AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83867

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83867.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 6.79e-17 77.4
MS.gene83867.t1 MTR_3g463400 59.259 54 21 1 121 174 132 184 4.04e-15 72.4
MS.gene83867.t1 MTR_5g070020 59.259 54 21 1 121 174 121 173 1.03e-14 71.2
MS.gene83867.t1 MTR_7g451170 59.259 54 21 1 121 174 190 242 2.42e-14 70.1
MS.gene83867.t1 MTR_5g049190 54.237 59 26 1 116 174 13 70 3.65e-14 68.6
MS.gene83867.t1 MTR_3g077650 57.407 54 22 1 121 174 180 232 2.85e-13 67.0
MS.gene83867.t1 MTR_7g035350 53.704 54 24 1 121 174 224 276 3.59e-13 67.0
MS.gene83867.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 5.71e-13 66.2
MS.gene83867.t1 MTR_4g105660 41.379 87 40 3 101 177 149 234 1.17e-12 65.5
MS.gene83867.t1 MTR_1g057980 52.830 53 24 1 122 174 80 131 3.09e-12 63.5
MS.gene83867.t1 MTR_7g037130 51.852 54 25 1 121 174 144 196 5.84e-11 60.5
MS.gene83867.t1 MTR_0008s0390 42.188 64 36 1 112 174 4 67 8.73e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83867.t1 AT3G27785 60.345 58 22 1 117 174 184 240 2.35e-15 73.2
MS.gene83867.t1 AT5G11050 57.407 54 22 1 121 174 104 156 3.26e-14 70.1
MS.gene83867.t1 AT5G58850 55.556 54 23 1 121 174 104 156 3.88e-14 69.7
MS.gene83867.t1 AT4G18770 49.180 61 30 1 114 174 209 268 2.06e-13 67.8
MS.gene83867.t1 AT5G40360 31.852 135 64 4 67 174 76 209 1.24e-12 65.1

