AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43204

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43204.t1 MTR_7g018500 94.933 375 16 3 1 373 1 374 0.0 550
MS.gene43204.t1 MTR_6g017055 48.315 356 103 16 73 366 67 403 3.08e-74 236
MS.gene43204.t1 MTR_1g103380 35.602 382 163 14 43 356 119 485 5.80e-43 156
MS.gene43204.t1 MTR_4g111935 33.459 266 141 11 5 245 14 268 5.10e-27 110
MS.gene43204.t1 MTR_2g078200 53.846 65 30 0 115 179 15 79 6.90e-17 80.5
MS.gene43204.t1 MTR_2g090960 51.562 64 31 0 115 178 19 82 1.70e-16 80.1
MS.gene43204.t1 MTR_4g079580 52.308 65 31 0 115 179 17 81 2.14e-16 79.7
MS.gene43204.t1 MTR_8g463380 52.308 65 31 0 115 179 49 113 2.18e-16 80.5
MS.gene43204.t1 MTR_6g015350 47.561 82 41 1 119 200 48 127 4.46e-16 79.0
MS.gene43204.t1 MTR_7g015010 51.667 60 29 0 119 178 56 115 1.96e-14 73.9
MS.gene43204.t1 MTR_4g109660 48.333 60 31 0 119 178 55 114 5.66e-13 69.3
MS.gene43204.t1 MTR_3g026050 48.333 60 31 0 119 178 56 115 2.58e-12 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43204.t1 AT1G67260 40.789 228 105 9 113 312 80 305 7.89e-34 129
MS.gene43204.t1 AT1G67260 40.789 228 105 9 113 312 80 305 7.89e-34 129
MS.gene43204.t1 AT1G67260 40.789 228 105 9 113 312 80 305 9.75e-34 128
MS.gene43204.t1 AT1G68800 54.867 113 42 4 120 229 112 218 1.89e-25 106
MS.gene43204.t1 AT1G68800 54.867 113 42 4 120 229 112 218 2.06e-25 105
MS.gene43204.t1 AT3G18550 39.216 153 69 3 113 241 141 293 8.26e-22 96.7
MS.gene43204.t1 AT3G18550 36.943 157 71 3 113 241 141 297 1.44e-20 93.2
MS.gene43204.t1 AT3G18550 36.943 157 71 3 113 241 141 297 1.71e-20 92.8
MS.gene43204.t1 AT3G18550 36.943 157 71 3 113 241 141 297 1.71e-20 92.8
MS.gene43204.t1 AT4G18390 37.671 146 87 3 103 248 27 168 3.20e-18 85.5
MS.gene43204.t1 AT4G18390 37.671 146 87 3 103 248 27 168 3.20e-18 85.5
MS.gene43204.t1 AT1G30210 53.968 63 29 0 116 178 46 108 1.54e-16 80.1
MS.gene43204.t1 AT1G30210 53.968 63 29 0 116 178 46 108 1.54e-16 80.1
MS.gene43204.t1 AT1G53230 51.515 66 32 0 115 180 44 109 2.40e-16 80.1
MS.gene43204.t1 AT1G53230 51.515 66 32 0 115 180 44 109 2.40e-16 80.1
MS.gene43204.t1 AT3G15030 52.308 65 31 0 115 179 40 104 2.82e-16 80.1
MS.gene43204.t1 AT3G15030 52.308 65 31 0 115 179 40 104 2.82e-16 80.1
MS.gene43204.t1 AT3G15030 52.308 65 31 0 115 179 40 104 2.82e-16 80.1
MS.gene43204.t1 AT3G15030 52.308 65 31 0 115 179 40 104 2.82e-16 80.1
