AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene30554

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30554.t1 MTR_4g064873 93.258 178 7 2 1 178 1 173 1.78e-117 330
MS.gene30554.t1 MTR_7g063220 37.107 159 57 5 20 178 23 138 3.83e-20 82.0
MS.gene30554.t1 MTR_1g075430 60.317 63 21 2 10 69 8 69 3.00e-16 73.2
MS.gene30554.t1 MTR_1g044225 44.304 79 43 1 13 90 18 96 2.00e-14 67.8
MS.gene30554.t1 MTR_3g068095 65.909 44 13 1 21 64 55 96 2.79e-13 66.2
MS.gene30554.t1 MTR_1g070250 70.732 41 11 1 21 60 38 78 3.94e-13 64.7
MS.gene30554.t1 MTR_4g021270 74.286 35 9 0 21 55 59 93 4.25e-13 66.2
MS.gene30554.t1 MTR_2g076060 30.460 174 85 6 21 162 50 219 4.52e-13 65.1
MS.gene30554.t1 MTR_5g014400 32.768 177 79 6 21 165 80 248 4.85e-13 65.5
MS.gene30554.t1 MTR_5g080660 72.973 37 10 0 21 57 47 83 7.08e-13 64.7
MS.gene30554.t1 MTR_1g070265 66.667 33 11 0 21 53 35 67 1.95e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30554.t1 AT3G53820 35.220 159 63 7 21 174 19 142 1.98e-17 75.1
MS.gene30554.t1 AT3G09290 80.000 35 7 0 21 55 33 67 1.24e-15 71.2
MS.gene30554.t1 AT5G06070 72.222 36 10 0 21 56 53 88 2.40e-13 65.9
MS.gene30554.t1 AT5G43540 55.357 56 17 2 23 70 35 90 8.68e-13 62.8
MS.gene30554.t1 AT2G37740 59.091 44 18 0 11 54 27 70 1.61e-12 64.7
MS.gene30554.t1 AT3G23130 68.571 35 11 0 21 55 45 79 2.56e-12 62.8
MS.gene30554.t1 AT4G17810 32.414 145 83 4 21 165 44 173 5.91e-12 61.2
MS.gene30554.t1 AT2G42410 56.098 41 18 0 21 61 73 113 2.47e-11 60.8
MS.gene30554.t1 AT2G42410 56.098 41 18 0 21 61 47 87 2.48e-11 60.5
MS.gene30554.t1 AT2G42410 56.098 41 18 0 21 61 47 87 2.48e-11 60.5
MS.gene30554.t1 AT4G17810 64.103 39 13 1 21 58 44 82 2.73e-11 60.1

