG+AGG 0.679932 7.2:-14582517 None:intergenic
GAAAGACGTGAAGTCCAACT+GGG 0.680650 7.2:+14582746 MS.gene40393:CDS
CACGGTGGAAACCAACGAGG+AGG 0.688972 7.2:-14582586 None:intergenic
ATTTGTCGGTGCTGGCACGG+TGG 0.715454 7.2:-14582601 None:intergenic
TGGCACGGTGGAAACCAACG+AGG 0.765920 7.2:-14582589 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTGTTAGAATCATTTGT+CGG - chr7.2:14582618-14582637 None:intergenic 20.0%
!!! AAAAAGAAGACAGTTTTGAA+CGG + chr7.2:14582633-14582652 MS.gene40393:CDS 25.0%
AATAAACTTGTGAGTGTTCT+TGG - chr7.2:14582814-14582833 None:intergenic 30.0%
ATAAACTTGTGAGTGTTCTT+GGG - chr7.2:14582813-14582832 None:intergenic 30.0%
GTATGAAAGTTGAGAAACAT+AGG - chr7.2:14582305-14582324 None:intergenic 30.0%
TTGAGAAACATAGGTAATTG+AGG - chr7.2:14582296-14582315 None:intergenic 30.0%
!! AGTGTTGAAGTTTTTGATCA+TGG - chr7.2:14582403-14582422 None:intergenic 30.0%
ATGGAGGATTGTGATCAATT+TGG - chr7.2:14582362-14582381 None:intergenic 35.0%
! ATAGGTAATTGAGGTGTTTG+AGG - chr7.2:14582287-14582306 None:intergenic 35.0%
! CTTCTTGTTCTAAGTGTAGT+TGG - chr7.2:14582255-14582274 None:intergenic 35.0%
!! TGTGATCAATTTGGTGATGT+TGG - chr7.2:14582353-14582372 None:intergenic 35.0%
!! TTTGATCATGGTTGATGACT+TGG - chr7.2:14582391-14582410 None:intergenic 35.0%
ACTGCCGAAAATCCATGTAA+GGG - chr7.2:14582689-14582708 None:intergenic 40.0%
TTAGAATCATTTGTCGGTGC+TGG - chr7.2:14582612-14582631 None:intergenic 40.0%
TTCACGTCTTTCATCAACTC+TGG - chr7.2:14582738-14582757 None:intergenic 40.0%
AGAGGAGAAAAAGAAGCGGT+TGG - chr7.2:14582502-14582521 None:intergenic 45.0%
CGAAAATCCATGTAAGGGTC+CGG - chr7.2:14582684-14582703 None:intergenic 45.0%
GAAAGACGTGAAGTCCAACT+GGG + chr7.2:14582746-14582765 MS.gene40393:CDS 45.0%
GACTGCCGAAAATCCATGTA+AGG - chr7.2:14582690-14582709 None:intergenic 45.0%
GCTAAGAAGAAGCTCGTGTA+AGG - chr7.2:14582775-14582794 None:intergenic 45.0%
TGAAAGACGTGAAGTCCAAC+TGG + chr7.2:14582745-14582764 MS.gene40393:CDS 45.0%
TGTTGAAGAGGAGGAGATTG+AGG - chr7.2:14582330-14582349 None:intergenic 45.0%
! CGGACCCTTACATGGATTTT+CGG + chr7.2:14582682-14582701 MS.gene40393:CDS 45.0%
! GGATGAGGTGGATTCAACTA+TGG - chr7.2:14582541-14582560 None:intergenic 45.0%
! GGTGGATTCAACTATGGAGT+TGG - chr7.2:14582535-14582554 None:intergenic 45.0%
!! GTTGATGACTTGGAGAGTGA+TGG - chr7.2:14582381-14582400 None:intergenic 45.0%