MS.gene43204.t1 AT2G31070 51.562 64 31 0 115 178 24 87 6.16e-16 78.6
MS.gene43204.t1 AT3G02150 53.333 60 28 0 119 178 73 132 1.03e-14 74.3
MS.gene43204.t1 AT3G02150 53.333 60 28 0 119 178 73 132 1.67e-14 74.3
MS.gene43204.t1 AT5G60970 46.667 60 32 0 119 178 62 121 9.23e-13 69.3
MS.gene43204.t1 AT5G08070 45.000 60 33 0 119 178 32 91 2.32e-11 63.9
MS.gene43204.t1 AT5G08070 45.000 60 33 0 119 178 32 91 2.32e-11 63.9

Find 61 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTCAACTTATTGCTCTTT+AGG 0.129653 7.2:-79113113 MS.gene43204:CDS
GCCCAATTTGTTGGTGTATC+AGG 0.208941 7.2:+79112885 None:intergenic
GTTGGTGTATCAGGATTAAT+TGG 0.216086 7.2:+79112894 None:intergenic
CTCCAATGTTATCACCAAAT+TGG 0.217754 7.2:-79112158 MS.gene43204:CDS
ATCCTGATACACCAACAAAT+TGG 0.224168 7.2:-79112887 MS.gene43204:CDS
CTTCGAAGACGAAGGATTCT+AGG 0.286350 7.2:-79112452 MS.gene43204:CDS
TTCTTAGCTGGTTTCTTGAC+AGG 0.328037 7.2:+79112780 None:intergenic
TGTGAAGAAGAAGATGAATT+AGG 0.330614 7.2:+79113071 None:intergenic
TTCGATCTTCAAGACATGTT+AGG 0.334610 7.2:-79112675 MS.gene43204:CDS
CTATGCCTGTCTTTCTTAGC+TGG 0.335007 7.2:+79112768 None:intergenic
TTTGAAGTTTCATCCTCATT+AGG 0.336904 7.2:+79112315 None:intergenic
TTATTATTAGCATCCCAATT+TGG 0.341400 7.2:+79112144 None:intergenic
TCATGAGAATCACTATTATT+AGG 0.353829 7.2:+79112183 None:intergenic
AATATCAGCTAATATCGATT+TGG 0.375751 7.2:+79111875 None:intergenic
TCAGGGGTAAGAAAAGTAAA+AGG 0.386359 7.2:+79113038 None:intergenic
GAGCCATTCAAGTGTGTTGC+TGG 0.409129 7.2:+79112641 None:intergenic
TTCAAATCTTTGGAAAATCA+TGG 0.409744 7.2:-79111916 MS.gene43204:CDS
AAAGTTGTTGATGTTGTTGT+TGG 0.410045 7.2:+79112974 None:intergenic
TCCAATGTTATCACCAAATT+GGG 0.411724 7.2:-79112157 MS.gene43204:CDS
CTAAAGATAGAAAGATGAAA+AGG 0.414926 7.2:-79112488 MS.gene43204:CDS
TCCTGATACACCAACAAATT+GGG 0.420639 7.2:-79112886 MS.gene43204:CDS
TCTTGATATTGCAGAAAAGT+TGG 0.424180 7.2:+79112095 None:intergenic
TCTTCTTCGTCTTCCGATGA+AGG 0.430527 7.2:-79112528 MS.gene43204:CDS
TCGATCTTCAAGACATGTTA+GGG 0.442491 7.2:-79112674 MS.gene43204:CDS
GGTGTTGTTAGTGTTGTTGT+TGG 0.445348 7.2:+79112995 None:intergenic
TCAGCAACAGCCCAATTTGT+TGG 0.449965 7.2:+79112876 None:intergenic
AGCAAGAACAACATAGCTTC+TGG 0.450038 7.2:-79112579 MS.gene43204:CDS
TGATGAGTTGTTTGTGTGTA+GGG 0.490224 7.2:+79112924 None:intergenic
AATAACAATGATGCTGTCAC+TGG 0.496363 7.2:-79112123 MS.gene43204:CDS