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCAATTACCATCTAATT+TGG 0.170331 4.2:+40448664 MS.gene30554:CDS
CTGGTACCCGTTGGCTTTGA+TGG 0.228413 4.2:-40448983 None:intergenic
AATTAGATGGTAATTGAGTT+TGG 0.335367 4.2:-40448661 None:intergenic
TTAGACCTTGAACTAAGATT+AGG 0.355982 4.2:+40448944 MS.gene30554:CDS
ACAATATTAGTATTCAAGTT+TGG 0.372182 4.2:-40448722 None:intergenic
TAGACCTTGAACTAAGATTA+GGG 0.384535 4.2:+40448945 MS.gene30554:CDS
AATTACACTCATAAGATCTA+AGG 0.395050 4.2:-40448538 None:intergenic
CCCTTTGAACTTGACCTTGT+GGG 0.399837 4.2:-40448865 None:intergenic
GCTTTGCTTTGTCTTTCCTA+TGG 0.427666 4.2:-40448613 None:intergenic
GGAAATTATTACTACACAAA+AGG 0.438306 4.2:+40448886 MS.gene30554:CDS
GAGTCTGATCAACATGATAA+AGG 0.445854 4.2:+40448485 MS.gene30554:CDS
GAACTTCCCTCCAAATTAGA+TGG 0.446674 4.2:-40448674 None:intergenic
ATTTGTGTTTCATTTCTAGT+TGG 0.455559 4.2:-40448836 None:intergenic
TTCTCTAATGCACAAGCTCT+TGG 0.469634 4.2:+40448575 MS.gene30554:CDS
AGAATTTCATCACCTCTAGA+AGG 0.475968 4.2:-40448770 None:intergenic
TCCCACAAGGTCAAGTTCAA+AGG 0.482764 4.2:+40448864 MS.gene30554:CDS
TCAATTACCATCTAATTTGG+AGG 0.483513 4.2:+40448667 MS.gene30554:CDS
CACCTCTAGAAGGAGCTTGT+TGG 0.486575 4.2:-40448760 None:intergenic
CCCACAAGGTCAAGTTCAAA+GGG 0.499228 4.2:+40448865 MS.gene30554:CDS
TTTGATGGATCATGTGGCTC+AGG 0.503162 4.2:-40448968 None:intergenic
CAGGCCCTAATCTTAGTTCA+AGG 0.522982 4.2:-40448949 None:intergenic
CATGATCCATCAAAGCCAAC+GGG 0.534522 4.2:+40448977 MS.gene30554:CDS
TCTAATGCACAAGCTCTTGG+TGG 0.538110 4.2:+40448578 MS.gene30554:CDS
TCCCTTTGAACTTGACCTTG+TGG 0.538332 4.2:-40448866 None:intergenic
TCCGATGAAGAATCTTGAGC+AGG 0.539565 4.2:-40448920 None:intergenic
ACCTGCTCAAGATTCTTCAT+CGG 0.568940 4.2:+40448919 MS.gene30554:CDS
CAATTACCATCTAATTTGGA+GGG 0.604261 4.2:+40448668 MS.gene30554:CDS
GTGGACACATGAATATCCAT+AGG 0.606044 4.2:+40448597 MS.gene30554:CDS
CACCAACAAGCTCCTTCTAG+AGG 0.609713 4.2:+40448758 MS.gene30554:CDS
ACATGATCCATCAAAGCCAA+CGG 0.613032 4.2:+40448976 MS.gene30554:CDS
GTTGGCTTTGATGGATCATG+TGG 0.637580 4.2:-40448974 None:intergenic
TCTGATCAACATGATAAAGG+TGG 0.671643 4.2:+40448488 MS.gene30554:CDS
ACACAAATTAATATCCCACA+AGG 0.716304 4.2:+40448851 MS.gene30554:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACAATATTAGTATTCAAGTT+TGG - chr4.2:40448725-40448744 None:intergenic 20.0%
! AACTCAATTACCATCTAATT+TGG + chr4.2:40448664-40448683 MS.gene30554:CDS 25.0%
! AATTACACTCATAAGATCTA+AGG - chr4.2:40448541-40448560 None:intergenic 25.0%
! AATTAGATGGTAATTGAGTT+TGG - chr4.2:40448664-40448683 None:intergenic 25.0%
! GGAAATTATTACTACACAAA+AGG + chr4.2:40448886-40448905 MS.gene30554:CDS 25.0%
!!! ATTTGTGTTTCATTTCTAGT+TGG - chr4.2:40448839-40448858 None:intergenic 25.0%
ACACAAATTAATATCCCACA+AGG + chr4.2:40448851-40448870 MS.gene30554:CDS 30.0%
CAATTACCATCTAATTTGGA+GGG + chr4.2:40448668-40448687 MS.gene30554:CDS 30.0%
TAGACCTTGAACTAAGATTA+GGG + chr4.2:40448945-40448964 MS.gene30554:CDS 30.0%
TCAATTACCATCTAATTTGG+AGG + chr4.2:40448667-40448686 MS.gene30554:CDS 30.0%
TTAGACCTTGAACTAAGATT+AGG + chr4.2:40448944-40448963 MS.gene30554:CDS 30.0%
AGAATTTCATCACCTCTAGA+AGG - chr4.2:40448773-40448792 None:intergenic 35.0%
GAGTCTGATCAACATGATAA+AGG + chr4.2:40448485-40448504 MS.gene30554:CDS 35.0%
TCTGATCAACATGATAAAGG+TGG + chr4.2:40448488-40448507 MS.gene30554:CDS 35.0%
! GAGTGTAATTTTTGCAAGAG+AGG + chr4.2:40448551-40448570 MS.gene30554:CDS 35.0%
ACATGATCCATCAAAGCCAA+CGG + chr4.2:40448976-40448995 MS.gene30554:CDS 40.0%
ACCTGCTCAAGATTCTTCAT+CGG + chr4.2:40448919-40448938 MS.gene30554:CDS 40.0%
GAACTTCCCTCCAAATTAGA+TGG - chr4.2:40448677-40448696 None:intergenic 40.0%
GCTTTGCTTTGTCTTTCCTA+TGG - chr4.2:40448616-40448635 None:intergenic 40.0%
GTGGACACATGAATATCCAT+AGG + chr4.2:40448597-40448616 MS.gene30554:CDS 40.0%
TTCTCTAATGCACAAGCTCT+TGG + chr4.2:40448575-40448594 MS.gene30554:CDS 40.0%
!! AAGAATTTTCTGGTACCCGT+TGG - chr4.2:40448995-40449014 None:intergenic 40.0%
!! GTTGGTGATTCAGCAAAAAG+TGG - chr4.2:40448821-40448840 None:intergenic 40.0%
CAGGCCCTAATCTTAGTTCA+AGG - chr4.2:40448952-40448971 None:intergenic 45.0%
CATGATCCATCAAAGCCAAC+GGG + chr4.2:40448977-40448996 MS.gene30554:CDS 45.0%
CCCACAAGGTCAAGTTCAAA+GGG + chr4.2:40448865-40448884 MS.gene30554:CDS 45.0%
CCCTTTGAACTTGACCTTGT+GGG - chr4.2:40448868-40448887 None:intergenic 45.0%
TCCCACAAGGTCAAGTTCAA+AGG + chr4.2:40448864-40448883 MS.gene30554:CDS 45.0%
TCCCTTTGAACTTGACCTTG+TGG - chr4.2:40448869-40448888 None:intergenic 45.0%
TCCGATGAAGAATCTTGAGC+AGG - chr4.2:40448923-40448942 None:intergenic 45.0%
TCTAATGCACAAGCTCTTGG+TGG + chr4.2:40448578-40448597 MS.gene30554:CDS 45.0%
! TTTGATGGATCATGTGGCTC+AGG - chr4.2:40448971-40448990 None:intergenic 45.0%
!! GTTGGCTTTGATGGATCATG+TGG - chr4.2:40448977-40448996 None:intergenic 45.0%
CACCAACAAGCTCCTTCTAG+AGG + chr4.2:40448758-40448777 MS.gene30554:CDS 50.0%
! CACCTCTAGAAGGAGCTTGT+TGG - chr4.2:40448763-40448782 None:intergenic 50.0%
!! CTGGTACCCGTTGGCTTTGA+TGG - chr4.2:40448986-40449005 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 40448482 40449018 40448482 ID=MS.gene30554
chr4.2 mRNA 40448482 40449018 40448482 ID=MS.gene30554.t1;Parent=MS.gene30554
chr4.2 exon 40448482 40449018 40448482 ID=MS.gene30554.t1.exon1;Parent=MS.gene30554.t1
chr4.2 CDS 40448482 40449018 40448482 ID=cds.MS.gene30554.t1;Parent=MS.gene30554.t1
Gene Sequence