!! TGATGTTGGTGTTGAAGAGG+AGG - chr7.2:14582339-14582358 None:intergenic 45.0%
!! TGGTGATGTTGGTGTTGAAG+AGG - chr7.2:14582342-14582361 None:intergenic 45.0%
!!! AGTTTTGAACGGAAGTGTGG+CGG + chr7.2:14582644-14582663 MS.gene40393:CDS 45.0%
!!! GACAGTTTTGAACGGAAGTG+TGG + chr7.2:14582641-14582660 MS.gene40393:CDS 45.0%
ATACTCACCGGACCCTTACA+TGG + chr7.2:14582674-14582693 MS.gene40393:CDS 50.0%
CAACGAGGAGGAAGAAGATG+AGG - chr7.2:14582577-14582596 None:intergenic 50.0%
CCGGAGAGGAGAAAAAGAAG+CGG - chr7.2:14582506-14582525 None:intergenic 50.0%
CTCATCTTCTTCCTCCTCGT+TGG + chr7.2:14582575-14582594 MS.gene40393:CDS 50.0%
GCAGTCAATGCAAGAGATGG+TGG + chr7.2:14582704-14582723 MS.gene40393:CDS 50.0%
GGAGAAAAAGAAGCGGTTGG+AGG - chr7.2:14582499-14582518 None:intergenic 50.0%
TAAGGGTCCGGTGAGTATGT+TGG - chr7.2:14582672-14582691 None:intergenic 50.0%
TCGGCAGTCAATGCAAGAGA+TGG + chr7.2:14582701-14582720 MS.gene40393:CDS 50.0%
! AATCTGGTTCGATGGAGTGG+TGG - chr7.2:14582434-14582453 None:intergenic 50.0%
! CCGCTTCTTTTTCTCCTCTC+CGG + chr7.2:14582503-14582522 MS.gene40393:CDS 50.0%
! CGCTTCTTTTTCTCCTCTCC+GGG + chr7.2:14582504-14582523 MS.gene40393:CDS 50.0%
! CTCGTGTAAGGTATCCCAGT+TGG - chr7.2:14582763-14582782 None:intergenic 50.0%
! GATGACTTGGAGAGTGATGG+AGG - chr7.2:14582378-14582397 None:intergenic 50.0%
! GCTTCTTTTTCTCCTCTCCG+GGG + chr7.2:14582505-14582524 MS.gene40393:CDS 50.0%
! GGGTTTGGAATCTGGTTCGA+TGG - chr7.2:14582442-14582461 None:intergenic 50.0%
! TGAGGTTCGGGTTTGGAATC+TGG - chr7.2:14582450-14582469 None:intergenic 50.0%
! TGGAATCTGGTTCGATGGAG+TGG - chr7.2:14582437-14582456 None:intergenic 50.0%
!! ATCATTTGTCGGTGCTGGCA+CGG - chr7.2:14582607-14582626 None:intergenic 50.0%
ACTATGGAGTTGGAACGCCC+CGG - chr7.2:14582525-14582544 None:intergenic 55.0%
AGAAGATGAGGAGGAGGAGG+AGG - chr7.2:14582565-14582584 None:intergenic 55.0%
CGAGGAGGAAGAAGATGAGG+AGG - chr7.2:14582574-14582593 None:intergenic 55.0%
GGAAGAAGATGAGGAGGAGG+AGG - chr7.2:14582568-14582587 None:intergenic 55.0%
GGAGGAAGAAGATGAGGAGG+AGG - chr7.2:14582571-14582590 None:intergenic 55.0%
!! AATGTCGGCGGGTTGAGGTT+CGG - chr7.2:14582463-14582482 None:intergenic 55.0%
AGATGAGGAGGAGGAGGAGG+AGG - chr7.2:14582562-14582581 None:intergenic 60.0%
ATAGCGGTGGCAATGTCGGC+GGG - chr7.2:14582474-14582493 None:intergenic 60.0%
CACGGTGGAAACCAACGAGG+AGG - chr7.2:14582589-14582608 None:intergenic 60.0%