CATTAGGCATCAATTGATGA+AGG 0.499616 7.2:+79112331 None:intergenic
CCTAAAGAGCAATAAGTTGA+AGG 0.500471 7.2:+79113113 None:intergenic
TCAAGAACGAATCTATCATC+AGG 0.510472 7.2:-79112078 MS.gene43204:intron
ATCTTCTTCATCTCCTTCAT+CGG 0.512276 7.2:+79112515 None:intergenic
AAAGATGAAAAGGGCACAGA+AGG 0.517893 7.2:-79112478 MS.gene43204:CDS
AGCAAGATTCACACATCTCA+AGG 0.519514 7.2:-79112747 MS.gene43204:CDS
TAAAGATAGAAAGATGAAAA+GGG 0.526209 7.2:-79112487 MS.gene43204:CDS
TCAAATCTTTGGAAAATCAT+GGG 0.526493 7.2:-79111915 MS.gene43204:CDS
GAACTTCCTCGCGATCTCGA+TGG 0.528472 7.2:+79112698 None:intergenic
TGACATCTTTAACTTCATTG+AGG 0.528826 7.2:-79112277 MS.gene43204:CDS
TAGGGAACAGAAATAGCTGC+TGG 0.529350 7.2:+79112942 None:intergenic
AGAAAACAAGAGCAAGAGCA+AGG 0.530089 7.2:-79112428 MS.gene43204:CDS
AAGCCAGCAACACACTTGAA+TGG 0.532128 7.2:-79112644 MS.gene43204:CDS
AGAAACCAGCTAAGAAAGAC+AGG 0.535037 7.2:-79112773 MS.gene43204:CDS
TCATCAATTGATGCCTAATG+AGG 0.536962 7.2:-79112328 MS.gene43204:CDS
TTCGAAGACGAAGGATTCTA+GGG 0.537014 7.2:-79112451 MS.gene43204:CDS
GGGGTAAGAAAAGTAAAAGG+AGG 0.548490 7.2:+79113041 None:intergenic
TTAGGATTATAACAAGGGTA+AGG 0.556043 7.2:+79113089 None:intergenic
TCCCAATTTGGTGATAACAT+TGG 0.563066 7.2:+79112156 None:intergenic
ATGAATTAGGATTATAACAA+GGG 0.570279 7.2:+79113084 None:intergenic
GGGTAAGAAAAGTAAAAGGA+GGG 0.575339 7.2:+79113042 None:intergenic
ATGATGAGTTGTTTGTGTGT+AGG 0.581066 7.2:+79112923 None:intergenic
CAGCTAATATCGATTTGGAC+TGG 0.588709 7.2:+79111880 None:intergenic
GAAAACAAGAGCAAGAGCAA+GGG 0.591086 7.2:-79112427 MS.gene43204:CDS
GATGAATTAGGATTATAACA+AGG 0.592158 7.2:+79113083 None:intergenic
CTCAAGGTTTGAGAGACAGA+AGG 0.592962 7.2:-79112731 MS.gene43204:CDS
GACTTTCCATCGAGATCGCG+AGG 0.608900 7.2:-79112704 MS.gene43204:CDS
TCAAGGTTTGAGAGACAGAA+GGG 0.615028 7.2:-79112730 MS.gene43204:CDS
AATCTTTGGAAAATCATGGG+AGG 0.624471 7.2:-79111912 MS.gene43204:CDS
GAAGGAATCTTCGAAGACGA+AGG 0.639563 7.2:-79112460 MS.gene43204:CDS
GCTTCTGGCGATGACGACGA+TGG 0.659720 7.2:-79112564 MS.gene43204:CDS
ATGTTGAAACAAGATCTAAG+TGG 0.698091 7.2:-79112843 MS.gene43204:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATAAAATTAATTAACAAAA+AGG - chr7.2:79112989-79113008 MS.gene43204:CDS 10.0%
!!! TTTTAGGTTTAAACTTTTTA+GGG - chr7.2:79113062-79113081 MS.gene43204:CDS 15.0%
!!! TTTTTAGGTTTAAACTTTTT+AGG - chr7.2:79113061-79113080 MS.gene43204:CDS 15.0%