Find 37 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATAGGGAACTTGTGAAAT+TGG 0.218457 6.1:-9573089 MS.gene83867:intron
CGCTCCAAACATGGATATTC+TGG 0.220757 6.1:+9573715 None:intergenic
TTCAAGATATTGGGATTATT+AGG 0.258151 6.1:+9573586 None:intergenic
TAGACGCATGTTCAAGATAT+TGG 0.258678 6.1:+9573576 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.1:-9572975 MS.gene83867:CDS
GGAACATAAACCTTAATGTT+TGG 0.342814 6.1:+9572965 None:intergenic
CCAGACGTCAACAAAGCTTA+TGG 0.359040 6.1:-9573433 MS.gene83867:CDS
AGACGCATGTTCAAGATATT+GGG 0.359386 6.1:+9573577 None:intergenic
GTTTCCAGAATATCCATGTT+TGG 0.387556 6.1:-9573719 MS.gene83867:CDS
CCATAAGCTTTGTTGACGTC+TGG 0.394101 6.1:+9573433 None:intergenic
AAATGGATGACATGCATGTT+AGG 0.397171 6.1:+9573550 None:intergenic
TTCGTCAATCTTGCAATTTG+AGG 0.432664 6.1:+9573040 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.1:-9573003 MS.gene83867:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.1:+9573680 None:intergenic
ATGATGACATGCCACATAAA+TGG 0.444183 6.1:+9573533 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.1:+9573602 None:intergenic
TTGTTGACGTCTGGTGCAAA+TGG 0.494806 6.1:+9573442 None:intergenic
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.1:+9572969 None:intergenic
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.1:+9573658 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.1:+9573679 None:intergenic
ATTCTGGAAACAGATTCAAA+AGG 0.540825 6.1:+9573731 None:intergenic
TCGAAAGATTGAGAAATGAC+AGG 0.547098 6.1:+9573502 None:intergenic
GTGAAATTGGTGAACCAACA+TGG 0.548528 6.1:-9573076 MS.gene83867:CDS
TGAATCACACGCTCCAAACA+TGG 0.559827 6.1:+9573706 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.1:+9573655 None:intergenic
ATGCATGTCATCCATTTATG+TGG 0.566202 6.1:-9573544 MS.gene83867:CDS
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.1:+9573640 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.1:+9573652 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.1:+9573626 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.1:+9573639 None:intergenic
ACAAAGCTTATGGAATCAGA+AGG 0.604961 6.1:-9573423 MS.gene83867:CDS
ATTGCAAGATTGACGAAGCG+AGG 0.637873 6.1:-9573034 MS.gene83867:CDS
TGAAATTGGTGAACCAACAT+GGG 0.667572 6.1:-9573075 MS.gene83867:CDS
CTTATGGAATCAGAAGGCAA+TGG 0.671225 6.1:-9573417 MS.gene83867:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.1:+9573681 None:intergenic
AAGGCAATGGACAACCAATG+AGG 0.693483 6.1:-9573404 MS.gene83867:CDS
GTGTGATTCATACCCCACAA+AGG 0.701235 6.1:-9573693 MS.gene83867:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGGTTTTTTAATGTTAAAA+GGG - chr6.1:9573508-9573527 MS.gene83867:CDS 15.0%
!!! TAAGGTTTTTTAATGTTAAA+AGG - chr6.1:9573507-9573526 MS.gene83867:CDS 15.0%
!!! TTAATTTGTGATTTCATATA+GGG - chr6.1:9573626-9573645 MS.gene83867:CDS 15.0%
!! CTTGAAAAAATCCAAATAAA+GGG + chr6.1:9573403-9573422 None:intergenic 20.0%
!! TCTTGAAAAAATCCAAATAA+AGG + chr6.1:9573404-9573423 None:intergenic 20.0%
!!! AGGTTTTTTAATGTTAAAAG+GGG - chr6.1:9573509-9573528 MS.gene83867:CDS 20.0%
!!! CTTAATTTGTGATTTCATAT+AGG - chr6.1:9573625-9573644 MS.gene83867:CDS 20.0%
!!! TATATCTTTTTCCCTTTATT+TGG - chr6.1:9573389-9573408 MS.gene83867:intron 20.0%
! AACCTTATATTGACGAAAAA+TGG + chr6.1:9573494-9573513 None:intergenic 25.0%
! TTCAAGATATTGGGATTATT+AGG + chr6.1:9573147-9573166 None:intergenic 25.0%
!! GAGTGTTTAATCTTAATTTG+TGG - chr6.1:9573534-9573553 MS.gene83867:CDS 25.0%
!! TTTTACATACATATCCTCAT+TGG + chr6.1:9573343-9573362 None:intergenic 25.0%
!!! GGTTTTTTAATGTTAAAAGG+GGG - chr6.1:9573510-9573529 MS.gene83867:CDS 25.0%
!!! TACCATTTTTCGTCAATATA+AGG - chr6.1:9573489-9573508 MS.gene83867:CDS 25.0%
ATATAGGGAACTTGTGAAAT+TGG - chr6.1:9573641-9573660 MS.gene83867:CDS 30.0%
CATAAACCTTAATGTTTGGA+CGG + chr6.1:9573764-9573783 None:intergenic 30.0%
GGAACATAAACCTTAATGTT+TGG + chr6.1:9573768-9573787 None:intergenic 30.0%
TATTAGGTACACTCAAGATA+TGG + chr6.1:9573131-9573150 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG + chr6.1:9573093-9573112 None:intergenic 30.0%
! ATTCTGGAAACAGATTCAAA+AGG + chr6.1:9573002-9573021 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG + chr6.1:9573107-9573126 None:intergenic 30.0%
! TAACTGTGCTGTTCAATTAT+TGG - chr6.1:9573454-9573473 MS.gene83867:CDS 30.0%
!!! TGTTGAGAAAAGCATTTTGA+TGG + chr6.1:9573266-9573285 None:intergenic 30.0%
AAATGGATGACATGCATGTT+AGG + chr6.1:9573183-9573202 None:intergenic 35.0%
ACAAAGCTTATGGAATCAGA+AGG - chr6.1:9573307-9573326 MS.gene83867:intron 35.0%
AGACGCATGTTCAAGATATT+GGG + chr6.1:9573156-9573175 None:intergenic 35.0%
ATGATGACATGCCACATAAA+TGG + chr6.1:9573200-9573219 None:intergenic 35.0%
ATGCATGTCATCCATTTATG+TGG - chr6.1:9573186-9573205 MS.gene83867:intron 35.0%
GTTGAGATGGTAGTTTAACA+AGG + chr6.1:9573094-9573113 None:intergenic 35.0%
GTTTCCAGAATATCCATGTT+TGG - chr6.1:9573011-9573030 MS.gene83867:CDS 35.0%
TAGACGCATGTTCAAGATAT+TGG + chr6.1:9573157-9573176 None:intergenic 35.0%
TCGAAAGATTGAGAAATGAC+AGG + chr6.1:9573231-9573250 None:intergenic 35.0%
TGAAATTGGTGAACCAACAT+GGG - chr6.1:9573655-9573674 MS.gene83867:CDS 35.0%
TTCGTCAATCTTGCAATTTG+AGG + chr6.1:9573693-9573712 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG + chr6.1:9573081-9573100 None:intergenic 35.0%
!! AGCATTTTGATGGAAACATC+TGG + chr6.1:9573256-9573275 None:intergenic 35.0%
AACGAGAATTGACCTTTGTG+GGG + chr6.1:9573052-9573071 None:intergenic 40.0%
CAAAACAGTGTCGTGATAGA+TGG - chr6.1:9573727-9573746 MS.gene83867:CDS 40.0%
CTTATGGAATCAGAAGGCAA+TGG - chr6.1:9573313-9573332 MS.gene83867:intron 40.0%
GAACGAGAATTGACCTTTGT+GGG + chr6.1:9573053-9573072 None:intergenic 40.0%
GTGAAATTGGTGAACCAACA+TGG - chr6.1:9573654-9573673 MS.gene83867:CDS 40.0%
TCATCTCCGTCCAAACATTA+AGG - chr6.1:9573755-9573774 MS.gene83867:CDS 40.0%
! ACCAACATGGGCTGAAAAAA+TGG - chr6.1:9573667-9573686 MS.gene83867:CDS 40.0%
AAGGCAATGGACAACCAATG+AGG - chr6.1:9573326-9573345 MS.gene83867:intron 45.0%
ATTGCAAGATTGACGAAGCG+AGG - chr6.1:9573696-9573715 MS.gene83867:CDS 45.0%
CCAGACGTCAACAAAGCTTA+TGG - chr6.1:9573297-9573316 MS.gene83867:intron 45.0%
CGCTCCAAACATGGATATTC+TGG + chr6.1:9573018-9573037 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG + chr6.1:9573054-9573073 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG - chr6.1:9573037-9573056 MS.gene83867:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG + chr6.1:9573027-9573046 None:intergenic 45.0%
TTGTTGACGTCTGGTGCAAA+TGG + chr6.1:9573291-9573310 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG + chr6.1:9573078-9573097 None:intergenic 45.0%
!! CCATAAGCTTTGTTGACGTC+TGG + chr6.1:9573300-9573319 None:intergenic 45.0%
!!! GCCATTTTTTCAGCCCATGT+TGG + chr6.1:9573671-9573690 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG + chr6.1:9573075-9573094 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 9572961 9573791 9572961 ID=MS.gene83867
chr6.1 mRNA 9572961 9573791 9572961 ID=MS.gene83867.t1;Parent=MS.gene83867
chr6.1 exon 9573400 9573791 9573400 ID=MS.gene83867.t1.exon1;Parent=MS.gene83867.t1
chr6.1 CDS 9573400 9573791 9573400 ID=cds.MS.gene83867.t1;Parent=MS.gene83867.t1
chr6.1 exon 9572961 9573105 9572961 ID=MS.gene83867.t1.exon2;Parent=MS.gene83867.t1
chr6.1 CDS 9572961 9573105 9572961 ID=cds.MS.gene83867.t1;Parent=MS.gene83867.t1
Gene Sequence