>MS.gene30554

ATGGAGTCTGATCAACATGATAAAGGTGGTGATGATCAAGATGCAAAACAAGTGAACCTTAGATCTTATGAGTGTAATTTTTGCAAGAGAGGATTCTCTAATGCACAAGCTCTTGGTGGACACATGAATATCCATAGGAAAGACAAAGCAAAGCTCAAACAACAATCTTCAACAAATTACCAAACTCAATTACCATCTAATTTGGAGGGAAGTTCTAGTGAAGAGATCAACAAATTATTACCAAACTTGAATACTAATATTGTGTCTCAACAAGATCACCAACAAGCTCCTTCTAGAGGTGATGAAATTCTTGTAACTCAAGTGAGAACACAACTTCCACTTTTTGCTGAATCACCAACTAGAAATGAAACACAAATTAATATCCCACAAGGTCAAGTTCAAAGGGAAATTATTACTACACAAAAGGCTTTGTTATTACCTGCTCAAGATTCTTCATCGGAGTTAGACCTTGAACTAAGATTAGGGCCTGAGCCACATGATCCATCAAAGCCAACGGGTACCAGAAAATTCTTTTAA
Protein sequence

>MS.gene30554.t1

MESDQHDKGGDDQDAKQVNLRSYECNFCKRGFSNAQALGGHMNIHRKDKAKLKQQSSTNYQTQLPSNLEGSSSEEINKLLPNLNTNIVSQQDHQQAPSRGDEILVTQVRTQLPLFAESPTRNETQINIPQGQVQREIITTQKALLLPAQDSSSELDLELRLGPEPHDPSKPTGTRKFF