!! ATGAATTAGGATTATAACAA+GGG + chr7.2:79111921-79111940 None:intergenic 20.0%
!! TAAAGATAGAAAGATGAAAA+GGG - chr7.2:79112515-79112534 MS.gene43204:CDS 20.0%
!!! TTGTGATACTTACAATTTTT+AGG - chr7.2:79113046-79113065 MS.gene43204:CDS 20.0%
! CTAAAGATAGAAAGATGAAA+AGG - chr7.2:79112514-79112533 MS.gene43204:CDS 25.0%
! GATGAATTAGGATTATAACA+AGG + chr7.2:79111922-79111941 None:intergenic 25.0%
! TCATGAGAATCACTATTATT+AGG + chr7.2:79112822-79112841 None:intergenic 25.0%
! TTATTATTAGCATCCCAATT+TGG + chr7.2:79112861-79112880 None:intergenic 25.0%
!! TCAAATCTTTGGAAAATCAT+GGG - chr7.2:79113087-79113106 MS.gene43204:CDS 25.0%
!! TTCAAATCTTTGGAAAATCA+TGG - chr7.2:79113086-79113105 MS.gene43204:CDS 25.0%
!!! TGTTGATTTTGATCAATTTC+AGG + chr7.2:79112648-79112667 None:intergenic 25.0%
AAAGTTGTTGATGTTGTTGT+TGG + chr7.2:79112031-79112050 None:intergenic 30.0%
ATGTTGAAACAAGATCTAAG+TGG - chr7.2:79112159-79112178 MS.gene43204:CDS 30.0%
TCCAATGTTATCACCAAATT+GGG - chr7.2:79112845-79112864 MS.gene43204:CDS 30.0%
TCTTGATATTGCAGAAAAGT+TGG + chr7.2:79112910-79112929 None:intergenic 30.0%
TGTGAAGAAGAAGATGAATT+AGG + chr7.2:79111934-79111953 None:intergenic 30.0%
TTAGGATTATAACAAGGGTA+AGG + chr7.2:79111916-79111935 None:intergenic 30.0%
! TGACATCTTTAACTTCATTG+AGG - chr7.2:79112725-79112744 MS.gene43204:CDS 30.0%
! TTTGAAGTTTCATCCTCATT+AGG + chr7.2:79112690-79112709 None:intergenic 30.0%
!!! TAGAAGAAGCATTTTGATCA+GGG + chr7.2:79111984-79112003 None:intergenic 30.0%
!!! TTAGAAGAAGCATTTTGATC+AGG + chr7.2:79111985-79112004 None:intergenic 30.0%
!!! TTTTTAGGGCTTCAAATCTT+TGG - chr7.2:79113076-79113095 MS.gene43204:CDS 30.0%
AATAACAATGATGCTGTCAC+TGG - chr7.2:79112879-79112898 MS.gene43204:CDS 35.0%
ATCCTGATACACCAACAAAT+TGG - chr7.2:79112115-79112134 MS.gene43204:CDS 35.0%
ATCTTCTTCATCTCCTTCAT+CGG + chr7.2:79112490-79112509 None:intergenic 35.0%
ATGATGAGTTGTTTGTGTGT+AGG + chr7.2:79112082-79112101 None:intergenic 35.0%
CATTAGGCATCAATTGATGA+AGG + chr7.2:79112674-79112693 None:intergenic 35.0%
CCTTCAACTTATTGCTCTTT+AGG - chr7.2:79111889-79111908 MS.gene43204:CDS 35.0%
CTCCAATGTTATCACCAAAT+TGG - chr7.2:79112844-79112863 MS.gene43204:CDS 35.0%
GGGTAAGAAAAGTAAAAGGA+GGG + chr7.2:79111963-79111982 None:intergenic 35.0%
GTTGGTGTATCAGGATTAAT+TGG + chr7.2:79112111-79112130 None:intergenic 35.0%
TCAAGAACGAATCTATCATC+AGG - chr7.2:79112924-79112943 MS.gene43204:CDS 35.0%
TCAGGGGTAAGAAAAGTAAA+AGG + chr7.2:79111967-79111986 None:intergenic 35.0%