>MS.gene83867

ATGGAACTCAATATTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTGTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTGAACATGCGTCTATCTCCTAACATGCATGTCATCCATTTATGTGGCATGTCATCATCAACATCGCCTGTCATTTCTCAATCTTTCGAAACCAGATGTTTCCATCAAAATGCTTTTCTCAACACTCCATTTGCACCAGACGTCAACAAAGCTTATGGAATCAGAAGGCAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTCTTAATCTCTCTCTATATCTTTTTCCCTTTATTTGGATTTTTTCAAGAAAAAAAAAATATAATAGAATTAAATTACATTAACTGTGCTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCGTCAATATAAGGTTTTTTAATGTTAAAAGGGGGTGAGTGTTTAATCTTAATTTGTGGTAGTTTTATAGATACCATTTTTCGTCAATATAAGGTTTTTTAATGTTAAAAGGGGGTGAGTGTTTAATCTTAATTTGTGATTTCATATAGGGAACTTGTGAAATTGGTGAACCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGACGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAGGTTTATGTTCCCTAA
Protein sequence

>MS.gene83867.t1

MELNINNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNMRLSPNMHVIHLCGMSSSTSPVISQSFETRCFHQNAFLNTPFAPDVNKAYGIRRQWTTNEDMELVKLVNQHGLKKWPQIARLTKRGRNAKQCRDRWLNHLRPNIKVYVP