GAAGCGGTTGGAGGCGATAG+CGG - chr7.2:14582490-14582509 None:intergenic 60.0%
TGGCACGGTGGAAACCAACG+AGG - chr7.2:14582592-14582611 None:intergenic 60.0%
! CTGGTTCGATGGAGTGGTGG+TGG - chr7.2:14582431-14582450 None:intergenic 60.0%
! GATAGCGGTGGCAATGTCGG+CGG - chr7.2:14582475-14582494 None:intergenic 60.0%
! GGCGATAGCGGTGGCAATGT+CGG - chr7.2:14582478-14582497 None:intergenic 60.0%
! GGCGGTGCCAACATACTCAC+CGG + chr7.2:14582662-14582681 MS.gene40393:CDS 60.0%
!! ATGTCGGCGGGTTGAGGTTC+GGG - chr7.2:14582462-14582481 None:intergenic 60.0%
!! ATTTGTCGGTGCTGGCACGG+TGG - chr7.2:14582604-14582623 None:intergenic 60.0%
GGAGGAGGAGGAGGAGGATG+AGG - chr7.2:14582556-14582575 None:intergenic 65.0%
GGAGGAGGAGGAGGATGAGG+TGG - chr7.2:14582553-14582572 None:intergenic 65.0%
!! GGCGGGTTGAGGTTCGGGTT+TGG - chr7.2:14582457-14582476 None:intergenic 65.0%
!! GTGGCAATGTCGGCGGGTTG+AGG - chr7.2:14582468-14582487 None:intergenic 65.0%
GGAGTTGGAACGCCCCGGAG+AGG - chr7.2:14582520-14582539 None:intergenic 70.0%
! GCGGTTGGAGGCGATAGCGG+TGG - chr7.2:14582487-14582506 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 14582249 14582905 14582249 ID=MS.gene40393
chr7.2 mRNA 14582249 14582905 14582249 ID=MS.gene40393.t1;Parent=MS.gene40393
chr7.2 exon 14582249 14582905 14582249 ID=MS.gene40393.t1.exon1;Parent=MS.gene40393.t1
chr7.2 CDS 14582249 14582905 14582249 ID=cds.MS.gene40393.t1;Parent=MS.gene40393.t1
Gene Sequence

>MS.gene40393

ATGCCAACTACACTTAGAACAAGAAGAAGAAACAACCTCAAACACCTCAATTACCTATGTTTCTCAACTTTCATACAACCTCAATCTCCTCCTCTTCAACACCAACATCACCAAATTGATCACAATCCTCCATCACTCTCCAAGTCATCAACCATGATCAAAAACTTCAACACTCTCTACCACCACCACTCCATCGAACCAGATTCCAAACCCGAACCTCAACCCGCCGACATTGCCACCGCTATCGCCTCCAACCGCTTCTTTTTCTCCTCTCCGGGGCGTTCCAACTCCATAGTTGAATCCACCTCATCCTCCTCCTCCTCCTCCTCATCTTCTTCCTCCTCGTTGGTTTCCACCGTGCCAGCACCGACAAATGATTCTAACAAAAAGAAGACAGTTTTGAACGGAAGTGTGGCGGTGCCAACATACTCACCGGACCCTTACATGGATTTTCGGCAGTCAATGCAAGAGATGGTGGAAGCGCAACCAGAGTTGATGAAAGACGTGAAGTCCAACTGGGATACCTTACACGAGCTTCTTCTTAGCTATCTCGCGATTAATCCCAAGAACACTCACAAGTTTATTCTCGATGCTTTTTCTGATCTTATTGTTACTCTCATGTCATTTTCTTCTTCTTCTTCACCATCTTCTTCGTGA
Protein sequence

>MS.gene40393.t1

MPTTLRTRRRNNLKHLNYLCFSTFIQPQSPPLQHQHHQIDHNPPSLSKSSTMIKNFNTLYHHHSIEPDSKPEPQPADIATAIASNRFFFSSPGRSNSIVESTSSSSSSSSSSSSSLVSTVPAPTNDSNKKKTVLNGSVAVPTYSPDPYMDFRQSMQEMVEAQPELMKDVKSNWDTLHELLLSYLAINPKNTHKFILDAFSDLIVTLMSFSSSSSPSSS