TCATCAATTGATGCCTAATG+AGG - chr7.2:79112674-79112693 MS.gene43204:CDS 35.0%
TCCTGATACACCAACAAATT+GGG - chr7.2:79112116-79112135 MS.gene43204:CDS 35.0%
TCGATCTTCAAGACATGTTA+GGG - chr7.2:79112328-79112347 MS.gene43204:CDS 35.0%
TGATGAGTTGTTTGTGTGTA+GGG + chr7.2:79112081-79112100 None:intergenic 35.0%
TTCGATCTTCAAGACATGTT+AGG - chr7.2:79112327-79112346 MS.gene43204:CDS 35.0%
! AATCTTTGGAAAATCATGGG+AGG - chr7.2:79113090-79113109 MS.gene43204:CDS 35.0%
! CCTAAAGAGCAATAAGTTGA+AGG + chr7.2:79111892-79111911 None:intergenic 35.0%
! TCCCAATTTGGTGATAACAT+TGG + chr7.2:79112849-79112868 None:intergenic 35.0%
!!! AGAAGAAGCATTTTGATCAG+GGG + chr7.2:79111983-79112002 None:intergenic 35.0%
AGAAAACAAGAGCAAGAGCA+AGG - chr7.2:79112574-79112593 MS.gene43204:CDS 40.0%
AGAAACCAGCTAAGAAAGAC+AGG - chr7.2:79112229-79112248 MS.gene43204:CDS 40.0%
AGCAAGAACAACATAGCTTC+TGG - chr7.2:79112423-79112442 MS.gene43204:CDS 40.0%
AGCAAGATTCACACATCTCA+AGG - chr7.2:79112255-79112274 MS.gene43204:CDS 40.0%
GAAAACAAGAGCAAGAGCAA+GGG - chr7.2:79112575-79112594 MS.gene43204:CDS 40.0%
GGGGTAAGAAAAGTAAAAGG+AGG + chr7.2:79111964-79111983 None:intergenic 40.0%
TCAAGGTTTGAGAGACAGAA+GGG - chr7.2:79112272-79112291 MS.gene43204:CDS 40.0%
TTCGAAGACGAAGGATTCTA+GGG - chr7.2:79112551-79112570 MS.gene43204:CDS 40.0%
! AAAGATGAAAAGGGCACAGA+AGG - chr7.2:79112524-79112543 MS.gene43204:CDS 40.0%
! TTCTTAGCTGGTTTCTTGAC+AGG + chr7.2:79112225-79112244 None:intergenic 40.0%
!! GGTGTTGTTAGTGTTGTTGT+TGG + chr7.2:79112010-79112029 None:intergenic 40.0%
AAGCCAGCAACACACTTGAA+TGG - chr7.2:79112358-79112377 MS.gene43204:CDS 45.0%
CTATGCCTGTCTTTCTTAGC+TGG + chr7.2:79112237-79112256 None:intergenic 45.0%
CTCAAGGTTTGAGAGACAGA+AGG - chr7.2:79112271-79112290 MS.gene43204:CDS 45.0%
CTTCGAAGACGAAGGATTCT+AGG - chr7.2:79112550-79112569 MS.gene43204:CDS 45.0%
GAAGGAATCTTCGAAGACGA+AGG - chr7.2:79112542-79112561 MS.gene43204:CDS 45.0%
TAGGGAACAGAAATAGCTGC+TGG + chr7.2:79112063-79112082 None:intergenic 45.0%
TCAGCAACAGCCCAATTTGT+TGG + chr7.2:79112129-79112148 None:intergenic 45.0%
TCTTCTTCGTCTTCCGATGA+AGG - chr7.2:79112474-79112493 MS.gene43204:CDS 45.0%
!! GCCCAATTTGTTGGTGTATC+AGG + chr7.2:79112120-79112139 None:intergenic 45.0%
GAGCCATTCAAGTGTGTTGC+TGG + chr7.2:79112364-79112383 None:intergenic 50.0%
GAACTTCCTCGCGATCTCGA+TGG + chr7.2:79112307-79112326 None:intergenic 55.0%
GACTTTCCATCGAGATCGCG+AGG - chr7.2:79112298-79112317 MS.gene43204:CDS 55.0%
GCTTCTGGCGATGACGACGA+TGG - chr7.2:79112438-79112457 MS.gene43204:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 79111883 79113141 79111883 ID=MS.gene43204
chr7.2 mRNA 79111883 79113141 79111883 ID=MS.gene43204.t1;Parent=MS.gene43204
chr7.2 exon 79112079 79113141 79112079 ID=MS.gene43204.t1.exon1;Parent=MS.gene43204.t1
chr7.2 CDS 79112079 79113141 79112079 ID=cds.MS.gene43204.t1;Parent=MS.gene43204.t1
chr7.2 exon 79111883 79111941 79111883 ID=MS.gene43204.t1.exon2;Parent=MS.gene43204.t1
chr7.2 CDS 79111883 79111941 79111883 ID=cds.MS.gene43204.t1;Parent=MS.gene43204.t1
Gene Sequence

>MS.gene43204

ATGTTTCCTTCAACTTATTGCTCTTTAGGTCCTTACCCTTGTTATAATCCTAATTCATCTTCTTCTTCACACTCATACCCTCCTTTTACTTTTCTTACCCCTGATCAAAATGCTTCTTCTAACACCAACAACAACACTAACAACACCAACAACAACATCAACAACTTTCTTCATGATCCAGCAGCTATTTCTGTTCCCTACACACAAACAACTCATCATCATGTTCCAATTAATCCTGATACACCAACAAATTGGGCTGTTGCTGATTATGCAGCTATGTTGAAACAAGATCTAAGTGGTTCTTCTCATTACAATCTCTCAAATTTGCTCACAAAGAAACCTGTCAAGAAACCAGCTAAGAAAGACAGGCATAGCAAGATTCACACATCTCAAGGTTTGAGAGACAGAAGGGTGAGACTTTCCATCGAGATCGCGAGGAAGTTCTTCGATCTTCAAGACATGTTAGGGTTTGACAAAGCCAGCAACACACTTGAATGGCTCTTCAATAAATCAAAAGAAGCAATTGAAGAGTTAACTAGAAGCAAGAACAACATAGCTTCTGGCGATGACGACGATGGTGATCATAGCTTCTCTTCTTCGTCTTCCGATGAAGGAGATGAAGAAGATTATACTAAAGATAGAAAGATGAAAAGGGCACAGAAGGAATCTTCGAAGACGAAGGATTCTAGGGAGAAAACAAGAGCAAGAGCAAGGGAAAGAGCAAGTGAGATGAAGATGCAAGAAGATTTGAAAGAAAAATATCCTGAAATTGATCAAAATCAACAAATCCTTCATCAATTGATGCCTAATGAGGATGAAACTTCAAAATCACTTCAAAGAGATGACATCTTTAACTTCATTGAGGAATCTATTGTGATTAAGAGAAAGTTGAAGAAATCTTCTTCTCATCATTATCAACAAAACACTAATTTGATGCCTAATAATAGTGATTCTCATGACTCTCCAATGTTATCACCAAATTGGGATGCTAATAATAATAACAATGATGCTGTCACTGGAAGATCCAACTTTTCTGCAATATCAAGAACGAATCTATCATCAGGTAATTTTTGTTTTTATTTGATAATTGTTTCACTGTTTCAAAACATAAAATTAATTAACAAAAAGGCTAATTTTTTATTTTATTTTTATTTTTGTGAATTTTGTGATACTTACAATTTTTAGGTTTAAACTTTTTAGGGCTTCAAATCTTTGGAAAATCATGGGAGGATTGCAATACCAGTCCAAATCGATATTAG
Protein sequence

>MS.gene43204.t1

MFPSTYCSLGPYPCYNPNSSSSSHSYPPFTFLTPDQNASSNTNNNTNNTNNNINNFLHDPAAISVPYTQTTHHHVPINPDTPTNWAVADYAAMLKQDLSGSSHYNLSNLLTKKPVKKPAKKDRHSKIHTSQGLRDRRVRLSIEIARKFFDLQDMLGFDKASNTLEWLFNKSKEAIEELTRSKNNIASGDDDDGDHSFSSSSSDEGDEEDYTKDRKMKRAQKESSKTKDSREKTRARARERASEMKMQEDLKEKYPEIDQNQQILHQLMPNEDETSKSLQRDDIFNFIEESIVIKRKLKKSSSHHYQQNTNLMPNNSDSHDSPMLSPNWDANNNNNDAVTGRSNFSAISRTNLSSGLQIFGKSWEDCNTSPNRY